WO2012036884A2 - Bioproduction of aromatic chemicals from lignin-derived compounds - Google Patents

Bioproduction of aromatic chemicals from lignin-derived compounds Download PDF

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Publication number
WO2012036884A2
WO2012036884A2 PCT/US2011/049619 US2011049619W WO2012036884A2 WO 2012036884 A2 WO2012036884 A2 WO 2012036884A2 US 2011049619 W US2011049619 W US 2011049619W WO 2012036884 A2 WO2012036884 A2 WO 2012036884A2
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Prior art keywords
lignin
daltons
polypeptide
amino acid
beta
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PCT/US2011/049619
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French (fr)
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WO2012036884A3 (en
Inventor
Ranjini Chatterjee
Kenneth Zahn
Kenneth Mitchell
Gary Y. Liu
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Aligna Technologies, Inc.
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Priority to CN201180044555.0A priority Critical patent/CN103797026A/en
Priority to EP11825655.1A priority patent/EP2616481A4/en
Priority to CA2811403A priority patent/CA2811403A1/en
Priority to AU2011302522A priority patent/AU2011302522A1/en
Priority to JP2013529175A priority patent/JP2014506115A/en
Publication of WO2012036884A2 publication Critical patent/WO2012036884A2/en
Publication of WO2012036884A3 publication Critical patent/WO2012036884A3/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/1085—Transferases (2.) transferring alkyl or aryl groups other than methyl groups (2.5)
    • C12N9/1088—Glutathione transferase (2.5.1.18)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/02—Preparation of oxygen-containing organic compounds containing a hydroxy group
    • C12P7/22—Preparation of oxygen-containing organic compounds containing a hydroxy group aromatic
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/24—Preparation of oxygen-containing organic compounds containing a carbonyl group
    • C12P7/26—Ketones
    • C12P7/28—Acetone-containing products
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y205/00—Transferases transferring alkyl or aryl groups, other than methyl groups (2.5)
    • C12Y205/01—Transferases transferring alkyl or aryl groups, other than methyl groups (2.5) transferring alkyl or aryl groups, other than methyl groups (2.5.1)
    • C12Y205/01018—Glutathione transferase (2.5.1.18)

Definitions

  • the name of the attached file is ALIGP004US01_SEQLIST_AS-FILED.txt, and the file was created August 29, 201 1 , is 813 KB in size, and is hereby incorporated herein by reference in its entirety. Because the ASCII compliant text file serves as both the paper copy required by ⁇ 1 .821 (c) and the CRF required by ⁇ 1 .821 (e), the statement indicating that the paper copy and CRF copy of the sequence listing are identical is no longer necessary under 37 C.F.R. ⁇ 1 .821 (f), as per Federal Register /Vol. 74, No. 206 /Tuesday, October 27, 2009, Section I.
  • Oil refineries for example, are petroleum-based processes that primarily produce
  • gasoline are also used extensively to produce valuable and less well-known chemical products used in the manufacture of pharmaceuticals, agrochemicals, food ingredients, and plastics. A clean, green alternative to this market area would be appreciated worldwide.
  • Bioprocesses can present a clean, green alternative to the petroleum-based processes, a bioprocess being one that uses organisms, cells, organelles, or enzymes to carry out a commercial process.
  • Biorefineries for example, can produce, for example, chemicals, heat and power, as well as food, feed, fuel and industrial chemical products.
  • Examples of biorefineries can include wet and dry corn mills, pulp and paper mills, and the biofuels industry.
  • leather tanning hides are softened and hair is removed using proteases.
  • amylases are used in germinating barley.
  • cheese-making rennin is used to coagulated the proteins in mil.
  • the biofuels industry for example, has been a point of focus recently, naturally focusing on fuel products to replace petroleum-based fuels and, as a result, has not developed other valuable chemical products that also rely on petroleum- based processes.
  • a natural product such as the wood that is used in a pulp and paper mill, contains cellulose, hemicelluloses, and lignin.
  • a typical range of compositions for a hardwood may be about 40-44% cellulose, about 15-35% hemicelluloses, and about 18-25% lignin.
  • a typical range of compositions for a softwood may be about 40-44% cellulose, about 20-32% hemicelluloses, and about 25-35% lignin. Since all biofuels come from cellulosic
  • lignin remains underutilized.
  • Lignin is the single most abundant source of aromatic compounds in nature, and the use of lignin is currently limited to low value applications, such as combustion to generate process heat and energy for the biorefinery facilities.
  • lignin is sold as a natural component of animal feeds or fertilizers.
  • lignin is the only plant biomass component based on aromatic core structures, and such core structures are valuable in the production of industrial chemicals.
  • the aromatic compounds present in the lignin fraction of a biorefinery include toxic compounds that inhibit the growth and survival of industrial microbes. For at least these reasons, processes for converting lignin fractions to industrial products using industrial microbes have not been successful.
  • This invention is generally directed to a recombinant method of producing enzymes for use in the bioconversion of lignin-derived compounds to valuable aromatic chemicals.
  • the teachings are directed to an isolated recombinant polypeptide, comprising an amino acid sequence having at least 95% identity to SEQ ID NO:101 .
  • the sequence can conserve residues T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, G54, K100, A101 , N104, V1 1 1 , G1 12, M1 15, F1 16, P166, W107, Y184, Y187, R188, G191 , G192, and F195.
  • teachings are directed to an isolated recombinant
  • the conserved residues can include T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, G54; K100, A101 , N104, V1 1 1 , G1 12, M1 15, F1 16, P166, W107, Y184, Y187, R188, G191 , G192, and F195.
  • the teachings are directed to an isolated recombinant glutathione S-transferase enzyme, comprising an amino acid sequence having at least 95% identity to SEQ ID NO:101 .
  • the amino acid sequence can conserve residues T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, G54; K100, A101 , N104, V1 1 1 , G1 12, M1 15, F1 16, P166, W107, Y184, Y187, R188, G191 , G192, and F195; wherein, the amino acid sequence functions to cleave a beta-aryl ether.
  • the teachings are directed to an isolated recombinant glutathione S-transferase enzyme, comprising an amino acid sequence having at least 95% identity to SEQ ID NO:101 ; wherein, the amino acid sequence functions to cleave a beta-aryl ether.
  • teachings are directed to an isolated recombinant
  • polypeptide comprising (i) a length ranging from about 279 to about 281 amino acids; (ii) a first amino acid region consisting of residues 19-54 from SEQ ID NO:101 , or conservative substitutions thereof outside of conserved residues T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, and G54; wherein, the first amino acid region can be located in the recombinant polypeptide from about residue 14 to about residue 59; and, (iii) a second amino acid region consisting of residues 98-221 from SEQ ID NO:101 , or conservative substitutions thereof outside of conserved residues K100, A101 , N104, V1 1 1 , G1 12, M1 15, F1 16, P166, W107
  • the teachings are directed to an isolated recombinant glutathione S-transferase enzyme, comprising (i) a length ranging from about 279 to about 281 amino acids; (ii) a first amino acid region having at least 95% identity to residues 19-54 from SEQ ID NO:101 while conserving residues T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, and G54; wherein, the first amino acid region is located in the recombinant polypeptide from about residue 14 to about residue 59; and, (iii) a second amino acid region having at least 95% identity to residues 98-221 from SEQ ID NO:101 while conserving residues K100, A101 , N
  • the teachings are directed to an isolated recombinant glutathione S-transferase enzyme, comprising an amino acid sequence having at least 95% identity to SEQ ID NO:541 ; wherein, the amino acid sequence functions to cleave a beta-aryl ether.
  • teachings are directed to an isolated recombinant
  • polypeptide comprising (i) a length ranging from about 256 to about 260 amino acids; (ii) a first amino acid region consisting of residues 47-57 from SEQ ID NO:541 , or conservative substitutions thereof outside of conserved residues A47, I48, N49, P50, G52, V54, P55, V56, L57; wherein, the first amino acid region is located in the recombinant polypeptide from about residue 45 to about residue 57; (iii) a second amino acid region consisting of 63-76 from SEQ ID NO:541 ; and, (iv) a third amino acid region consisting of residues 99-230 from SEQ ID NO:541 , or conservative substitutions thereof outside of conserved residues R100, Y101 , K104, D107, M1 1 1 , N1 12, S1 15, M1 16, K176, L194, 1197, N198, S201 , H202, and M206; wherein, the second amino acid region is located in the second
  • the teachings are directed to an isolated recombinant glutathione S-transferase enzyme, comprising (i) a length ranging from about 279 to about 281 amino acids; (ii) a first amino acid region having at least 95% identity to 47-57 from SEQ ID NO:541 , or conservative substitutions thereof outside of conserved residues A47, I48, N49, P50, G52, V54, P55, V56, L57; wherein, the first amino acid region can be located in the recombinant polypeptide from about residue 45 to about residue 57; (iii) a second amino acid region consisting of 63-76 from SEQ ID NO:541 ; and, (iv) a third amino acid region having at least 95% identity to residues 99-230 from SEQ ID NO:541 , or conservative substitutions thereof outside of conserved residues R100, Y101 , K104, D107, M1 1 1 , N1 12, S1 15, M
  • an amino acid substitution outside of the conserved residues can be a conservative substitution.
  • the amino acid sequence can function to cleave a beta-aryl ether.
  • the teachings are also directed to a method of cleaving a beta-aryl ether bond, the
  • a polypeptide taught herein comprising contacting a polypeptide taught herein with a lignin-derived compound having (i) a beta-aryl ether bond and (ii) a molecular weight ranging from about 180 Daltons to about 3000 Daltons; wherein, the contacting occurs in a solvent environment in which the lignin- derived compound is soluble.
  • the lignin-derived compound has a molecular weight of about 180 Daltons to about 1000 Daltons.
  • the solvent environment comprises water. And, in some embodiments, the solvent environment comprises a polar organic solvent.
  • the teachings are also directed to a system for bioprocessing lignin-derived compounds, the system comprising a polypeptide taught herein, a lignin-derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; and, a solvent in which the lignin-derived compound is soluble; wherein, the system functions to cleave the beta-aryl ether bond by contacting the polypeptide with the lignin- derived compound in the solvent.
  • teachings are also directed to a recombinant polynucleotide comprising a nucleotide sequence that encodes a polypeptide taught herein.
  • teachings are also directed to a vector or plasmid comprising the polynucleotide, as well as a host cell transformed by the vector or plasmid to express the polypeptide.
  • the teachings are also directed to a method of cleaving a beta-aryl ether bond, the
  • a method comprising (i) culturing a host cell taught herein under conditions suitable to produce a polypeptide taught herein; (ii) recovering the polypeptide from the host cell culture; and, (iii) contacting the polypeptide of claim 1 with a lignin-derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; wherein, the contacting occurs in a solvent environment in which the lignin- derived compound is soluble.
  • the host cell can be E. Coli or an Azotobacter strain, such as Azotobacter vinelandii.
  • the lignin-derived compound can have a molecular weight of about 180 Daltons to about 1000 Daltons.
  • the teachings are also directed to a system for bioprocessing lignin-derived compounds, the system comprising (i) a transformed host cell taught herein; (ii) a lignin-derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; and, (iii) a solvent in which the lignin-derived compound is soluble; wherein, the system functions to cleave the beta-aryl ether bond by contacting a polypeptide taught herein with the lignin-derived compound in the solvent.
  • FIGs. 1 A and 1 B illustrate general concepts of the biorefinery and discovery processes discussed herein, according to some embodiments.
  • FIG. 2 illustrates the structures of some building block chemicals that can be produced using bioconversions, according to some embodiments.
  • FIG. 3 is an example of a beta-etherase catalyzed hydrolysis of a model lignin dimer, a- O-(B-methylumbelliferyl) acetovanillone (MUAV), according to some embodiments.
  • MUAV a- O-(B-methylumbelliferyl) acetovanillone
  • FIG. 4 illustrates unexpected results from biochemical activity assays for beta-etherase function for the S. paucimobilis positive control polypeptides, and the N. aromaticivorans putative beta-etherase polypeptide, according to some embodiments.
  • FIG. 5 illustrates beta-aryl-ether compounds to be tested as substrates representing native lignin structures, according to some embodiments.
  • FIG. 6 illustrates pathways of guaiacylglycerol ⁇ -guaiacyl ether (GGE) metabolism by S. paucimobilis, according to some embodiments.
  • GGE guaiacylglycerol ⁇ -guaiacyl ether
  • FIG. 7 illustrates an example of a biochemical process for the production of catechol from lignin oligomers, according to some embodiments.
  • FIG. 8 illustrates an example of a biochemical process for the production of vanillin from lignin oligomers, according to some embodiments.
  • FIG. 9 illustrates an example of a biochemical process for the production of 2,4- diaminotoluene from lignin oligomers, according to some embodiments.
  • FIG. 10 illustrates process schemes for additional product targets that include ortho- cresol, salicylic acid, and aminosalicylic acid, for the production of valuable chemicals from lignin oligomers, according to some embodiments.
  • This invention is generally directed to a recombinant method of producing enzymes for use in the bioconversion of lignin-derived compounds to valuable aromatic chemicals.
  • FIGs. 1 A and 1 B illustrate general concepts of the biorefinery and discovery processes discussed herein, according to some embodiments.
  • FIG. 1 A shows a generalized example of a use of recombinant microbial strains in biotransformations for the production of aromatic chemicals from lignin-derived compounds.
  • Biorefinery process 100 converts a soluble biorefinery lignin 105 through a series of biotransformations using a transformed host cell.
  • the biorefinery lignin 105 is a feedstock comprising a lignin-derived compound which can be, for example, a combination of lignin-derived monomers and oligomers.
  • FIG. 1 B shows a discovery process 120, which includes selecting a host cell strain that is tolerant to toxic lignin-derived compounds.
  • the strain acquisition 125 includes growth of the strain, sample preparation, and storage. A set of bacterial strains are obtained for testing strain tolerance to soluble biorefinery lignin samples.
  • the strains can be selected for (i) having well-characterized aromatic and xenobiotic metabolisms; (ii) annotated genome sequences; and (iii) prior use in fermentation processes at pilot or larger scales.
  • Examples of strains can include, but are not limited to, Azotobacter vinelandii (ATCC BAA-1303 DJ), Azotobacter chroococcum (ATCC 4412 (EB Fred) X-50), Pseudomonas putida (ATCC BAA-477 Pf-5), Pseudomonas fluorescens (ATCC 29837 NCTC 1 100). Stains can be streaked on relevant rich media plates as described by the accompanying ATCC literature for revival. Individual colonies (5 each) can be picked and cultured on relevant liquid media to saturation. Culture samples prepared in a final glycerol concentration of 12.5% can be flash-frozen and stored at -80°C.
  • the model substrate synthesis 150 for use in the biochemical screening for selective activity can be outsourced through a contract research organization (CRO).
  • CRO contract research organization
  • the enzyme discovery effort can initially be focused on identifying potential beta-etherase candidate genes identified through bioinformatic methods.
  • the identification of candidates having beta-etherase activity is the 1 st step towards generating lignin monomers from lignin oligomers present in soluble lignin streams.
  • the fluorescent substrate ⁇ -0-( ⁇ - methylumbelliferyl) acetovanillone (MUAV), for example, can be used in in vitro assays to identify beta-etherase function (Acme Biosciences, Mt. View, CA).
  • the gene synthesis, cloning, and transformation step 145 can include combining
  • bioinformatic methods with known information about enzymes showing a desired, selective enzyme activity.
  • bioinformatics can produce a putative beta-etherase sequence that shares a significant homology to the S. paucimobilis ligE and ligF beta- etherase sequences. See Masai, E., et al. Journal of Bacteriology (3):1768- 1775(2003)("Masai”), which is hereby incorporated herein in it's entirety by reference.
  • the S. paucimobilis sequences can be used as positive controls for biochemical assays to show relative activities in an enzyme discovery strategy.
  • the gene synthesis, cloning, and transformation step 145 can be performed using any method known to one of skill.
  • all genes can be synthesized directly as open reading frames (ORFs) from oligonucleotides by using standard PCR-based assembly methods, and using the E. coli codon bias.
  • the end sequences can contain adaptors (BamHI and Hind III) for restriction digestion and cloning into the E. coli expression vector pET24a (Novagen). Internal BamHI and Hind 111 sites can be excluded from the ORF sequences during design of the oligonucleotides.
  • Assembled genes can be cloned into the proprietary cloning vector (pGOV4), transformed into E.
  • E. coli CH3 chemically competent cells and DNA sequences determined (Tocore Inc.) from purified plasmid DNA. After sequence verification, restriction digestion can be used to excise each ORF fragment from the cloning vector, and the sequence can be sub-cloned into pET24a. The entire set of ligE and ligF bearing plasmids can then be transformed into E. coli BL21 (DE3) which can serve as the host strain for beta-etherase expression and biochemical testing.
  • the enzyme screening 155 is done to identify novel etherases 160.
  • the fluorescent substrate MUAV can be used to screen for and identify beta-etherase activity from the recombinant E. coli clones. Expression of the beta-etherase genes can be done in 5ml or 25ml samples of the recombinant E. coli strains in LB medium using induction with IPTG. Following induction, and cell harvest, cell pellets can be be lysed using the BPER
  • Cell extracts can be tested in the in vitro biochemical assay for beta-etherase activity on the fluorescent substrate MUAV.
  • Cell extracts of E. coli transformed with the S. paucimobilis ligE and ligF genes can be the assay positive controls.
  • Test or unknown samples can include, for example, E. coli strains expressing putative beta-etherase genes from N. aromaticovorans.
  • the lignin stream acquisition 130 includes a waste lignin stream from a biorefinery for testing.
  • a preliminary characterization of one source of such lignin has shown an aromatic monomer concentration of less than 1 g/L and an oligomer concentration of ⁇ 10g/L.
  • Oligomers appear to be associated with carbohydrates in 10:1 ratio for sugar:phenolics. Some information exists on compounds in the liquid stream, including benzoic acid, vanillin, syringic acid and ferulics, which are routinely quantified in soluble samples. An average molecular weight of -280 has been established for the monomers; and the oligomeric components remain to be characterized.
  • the strain tolerance testing 135 Strain tolerance will be determined by cell growth upon exposure to biorefinery lignin. Tolerance to the phenolic compounds in biorefinery lignin waste stream will be critically important to the bioprocess efficiency and high level production of aromatic chemicals by microbial systems. Cell growth will be quantified as a function of respiration by the reduction of soluble tetrazolium salts. XTT (2,3-Bis(2-methoxy- 4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide inner salt, Sigma) is reduced to a soluble purple formazan compound by respiring cells. The formazan product will be detected and quantified by absorbance at 450nm.
  • Strain tolerance testing 135 on soluble lignin can be done in liquid format in 48 well plates, for example. Each strain can be tested in replicates of 8, for example, and E. coli can be used as a negative control strain. Strains can first be grown in rich medium to saturation, washed, and OD600nm of the cultures determined. Equal numbers of bacteria can be inoculated into wells of the 48-well growth plate containing minimal medium excluding a carbon source. Increasing concentrations of soluble lignin fractions, in addition to a minus-lignin positive control, can be added to the wells containing each species to a final volume of 0.8ml.
  • a benzoic acid content analysis of the lignin fractions can be used as an internal indicator of the phenolic content of lignin wastes of different origin. Following incubation for 24-48 hours with shaking at 30°C, the cultures can be tested for growth upon exposure to the lignin fraction using an XTT assay kit. Culture samples can be removed from the 48 well growth plate and diluted appropriately in 96 well assay plates to which the XTT reagent can be be added. The soluble formazan produced will be quantified by absorbance at 450nm. Bacterial strains exhibiting the highest level of growth, and therefore tolerance, can be candidates for further development as host strains for lignin conversions.
  • strain demonstrated to have the best tolerance characteristics can be transformed with the beta-etherase gene identified as showing the highest biochemical activity.
  • Restriction digestion can be used to excise the ORF fragment from the cloning vector, and the sequence can be sub-cloned into the shuttle vector pMMB206. Constructs cloned in the shuttle vector can be transformed into Azotobacter or Pseudomonas strains by
  • the recombinant, lignin tolerant host strain can be re-tested for beta-etherase expression and activity using any methods known to one of skill, such as those described herein, adapted to the particular host strain being used.
  • a starting material might be pretreated lignocellulosic biomass.
  • the lignocellulose biomass material might include grasses, corn stover, rice hull, agricultural residues, softwoods and hardwoods.
  • the lignin- derived compounds might be derived from hardwood species such as poplar from the Upper Peninsula region of Michigan, or hardwoods such as poplar, lolloby pine, and eucalyptus from Virginia and Georgia areas, or mixed hardwoods including maple and oak species from upstate New York.
  • the pretreatment methods might encompass a range of physical, chemical and biological based processes.
  • Examples of pretreatment methods used to generate the feedstock for Aligna processes might include physical pretreatment, solvent fractionation, chemical pretreatment, biological pretreatment, ionic liquids pretreatment, supercritical fluids pretreatment, or a combination thereof, for example, which can be applied in stages.
  • Solvent fractionation methods include organosolve processes, phosphoric acid fractionation processes, and methods using ionic liquids to pretreat the lignocellulose biomass to differentially solubilize and partition various components of the biomass.
  • organosolve methods might be performed using alcohol, including ethanol, with an acid catalyst at temperature ranges from about 90 to about 20°C, and from about 155 to about 220°C with residence time of about 25 minutes to about 100 minutes.
  • Catalyst concentrations can vary from about 0.83% to about 1 .67% and alcohol concentrations can vary from about 25% to about 74% (v/v).
  • phosphoric acid fractionations of lignocellulose biomass might be performed using a series of different extractions using phosphoric acid, acetone, and water at temperature of around 50°C.
  • lignocellulose biomass might include use of ionic liquids containing anions like chloride, formate, acetate, or alkylphosphonate, with biomass:ionic liquids ratios of approximately 1 :10 (w/w).
  • the pretreatment might be performed at temperatures ranging from about 100°C to about 150°C.
  • Other ionic liquid compounds that might be used include 1 -butyl-3- methyl-imidazolium chloride and 1 -ethyl-3-methylimidazolium chloride.
  • Chemical pretreatments of lignocellulose biomass material might be performed using technologies that include acidic, alkaline and oxidative treatments.
  • acidic pretreatment methods of lignocellulose biomass such as those described below might be applied. Dilute acid pretreatments using sulfuric acid at concentrations in the
  • ammonia fiber expansion (AFEX) method might be applied in which concentrated ammonia at about 0.3kg to about 2kg of ammonia per kg of dry weight biomass is used at about 60°C to about 140°C in a high pressure reactor, and cooked for 5-45 minutes before rapid pressure release.
  • the ammonia recycle percolation (ARP) method might be used in flow through mode by percolating ammoniacal solutions at 5-15% concentrations at high temperatures and pressures.
  • Oxidative pretreatment methods such as alkaline wet oxidation might be used with sodium carbonate at a temperature ranging from about 170°C to about 220°C in a high pressure reactor using pressurized air/oxygen mixtures or hydrogen peroxide as the oxidants.
  • actinomycetes might be applied.
  • One type of product stream from such pretreatment methods might be soluble lignin, and might contain lignin-derived monomers and oligomers in the range of about 1 g/L to about 10g/L, and xylans.
  • the lignin-derived monomers might include compounds such as gallic acid, hydroxybenzoate, ferulic acid, hydroxymethyl furfural, hydroxymethyl furfural alcohol, vanillin, homovanillin, syringic acid, syringaldehyde, and furfural alcohol.
  • Supercritical fluid pretreatment methods might be used to process the biomass.
  • supercritical fluids for use in processing biomass include ethanol, acetone, water, and carbon dioxide at a temperature and pressures above the critical points for ethanol and carbon dioxide but at a temperature and/or pressure below that of the critical point for water.
  • a biomass steam can be pretreated at 195°C for 10 min at controlled pH, followed by enzymatic treatment using commercial cellulases and xylanases at dosings of 100mg protein/g total solid, and with incubation at 50°C at pH 5.0 with agitation of 500 rpm.
  • Stage 1 Use heat in an aqueous medium at a predetermined pH, temperature and pressure for the hydrothermal process;
  • Stage 2 Use at least one organic solvent from those described in 6-6c in water for the organosolve step;
  • Stage 3 Use yeast, white rot basidomycetes, actinomycetes, and cellulases and xylanases in native or recombinant forms for the biological pretreatment step.
  • Soluble lignin fractions derived using organosolve methods might produce soluble lignins in the molecular weight range of 188-1000, soluble in various polar solvents. Without intending to be bound by any theory or mechanism of action, organosolve processes are generally believed to maintain the lignin beta-aryl ether linkage.
  • explosion might be performed, for example, using high pressure steam in the range of about 200 psi to about 500psi, and at temperatures ranging from about 180°C to about 230°C for about 1 minute to about 20 minutes in batch or continuous reactors.
  • the lignin might be extracted from the steam-exploded material with alkali washing or extraction using organic solvents. Steam exploded lignins can exhibit properties similar to those described form organosolve lignins, retaining native bond structures and containing about 3 to about 12 aromatic units per oligomer unit.
  • Supercritical fluid pretreatment can produce soluble lignin fractions that can be used with the teachings provided herein. Such processes typically yield monomers and lignin oligomers having a molecular weight of about ⁇ 1000 Daltons.
  • Biological pretreatment can produce soluble lignin fractions that can be used with the teachings provided herein.
  • Such lignin streams might contain lignin monomers and oligomers in the range of about 1 g/L to about 10 g/L and have a molecular weight of about ⁇ 1000 Daltons, and xylans.
  • the lignin-derived monomers might include compounds such as gallic acid, hydroxybenzoate, ferulic acid, hydroxymethyl furfural, hydroxymethyl furfural alcohol, vanillin, homovanillin, syringic acid, syringaldehyde, and furfural alcohol.
  • Wood pulping processes produce a variety of lignin types, the type of lignin dependent on the type of process used. Chemical pulping processes include, for example, Kraft and sulfite pulping.
  • the lignin-derived compound can be derived from a spent pulping liquor or "black liquor” from Kraft pulping processes. Kraft lignin might be derived from batch or continuous processes using, for example, reaction temperatures in the range of about 150°C to about 200°C and reaction times of approximately 2 hours. Any range of molecular weights of lignin may be obtained, and the useful fraction may range, in some embodiments, from about 200 Daltons to about 4000 Daltons. A Kraft lignin having a molecular weight ranging from about 1000 Daltons to about 3000 Daltons might be used in a bioconversion.
  • lignin from a sulfite pulping process might be used.
  • a sulfite pulping process can include, for example, a chemical sulfonation using aqueous sulfur dioxide, bisulfite and monosulfite at a pH ranging from about 2 to about 12.
  • the sulfonated lignin might be recovered by precipitation with excess lime as lignosulfonates.
  • formaldehyde-based methylation of the lignin aromatics followed by sulfonation might be performed. Any range of molecular weights of lignin may be obtained, and the useful fraction may range, in some embodiments, from about 200 Daltons to about 4000 Daltons.
  • a sulfite lignin having a molecular weight ranging from about 1000 Daltons to about 3000 Daltons might be used in a bioconversion.
  • optimization of a system for a particular feedstock should include an understanding of the composition of the particular feedstock.
  • the composition of a native lignin can be significantly different than the composition of the lignin- derived compounds in a given lignin faction that is used for a feedstock. Accordingly, and understanding of the composition of the feedstock will assist in optimizing the conversion of the lignin-derived compounds to the valuable aromatic compounds. Any method known to one of skill can be used to characterize the compositions of the feedstock.
  • wet chemistry techniques such as thioacidolysis and nitrobenzene oxidation
  • gas chromatography which have been used traditionally
  • spectroscopic techniques such as NMR and FTIR.
  • Thioacidolysis for example, cleaves the ⁇ - ⁇ -4 linkages in lignin, giving rise to monomers and dimers which are then used to calculate the S and G content. Similar information can be obtained using nitrobenzene oxidation, but the ratios are thought to be less accurate.
  • the content of S, G, and H, as well as their relative ratios can be used to characterize feedstock compositions for purposes of determining a bioconversion system design.
  • Tables 1 A and 1 B summarize distributions of p-coumaryl alcohol or p-hydroxyl phenol (H), coniferyl alcohol or guaiacyl (G), and sinapyl alcohol or syringyl (S) lignin in several sources of biomass.
  • Table 1 A compares percent lignin in the biomass to the G:S:H.
  • Table 1 A compares location of a sample in the biomass, species, and environmental stress to the G:S:H.
  • the relative amounts of G, S, and H in lignin can be a good indicator of its overall composition and response to a treatment, such as the bioconversions taught herein
  • a treatment such as the bioconversions taught herein
  • the S/G ratio ranges from 1 .3 to 2.2. This is similar to the hardwood eucalyptus, but higher than herbaceous biomass switchgrass and Miscanthus. This is to be expected given the higher H contents in grass lignin.
  • An optimized nitrobenzene oxidation method has shown S/G ratios of 13 poplar samples from two different sites and obtained values ranging from 1 .01 to 1 .68.
  • Higher throughput methods can be used for rapid screening of feedstocks. Examples of such methods can include, but are not limited to, near-infrared (NIR), reflectance
  • S/G ratios Information on some structural characteristics of lignin, such as S/G ratios, can be rapidly obtained using these methods.
  • the average S:G:H ratio of 104 poplar lignin samples was determined using the modified thioacidolysis technique, and was found to be 68:32:0.02.
  • the S, G, and H components in the ratio can be expressed as mass percent. In some embodiments, the S, G, and H components in the ratio can be expressed as any relative unit, or unitless.
  • the ratios can be expressed in relative whole numbers or fractions as S:G:H, or any other order or combination of components, S/G, G/S, and the like.
  • the S/G ratio is used.
  • the S/G ratio can range from about 0.20 to about 20.0, from about 0.3 to about 18.0, from about 0.4 to about 15.0, from about 0.5 to about 15.0, from about 0.6 to about 12.0, from about 0.7 to about 10.0, from about 0.8 to about 8.0, from about 0.9 to about 9.0, from about 1 .0 to about 7.0, or any range therein.
  • the S/G ratio can be about 0.2, about 0.4, about 0.6, about 0.8, about 1 .0, about 1 .2, about 1 .4, about 1 .6, about 1 .8, about 2.0, about 2.2, about 2.4, about 2.6, about 2.8, about 3.0, about 3.2, about 3.4, about 3.6, about 3.8, about 4.0, about 4.2, about 4.4, about 4.6, about 4.8, about 5.0, about 5.2, about 5.4, about 5.6, about 5.8, about 6.0, about 6.2, about 6.4, about 6.6, about 6.8, about 7.0, about 7.2, about 7.4, about 7.6, about 7.8, about 8.0, about 8.2, about 8.4, about 8.6, about 8.8, about 9.0, about 9.2, about 9.4, about 9.6, about 9.8, about 10.0, and any ratio in-between on 0.1 increments, and any range of ratios therein.
  • Soluble lignin streams derived from biorefinery or Kraft processes might be used directly in microbial conversions without additional purification or, they might be further purified by one or more of the separation or fractionation techniques prior to microbial conversions.
  • membrane filtration might be applied to achieve a starting concentration of lignin monomers and oligomers in the 1 -60% (w/v) concentration range, and molecular weights ranging from about 180 Daltons to about 2000 Daltons, from about 200 Daltons to about 4000 Daltons, from about 250 Daltons to about 2500 Daltons, from about 180 Daltons to about 3500 Daltons, from about 300 Daltons to about 3000 Daltons, or any range therein.
  • soluble lignin streams might be partially purified by
  • the lignin monomers and oligomers can bind to the resin while highly polar impurities or inorganics that might be toxic to
  • microorganisms can remain un-bound. Subsequent elution, for example, with a methanol- water solvent system, can provide fractions of higher purity that are enriched in lignin monomers and oligomers.
  • a purpose of the present teaching includes the discovery of novel biochemical
  • Such commercial products include monomeric aromatic chemicals that can serve as building block chemicals.
  • aromatic chemicals can be produced using the principles provided by the teachings set-forth herein, and that a comprehensive teaching of every possible chemical that can be produced would be beyond the scope and purpose of this teaching.
  • FIGs. 2A and 2B illustrate (i) the structures of some building block chemicals that can be produced using bioconversions, and (ii) an example enzyme system from a Sphingomonaas paucimobilis gene cluster, according to some embodiments.
  • FIG. 2A shows that examples of some monomeric aromatic structures that can serve as building block chemicals derived from lignin include, but are not limited to, guaiacol, ⁇ -hydroxypropiovanillone, 4-hydroxy-3 methoxy mandelic acid, coniferaldehyde, ferulic acid, eugenol, propylguaicol, and 4- acetylguaiacol. It should be appreciated that each of these structures can be produced using the teachings provided herein.
  • FIG. 2B(i) shows the organization of the LigDFEG gene cluster in a Sphingomonaas paucimobilis strain.
  • FIG. 2B(ii) shows deduced functions of the gene products believed to be involved in a ⁇ -aryl ether bond cleavage in a model lignin structure, guaiacylglycerol ⁇ -guaiacyl ether (GGE).
  • GGE guaiacylglycerol ⁇ -guaiacyl ether
  • the vertical bars above the restriction map indicate the positions of the gene insertions of LigD, LigF, LigE, and LigG.
  • LigD shoed Ca-dehydrogenase activity, LigF and LigE showed ⁇ -etherase activity
  • LigG showed glutathione lyase activity.
  • 2 LEGEND (Abbreviations): restriction enzymes Ap (Apal), Bs (BstXI), E (EcoRI), Ec (Eco47lll), Ml (Mlul), P (Pstl), RV (EcoRV), S, (Sail), Sc (Sacl). Sell (Sacll), St (Stul), Sm (Smal), Tt (Tthllll), and X (Xhol); chemicals GGE
  • compounds, as taught herein, include mono-aromatic chemicals.
  • such chemicals include, but are not limited to, caprolactam, cumene, styrene, mononitro- and dinitrotoluenes and their derivatives, 2,4-diaminotoluene, 2,4-dinitrotoluene, terephthalic acid, catechol, vanillin, salicylic acid, aminosalicylic acid, cresol and isomers, alkylphenols, chlorinated phenols, nitrophenols, polyhydric phenols, nitrobenzene, aniline and secondary and tertiary aniline bases, benzothiazole and derivatives, alkylbenzene and alkylbenzene sulfonates, 4,4-diphenylmethane diisocyanate (MDI), chlorobenzenes and
  • MDI 4,4-diphenylmethane diisocyanate
  • dichlorobenzenes nitrochlorobenzenes, sulfonic acid derivatives of toluene, pseudocumene, mesitylene, nitrocumene, cumenesulfonic acid.
  • the enzymes are beta-etherase enzymes.
  • Lignin is the only plant biomass constituent based on aromatic core structures, and is comprised of branched phenylpropenyl (C9) units.
  • the guaiacol and syringol building blocks of lignin are linked through carbon-carbon (C-C) and carbon-oxygen (C-O, ether) bonds.
  • C-C carbon-carbon
  • C-O carbon-oxygen
  • beta-aryl ether linkage which comprises 50% to 70% of the bond type in lignin.
  • the efficient scission of the beta-aryl ether bond would generate the monomeric building blocks of lignin, and provide the chemical feedstock for subsequent conversion to a range of industrial products.
  • the beta-etherase enzyme system has multiple advantages for conversions of lignin oligomers to monomers over the laccase enzyme systems.
  • the beta-etherase enzyme system would achieve highly selective reductive bond scission catalysis for efficient and high yield conversions of lignin oligomers to monomers without the formation of side products, degradation of the aromatic core structures of lignin, or the use of electron transfer mediators required with use of the oxidative and radical chemistry-based laccase enzyme systems.
  • FIG. 3 is an example of a beta-etherase catalyzed hydrolysis of a model lignin dimer, a- O-(B-methylumbelliferyl) acetovanillone (MUAV), according to some embodiments.
  • MUAV a- O-(B-methylumbelliferyl) acetovanillone
  • Azotobacter strains will provide the art with valuable industrial strains that particulary well- suited for lignin conversion processes.
  • amino acids used herein can be identified by at least the following conventional three-letter abbreviations in Table 2:
  • the Recombinant Polypeptides [0081 ] The teachings herein are based on discovery of novel and non-obvious proteins, DNAs, and host cell systems that can function in the conversion of lignin-derived compounds into valuable aromatic compounds.
  • the systems can include natural, wild-type components or recombinant components, the recombinant components being isolatable from what occurs in nature.
  • isolated means altered “by the hand of man” from its natural state; i.e., if it occurs in nature, it has been changed or removed from its original environment, or both.
  • a naturally occurring polynucleotide or a polypeptide naturally present in a living animal in its natural state is not “isolated,” but the same polynucleotide or polypeptide separated from the coexisting materials of its natural state is “isolated”, as the term is used herein.
  • isolated means that it is separated from the chromosome and cell in which it naturally occurs.
  • a nucleic acid molecule contained in a clone that is a member of a mixed clone library e.g., a genomic or cDNA library
  • a mixed clone library e.g., a genomic or cDNA library
  • a chromosome isolated or removed from a cell or a cell lysate e.g., a
  • chromosome spread as in a karyotype
  • chromosome spread is not “isolated” for the purposes of the teachings herein.
  • a lone nucleic acid molecule contained in a preparation of mechanically or enzymatically cleaved genomic DNA, where the isolation of the nucleic molecule was not the goal is also not “isolated” for the purposes of the teachings herein.
  • polynucleotides can be joined to other polynucleotides, for mutagenesis, to form fusion proteins, and for propagation or expression in a host, for instance.
  • Isolated polynucleotides alone or joined to other polynucleotides such as vectors, can be introduced into host cells, in culture or in whole organisms, after which such DNAs still would be isolated, as the term is used herein, because they would not be in their naturally occurring form or environment.
  • the isolated polynucleotides and polypeptides may occur in a composition, such as a media formulation, solutions for introduction of polynucleotides or polypeptides, for example, into cells, compositions or solutions for chemical or enzymatic reactions, for instance, which are not naturally occurring compositions, and, therein remain "isolated" polynucleotides or polypeptides within the meaning of that term as it is used herein.
  • a "vector,” such as an expression vector, is used to transfer or transmit the DNA of
  • Vectors can be recombinantly designed to contain a polynucleotide encoding a desired polypeptide. These vectors can include a tag, a cleavage site, or a combination of these elements to facilitate, for example, the process of producing, isolating, and purifying a polypeptide.
  • the DNA of interest can be inserted as the expression component of a vector. Examples of vectors include plasmids, cosmids, viruses, and bacteriophages. If the vector is a virus or bacteriophage, the term vector can include the viral/bacteriophage coat.
  • expression vector is usually used to describe a DNA construct containing gene encoding an expression product of interest, usually a protein, that is expressed by the machinery of the host cell. This type of vector is frequently a plasmid, but the other forms of expression vectors, such as bacteriophage vectors and viral vectors (e.g., adenoviruses, replication defective retroviruses, and adeno-associated viruses), can be used.
  • bacteriophage vectors e.g., adenoviruses, replication defective retroviruses, and adeno-associated viruses
  • polypeptides taught herein can be natural or wildtype
  • the polynucleotides can be natural or wildtype, isolated and/or recombinant.
  • the teachings are directed to a vector than can include such a polynucleotide or a host cell transformed by such a vector.
  • the polypeptide can be an isolated recombinant polypeptide, comprising an amino acid sequence having at least 95% identity to SEQ ID NO:101 .
  • the sequence can conserve residues T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, G54, K100, A101 , N104, V1 1 1 , G1 12, M1 15, F1 16, P166, W107, Y184, Y187, R188, G191 , G192, and F195.
  • the polypeptide can be an isolated recombinant polypeptide, comprising SEQ ID NO:101 ; or conservative substitutions thereof outside of the conserved residues.
  • the conserved residues can include T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, G54; K100, A101 , N104, V1 1 1 , G1 12, M1 15, F1 16, P166, W107, Y184, Y187, R188, G191 , G192, and F195.
  • the polypeptide can be an isolated recombinant glutathione S- transferase enzyme, comprising an amino acid sequence having at least 95% identity to SEQ ID NO:101 .
  • the amino acid sequence can conserve residues T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, G54; K100, A101 , N104, V1 1 1 , G1 12, M1 15, F1 16, P166, W107, Y184, Y187, R188, G191 , G192, and F195; wherein, the amino acid sequence functions to cleave a beta-aryl ether.
  • the polypeptide can be an isolated recombinant glutathione S- transferase enzyme, comprising an amino acid sequence having at least 95% identity to SEQ ID NO:101 ; wherein, the amino acid sequence functions to cleave a beta-aryl ether.
  • the polypeptide can be an isolated recombinant polypeptide, comprising (i) a length ranging from about 279 to about 281 amino acids; (ii) a first amino acid region consisting of residues 19-54 from SEQ ID NO:101 , or conservative substitutions thereof outside of conserved residues T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, and G54; wherein, the first amino acid region can be located in the recombinant polypeptide from about residue 14 to about residue 59; and, (iii) a second amino acid region consisting of residues 98-221 from SEQ ID NO:101 , or conservative substitutions thereof outside of conserved residues K100, A101 , N
  • the polypeptide can be an isolated recombinant glutathione S- transferase enzyme, comprising (i) a length ranging from about 279 to about 281 amino acids; (ii) a first amino acid region having at least 95% identity to residues 19-54 from SEQ ID NO:101 while conserving residues T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, and G54; wherein, the first amino acid region is located in the recombinant polypeptide from about residue 14 to about residue 59; and, (iii) a second amino acid region having at least 95% identity to residues 98-221 from SEQ ID NO:101 while conserving residues K100, A101 , N104
  • the polypeptide can be an isolated recombinant glutathione S- transferase enzyme, comprising an amino acid sequence having at least 95% identity to SEQ ID NO:541 ; wherein, the amino acid sequence functions to cleave a beta-aryl ether.
  • the polypeptide can be an isolated recombinant polypeptide, comprising (i) a length ranging from about 256 to about 260 amino acids; (ii) a first amino acid region consisting of residues 47-57 from SEQ ID NO:541 , or conservative substitutions thereof outside of conserved residues A47, I48, N49, P50, G52, V54, P55, V56, L57;
  • the first amino acid region is located in the recombinant polypeptide from about residue 45 to about residue 57; (iii) a second amino acid region consisting of 63-76 from SEQ ID NO:541 ; and, (iv) a third amino acid region consisting of residues 99-230 from SEQ ID NO:541 , or conservative substitutions thereof outside of conserved residues R100, Y101 , K104, D107, M1 1 1 , N1 12, S1 15, M1 16, K176, L194, 1197, N198, S201 , H202, and M206; wherein, the second amino acid region is located in the recombinant polypeptide from about residue 94 to about residue 235.
  • the polypeptide can be an isolated recombinant glutathione S- transferase enzyme, comprising (i) a length ranging from about 279 to about 281 amino acids; (ii) a first amino acid region having at least 95% identity to 47-57 from SEQ ID NO:541 , or conservative substitutions thereof outside of conserved residues A47, I48, N49, P50, G52, V54, P55, V56, L57; wherein, the first amino acid region can be located in the recombinant polypeptide from about residue 45 to about residue 57; (iii) a second amino acid region consisting of 63-76 from SEQ ID NO:541 ; and, (iv) a third amino acid region having at least 95% identity to residues 99-230 from SEQ ID NO:541 , or conservative substitutions thereof outside of conserved residues R100, Y101 , K104, D107, M1 1 1 , N1 12, S1 15, M1
  • an amino acid substitution outside of the conserved residues can be a conservative substitution.
  • the amino acid sequence can function to cleave a beta-aryl ether.
  • the teachings include a method of preparing the polypeptides described herein,
  • the host cell comprises an exogenously-derived polynucleotide encoding the desired polypeptide.
  • the host cell is E. Coli.
  • the host cell can be an Azotobacter strain such as, for example, Azotobacter vinelandii.
  • a double-stranded DNA fragment encoding the primary amino acid sequence of recombinant polypeptide can be designed.
  • This DNA fragment can be manipulated to facilitate synthesis, cloning, expression or biochemical manipulation of the expression products.
  • the synthetic gene can be ligated to a suitable cloning vector and then the nucleotide sequence of the cloned gene can be determined and confirmed.
  • the gene can be then amplified using designed primers having specific restriction enzyme sequences introduced at both sides of insert gene, and the gene can be subcloned into a suitable subclone/expression vector.
  • the expression vector bearing the synthetic gene for the mutant can be inserted into a suitable expression host. Thereafter the expression host can be maintained under conditions suitable for production of the gene product and, in some embodiments, the protein can be (i) isolated and purified from the cells expressing the gene or (ii) used directly in a reaction environment that includes the host cell.
  • the nucleic acid may be inserted into a replicable vector for cloning (amplification of the DNA) for expression.
  • a replicable vector for cloning (amplification of the DNA) for expression.
  • Various vectors are publicly available.
  • DNA can be inserted into an appropriate restriction endonuclease site(s) using techniques known in the art, for example.
  • Vector components generally include, but are not limited to, one or more of a signal sequence, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence.
  • the signal sequence may be a prokaryotic signal sequence selected, for example, from the group of the alkaline phosphatase, penicillinase, Ipp, or heat-stable enterotoxin II leaders.
  • yeast secretion the signal sequence may be, e.g., the yeast invertase leader, alpha factor leader (including Saccharomyces and Kluyveromyces alpha-factor leaders, the latter described in U.S. Pat. No. 5,010,182), or acid phosphatase leader, the C. albicans glucoamylase leader (EP 362,179), or the signal described in WO 90/13646, for example.
  • mammalian signal sequences may be used to direct secretion of the protein, such as signal sequences from secreted polypeptides of the same or related species, as well as viral secretory leaders.
  • Both expression and cloning vectors contain a nucleic acid sequence that enables the vector to replicate in one or more selected host cells. Such sequences are well known for a variety of bacteria, yeast, and viruses. The origin of replication from a plasmid, e.g.
  • pBR322 for example, is suitable for most Gram-negative bacteria, and the 2 ⁇ plasmid origin is suitable for yeast, and various viral origins (SV40, polyoma, adenovirus, VSV or BPV) are useful for cloning vectors in mammalian cells.
  • various viral origins SV40, polyoma, adenovirus, VSV or BPV
  • Expression and cloning vectors will typically contain a selection gene, also
  • selectable marker termed a selectable marker.
  • Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e g., ampicillin, neomycin, methotrexate, or tetracycline, (b) complement auxotrophic deficiencies, or (c) supply critical nutrients not available from complex media, e.g., the gene encoding D-alanine racemase for Bacilli.
  • Suitable selectable markers for mammalian cells are those that enable the identification of cells competent to take the encoding nucleic acid, such as DHFR or thymidine kinase.
  • An appropriate host cell when wild-type DHFR is employed is the CHO cell line deficient in DHFR activity, prepared and propagated as described by Urlaub et al., Proc. Natl. Acad. Sci. USA, 77:4216 (1980).
  • a suitable selection gene for use in yeast is the trpl gene present in the yeast plasmid YRp7 (Stinchcomb et al., Nature, 282:39 (1979); Kingsman et al., Gene, 7:141 (1979); Tschemper et al., Gene, 10:157 (1980)).
  • the trpl gene provides a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan, for example, ATCC No. 44076 or PEP4-1 (Jones, Genetics, 85:12 (1977)).
  • Expression and cloning vectors usually contain a promoter operably linked to the encoding nucleic acid sequence to direct mRNA synthesis. Promoters recognized by a variety of potential host cells are well known. Promoters suitable for use with prokaryotic hosts include the .beta.-lactamase and lactose promoter systems (Chang et al., Nature, 275:615 (1978); Goeddel et al., Nature, 281 :544 (1979)), alkaline phosphatase, a tryptophan (trp) promoter system (Goeddel, Nucleic Acids Res., 8:4057 (1980); EP 36,776), and hybrid promoters such as the tac promoter (deBoer et al., Proc. Natl. Acad. Sci. USA, 80:21 25 (1983)). Promoters for use in bacterial systems also will contain a Shine-Dalgarno sequence operably linked to the encoding DNA.
  • yeast promoters which are inducible promoters having the additional advantage of transcription controlled by growth conditions, are the promoter regions for alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degradative enzymes associated with nitrogen metabolism, metallothionein, glyceraldehyde-3-phosphate dehydrogenase, and enzymes responsible for maltose and galactose utilization.
  • Suitable vectors and promoters for use in yeast expression are known in the art, e.g. see EP 73,657 for a further discussion.
  • PR087299 transcription from vectors in mammalian host cells is controlled, for example, by promoters obtained from the genomes of viruses such as polyoma virus, fowlpox virus (UK 2,21 1 ,504), adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), from heterologous mammalian promoters, e.g., the actin promoter or an
  • immunoglobulin promoter and from heat-shock promoters, provided such promoters are compatible with the host cell systems.
  • Enhancers are cis-acting elements of DNA, usually about from 10 to 300 bp, that act on a promoter to increase its transcription.
  • Many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, a- fetoprotein, and insulin).
  • an enhancer from a eukaryotic cell virus. Examples include the SV40 enhancer on the late side of the replication origin, the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers.
  • the enhancer may be spliced into the vector at a position 5' or 3' to the coding sequence but is preferably located at a site 5' from the promoter.
  • Expression vectors used in eukaryotic host cells yeast, fungi, insect, plant,
  • nucleated cells from other multicellular organisms will also contain sequences necessary for the termination of transcription and for stabilizing the mRNA.
  • sequences are commonly available from the 5' and, occasionally 3', untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of the mRNA encoding the mutants.
  • the expression control sequence can be selected from a group consisting of a lac system, T7 expression system, major operator and promoter regions of pBR322 origin, and other prokaryotic control regions. Still other methods, vectors, and host cells suitable for adaptation to the synthesis of the mutants in recombinant vertebrate cell culture are described in Gething et al., Nature, 293:620 625 (1981 ); Mantei et al., Nature, 281 :40 46 (1979); EP 1 17,060; and EP 1 17,058.
  • Mutants can be expressed as a fusion protein.
  • the amino acids can be expressed as a fusion protein.
  • Extra amino acids can serve as affinity tags or cleavage sites, for example.
  • Fusion proteins can be designed to: (1 ) assist in purification by acting as a temporary ligand for affinity purification, (2) produce a precise recombinant by removing extra amino acids using a cleavage site between the target gene and affinity tag, (3) increase the solubility of the product, and/or (4) increase expression of the product.
  • a proteolytic cleavage site can be included at the junction of the fusion region and the protein of interest to enable further purification of the product - separation of the recombinant protein from the fusion protein following affinity purification of the fusion protein.
  • Such enzymes can include Factor Xa, thrombin and enterokinase, cyanogen bromide, trypsin, or chymotrypsin, for example.
  • Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith, D. B. and Johnson, K. S.
  • GST glutathione S-transferase
  • maltose E binding protein protein A
  • six-histidine sequence respectively, to a target recombinant protein.
  • a polypeptide can be a fusion polypeptide having an affinity tag
  • the recovering step includes (1 ) capturing and purifying the fusion polypeptide, and (2) removing the affinity tag for high yield production of the desired polypeptide or an amino acid sequence that is at least 95% homologous to a desired polypeptide.
  • DNA encoding the mutants may be obtained from a cDNA library prepared from tissue possessing the mRNA for the mutants. As such, the DNA can be conveniently obtained from a cDNA library.
  • the encoding gene for the mutants may also be obtained from a genomic library or by known synthetic procedures (e.g., automated nucleic acid synthesis).
  • Libraries can be screened with probes designed to identify the gene of interest or the protein encoded by it. Screening the cDNA or genomic library with the selected probe may be conducted using standard hybridization procedures, such as described in Sambrook et al., Molecular Cloning: A Laboratory Manual (New York: Cold Spring Harbor Laboratory Press, 1989), which is herein incorporated by reference. An alternative means to isolate the gene encoding recombinant polypeptide mutants is to use PCR methodology [Sambrook et al., supra; Dieffenbach et al., PCR Primer: A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1995)].
  • Nucleic acids having a desired protein coding sequence may be obtained by screening selected cDNA or genomic libraries using a deduced amino acid sequence and, if necessary, a conventional primer extension procedure as described in Sambrook et al., supra, to detect precursors and processing intermediates of mRNA that may not have been reverse-transcribed into cDNA.
  • [001 12] The selection of expression vectors, control sequences, transformation methods, and the like, are dependent on the type of host cell used to express the gene. Following entry into a cell, all or part of the vector DNA, including the insert DNA, may be incorporated into the host cell chromosome, or the vector may be maintained extrachromosomally.
  • vectors that are maintained extrachromosomally are frequently capable of autonomous replication in the host cell.
  • Other vectors are integrated into the genome of a host cell upon and are replicated along with the host genome.
  • Host cells are transfected or transformed with the expression or cloning vectors described herein to produce the mutants.
  • the cells are cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.
  • the culture conditions such as media, temperature, pH and the like, can be selected by the skilled artisan without undue experimentation. In general, principles, protocols, and practical techniques for maximizing the productivity of cell cultures can be found in Mammalian Cell Biotechnology: a Practical Approach, M. Butler, ed. (IRL Press, 1991 ) and Sambrook et al., supra, each of which are incorporated by reference.
  • the host cells can be prokaryotic or eukaryotic and, suitable host cells for cloning or expressing the DNA in the vectors herein can include prokaryote, yeast, or higher eukaryote cells.
  • suitable host cells for cloning or expressing the DNA in the vectors herein can include prokaryote, yeast, or higher eukaryote cells.
  • Methods of eukaryotic cell transfection and prokaryotic cell transformation are known to the ordinarily skilled artisan, for example, CaCI2, CaP04, liposome-mediated and electroporation.
  • transformation is performed using standard techniques appropriate to such cells.
  • the calcium treatment employing calcium chloride, as described in Sambrook et al., supra, or electroporation is generally used for prokaryotes.
  • prokaryote examples include prokaryote, yeast, or higher eukaryote cells.
  • Suitable prokaryotes include, but are not limited to, eubacteria, such as Gram-negative or Gram-positive organisms, for example, Enterobacteriaceae such as E. coli.
  • Various E. coli strains are publicly available, such as E. coli K12 strain MM294 (ATCC 31 ,446); E. coli X1776 (ATCC 31 ,537); E. coli strain W31 10 (ATCC 27,325) and K5 772 (ATCC 53,635).
  • Other suitable prokaryotic host cells include Enterobacteriaceae such as Escherichia, e.g., E.
  • Strain W31 10 is one particularly preferred host or parent host because it is a common host strain for recombinant DNA product fermentations. Preferably, the host cell secretes minimal amounts of proteolytic enzymes.
  • strain W31 10 may be modified to effect a genetic mutation in the genes encoding proteins endogenous to the host, with examples of such hosts including E. coli W31 10 strain 1 A2, which has the complete genotype tonA; E. coli W31 10 strain 9E4, which has the complete genotype tonA ptr3; E.
  • coli W31 10 strain 27C7 (ATCC 55,244), which has the complete genotype tonA ptr3 phoA E15 (argF-lac)169 degP ompT kanr ;
  • E. coli W31 10 strain 37D6 which has the complete genotype tonA ptr3 phoA E15 (argF- lac)169 degP ompT rbs7 ilvC kanr ;
  • E. coli W31 10 strain 40B4 which is 37D6 with a non- kanamycin resistant degP deletion mutation; and an E. coli strain having mutant periplasmic protease as disclosed in U.S. Pat. No. 4,946,783.
  • in vitro methods of cloning e.g., PCR or other nucleic acid polymerase reactions, are suitable.
  • eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for the mutants.
  • Saccharomyces cerevisiae is a commonly used lower eukaryotic host microorganism. Others include
  • Schizosaccharomyces pombe (Beach and Nurse, Nature, 290: 140 (1981 ); EP 139,383 published 2 May 1985); Kluyveromyces hosts (U.S. Pat. No. 4,943,529; Fleer et al., Bio/Technology, 9:968 975 (1991 )) such as, e.g., K. lactis (MW98-8C, CBS683, CBS4574; Louvencourt et al., J. Bacteriol., 154(2):737 742 (1983)), K. fragilis (ATCC 12,424), K.
  • thermotolerans and K. marxianus
  • yarrowia EP 402,226
  • Pichia pastoris EP 183,070; Sreekrishna et al., J. Basic Microbiol., 28:265 278 [1988]
  • Candida Trichoderma reesia (EP 244,234); Neurospora crassa (Case et al., Proc. Natl. Acad. Sci.
  • Schwanniomyces such as Schwanniomyces occidentalis (EP 394,538); and filamentous fungi such as, e.g., Neurospora, Penicillium, Tolypocladium (WO 91 /00357), and Aspergillus hosts such as A. nidulans (Ballance et al., Biochem. Biophys. Res.
  • Methylotropic yeasts are suitable herein and include, but are not limited to, yeast capable of growth on methanol selected from the genera consisting of Hansenula, Candida, Kloeckera, Pichia, Saccharomyces, Torulopsis, and Rhodotorula. A list of specific species that are exemplary of this class of yeasts may be found in C. Anthony, The
  • Suitable host cells for the expression of glycosylated mutants can be derived from multicellular organisms.
  • Invertebrate cells include insect cells such as Drosophila S2 and Spodoptera Sf9, as well as plant cells.
  • Useful mammalian host cell lines include Chinese hamster ovary (CHO) and COS cells. More specific examples include monkey kidney CVI line transformed by SV40 (COS-7, ATCC CRL 1651 ); human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture, Graham et al., J. Gen Virol., 36:59 (1977)); Chinese hamster ovary cells/-DHFR (CHO, Urlaub and Chasin, Proc. Natl. Acad. Sci.
  • a nucleotide sequence will be hybridizable, under moderately stringent conditions, to a nucleic acid having a nucleotide sequence comprising or complementary to the desired nucleotide sequences.
  • an isolated nucleotide sequence will be hybridizable, under stringent conditions, to a nucleic acid having a nucleotide sequence comprising or complementary to the desired nucleotide sequences.
  • a nucleic acid molecule can be "hybridizable" to another nucleic acid molecule when a single-stranded form of the nucleic acid molecule can anneal to the other nucleic acid molecule under the appropriate conditions of temperature and ionic strength (see Sambrook et al., supra,). The conditions of temperature and ionic strength determine the "stringency" of-the hybridization. "Hybridization" requires that two nucleic acids contain complementary sequences.
  • mismatches between bases may occur.
  • the appropriate stringency for hybridizing nucleic acids depends on the length of the nucleic acids and the degree of complementation. Such variables are well known in the art. More specifically, the greater the degree of similarity or homology between two nucleotide sequences, the greater the value of Tm for hybrids of nucleic acids having those sequences. For hybrids of greater than 100 nucleotides in length, equations for calculating Tm have been derived (see Sambrook et al., supra). For hybridization with shorter nucleic acids, the position of mismatches becomes more important, and the length of the oligonucleotide determines its specificity (see Sambrook et al., supra).
  • the polynucleotides and polypeptides have at least 55, 60, 65, 70, 75, 80, 85, 90, 91 , 92, 93, 94, 95, 96, 97, 98, or 99 percent homology to a desired polynucleotide or polypeptide. In some embodiments, the polynucleotides and polypeptides have at least 55, 60, 65, 70, 75, 80, 85, 90, 91 , 92, 93, 94, 95, 96, 97, 98, or 99 percent identity to a desired polynucleotide or polypeptide.
  • the polynucleotides and polypeptides have at least 55, 60, 65, 70, 75, 80, 85, 90, 91 , 92, 93, 94, 95, 96, 97, 98, or 99 percent similarity to a desired polynucleotide or polypeptide. As described above, degenerate forms of the desired polynucleotide are also acceptable.
  • a polypeptide can be 90, 91 , 92, 93, 94, 95, 96, 97, 98, or 99 homologous, identical, or similar to a desired polypeptide as long as it shares the same function as the desired polypeptide, and the extent of the function can be less or more than that of the desired polypeptide.
  • a polypeptide can have a function that is 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any 0.1 % increment in-between, that of the desired polypeptide.
  • a polypeptide can have a function that is 1 10%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 300%, 400%, 500%, or more, or any 1 % increment in-between, that of the desired polypeptide.
  • the "function" is an enzymatic activity, measurable by any method known to one of skill such as, for example, a method used in the teachings herein.
  • the “desired polypeptide” or “desired polynucleotide” can be referred to as a "reference polypeptide” or “reference polynucleotide”, or the like, in some embodiments as a control for comparison of a polypeptide of interest, which may be considered a “test polypeptide” or “test polynucleotide” or the like.
  • the comparison is that of one set of bases or amino acids against another set for purposes of measuring homology, identity, or similarity.
  • the ability to hybridize is, of course, another way of comparing nucleotide sequences.
  • the terms “homology” and “homologous” can be used interchangeably in some embodiments.
  • the terms can refer to nucleic acid sequence matching and the degree to which changes in the nucleotide bases between polynucleotide sequences affects the gene expression. These terms also refer to modifications, such as deletion or insertion of one or more nucleotides, and the effects of those modifications on the functional properties of the resulting polynucleotide relative to the unmodified polynucleotide. Likewise the terms refer to polypeptide sequence matching and the degree to which changes in the polypeptide sequences, such as those seen when comparing the modified polypeptides to the unmodified polypeptide, affect the function of the polypeptide. It should appreciated to one of skill that the polypeptides, such as the mutants taught herein, can be produced from two non-homologous polynucleotide sequences within the limits of degeneracy.
  • similarity can be used to refer to a comparison between amino acid sequences, and takes into account not only identical amino acids in corresponding positions, but also functionally similar amino acids in corresponding positions. Thus similarity between polypeptide sequences indicates functional similarity, in addition to sequence similarity.
  • Levels of identity between gene sequences and levels of identity or similarity between amino acid sequences can be calculated using known methods. For example, publicly available computer based methods for determining identity and similarity include the BLASTP, BLASTN and FASTA (Atschul et al., J. Molec.
  • the Gap program with a Gap penalty of 12 and a Gap length penalty of 4 can be used for determining the amino acid sequence comparisons, and a Gap penalty of 50 and a Gap length penalty of 3 for the polynucleotide sequence comparisons.
  • the sequences can be aligned so that the highest order match is obtained. The match can be calculated using published techniques that include, for example, Computational Molecular Biology, Lesk, A.
  • similarity is similar to "identity”, but in contrast to identity, similarity can be used to refer to both identical matches and conservative substitution matches. For example, if two polypeptide sequences have 10/20 identical amino acids, and the remainder are all non-conservative substitutions, then the percent identity and similarity would both be 50%. On the other hand, if there are 5 five more positions where there are conservative substitutions, then the percent identity is 50%, whereas the percent similarity is 75%.
  • the term "substantial sequence identity” can refer to an optimal alignment, such as by the programs GAP or BESTFIT using default gap penalties, having at least 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99 percent sequence identity.
  • the difference in what is "substantial” regarding identity can often vary according to a
  • substantially percent identity can be used to refer to a DNA sequence that is sufficiently similar to a reference sequence at the nucleotide level to code for the same protein, or a protein having substantially the same function, in which the comparison can allow for allelic differences in the coding region.
  • the term can be used to refer to a comparison of sequences of two polypeptides optimally aligned.
  • sequence comparisons can be made to a reference
  • the reference sequence may be a subset of a larger sequence.
  • the comparison window can include at least 10 residue or base positions, and sometimes at least 15-20 amino acids or bases.
  • the reference or test sequence may represent, for example, a polypeptide or polynucleotide having one or more deletions, substitutions or additions.
  • variant refers to modifications to a peptide that allows the peptide to retain its binding properties, and such modifications include, but are not limited to, conservative substitutions in which one or more amino acids are substituted for other amino acids; deletion or addition of amino acids that have minimal influence on the binding properties or secondary structure; conjugation of a linker; post-translational modifications such as, for example, the addition of functional groups.
  • post-translational modifications can include, but are not limited to, the addition of modifying groups described below through processes such as, for example, glycosylation, acetylation, phosphorylation, modifications with fatty acids, formation of disulfide bonds between peptides, biotinylation, PEGylation, and combinations thereof.
  • the polypeptides can be modified with any of the various modifying groups known to one of skill.
  • substitution and “conservative substitution” can be used interchangeably in some embodiments. These terms can be used to refer to a conservative amino acid substitution, which is an amino acid substituted by an amino acid of similar charge density,
  • non-conservatively modified variant refers to a non- conservative amino acid substitution, which is an amino acid substituted by an amino acid of differing charge density, hydrophilicity/hydrophobicity, size, and/or configuration such as, for example, substituting valine for phenyalanine.
  • a substitution can be considered conservative if an amino acid falling into one of the following groups is substituted by an amino acid falling in the same group: hydrophilic (Ala, Pro, Gly, Glu, Asp, Gin, Asn, Ser, Thr), aliphatic (Val, lie, Leu, Met), basic (Lys, Arg, His), aromatic (Phe, Tyr, Trp), and sulphydryl (Cys).
  • hydrophilic Al, Pro, Gly, Glu, Asp, Gin, Asn, Ser, Thr
  • aliphatic Val, lie, Leu, Met
  • basic Lys, Arg, His
  • aromatic Phe, Tyr, Trp
  • Cys sulphydryl
  • the substitution of amino acids can be considered conservative where the side chain of the substitution has similar biochemical properties to the side chain of the substituted amino acid.
  • typical industrial fermentation processes might utilize the microbes Escherichia coli K12 or Escherichia coli B, or the yeast Saccharomyces cerevisiae, and recombinant versions of these microbes, which are well characterized industrial strains.
  • the problem is that the antimicrobial activities of aromatic compounds on such industrial microbes are toxic to the microbes, which negates an application to biotransformations of lignin-derived compounds.
  • lignocellulosic biomass might contain aromatic and nonaromatic compounds, such as gallic acid, hydroxymethylfurfural alcohol, hydroxymethylfurfural, furfural alcohol, 3,5-dihydroxybenzoate, furoic acid, 3,4-dihydroxybenzaldehyde, hydroxybenzoate, homovanillin, syringic acid, vanillin, and syringaldehyde.
  • aromatic and nonaromatic compounds such as gallic acid, hydroxymethylfurfural alcohol, hydroxymethylfurfural, furfural alcohol, 3,5-dihydroxybenzoate, furoic acid, 3,4-dihydroxybenzaldehyde, hydroxybenzoate, homovanillin, syringic acid, vanillin, and syringaldehyde.
  • aromatic and nonaromatic compounds such as gallic acid, hydroxymethylfurfural alcohol, hydroxymethylfurfural, furfural alcohol, 3,5-dihydroxybenzoate, furoic acid, 3,4-di
  • furfural, 4-hydroxybenzaldehyde, syringaldehyde, 5-hydroxymethylfurfural, and vanillin are each known to have antimicrobial activity against Escherichia coli, and might have an additive antimicrobial activity against Escherichia coli when present in combination.
  • veratraldehyde, cinnamic acid and the respective benzoic acid derivatives of vanillic acid, vanillylacetone, and the cinnamic acid derivatives o-coumaric acid, m-coumaric acid, and p-coumaric acid might be components of the phenolic streams from pretreated lignocellulosic biomass.
  • Veratraldehyde, cinnamic acid and the respective benzoic acid derivatives of vanillic acid, vanillylacetone, and cinnamic acid derivatives o-coumaric acid, m-coumaric acid, and p- coumaric acid each have significant antifungal activities against the yeast Saccharomyces cerevisiae, and might have an additive antifungal activity against the yeast Saccharomyces cerevisiae when present in combination.
  • benzaldehyde derivatives might be present in the phenolic streams from pretreated lignocellulosic biomass: 2,4,6-trihydroxybenzaldehyde, 2,5-dihydroxybenzaldehyde, 2,3,4-trihydroxybenzaldehyde, 2-hydroxy-5- methoxybenzaldehyde, 2,3-dihydroxybenzaldehyde, 2-hydroxy-3-methoxybenzaldehyde, 4- hydroxy-2,6-dimethoxybenzaldehyde, 2,5-dihydroxybenzaldehyde, 2,4- dihydroxybenzaldehyde, and 2-hydroxybenzaldehyde.
  • 2,4,6- trihydroxybenzaldehyde, 2,5-dihydroxybenzaldehyde, 2,3,4-trihydroxybenzaldehyde, 2- hydroxy-5-methoxybenzaldehyde, 2,3-dihydroxybenzaldehyde, 2-hydroxy-3- methoxybenzaldehyde, 4-hydroxy-2,6-dimethoxybenzaldehyde, 2,5-dihydroxybenzaldehyde, 2,4-dihydroxybenzaldehyde, and 2-hydroxybenzaldehyde have each demonstrated antibacterial activity against Escherichia coli, and might have an additive antibacterial activity against Escherichia coli when present in combination.
  • the antimicrobial activity of lignin-derived compounds creates a need for a strain of microbe that is tolerant to such activity in the reaction environment.
  • the teachings include the identification of recombinant or non-recombinant microbial species that are naturally capable of metabolizing aromatic compounds for the biotransformations of lignin- derived compounds to commercial products.
  • Some examples of microbial species particularly suited for biotransformations of phenolic streams from pretreated lignocellulosic biomass include, but are not limited to, Azotobacter chroococcum, Azotobacter vinelandii, Novosphingobium aromaticivorans, Pseudomonas aeruginosa, Pseudomonas putida, Pseudomonas fluorescens, Pseudomonas stutzerii, Pseudomonas diminuta, Pseudomonas pseudoalcaligenes, Rhodopseudomonas palustris, Spingomonas sp.A1 , Sphingomonas paucimobilis SYK-6, Sphingomonas japonicum, Sphingomonas alaskenesis, Sphingomonas wittichii, Streptomyces
  • alkylbenzenes alkylbenzenes; styrene; atrazine; caprolactam; and polycyclic aromatic hydrocarbons.
  • the microbes can be grown in a fermentor, for example, using methods known to one of skill.
  • the enzymes used in the bioprocessing are obtained from the microbes, and they can be intracellular, extracellular, or a combination thereof.
  • the enzymes can be recovered from the host cells using methods known to one of skill in the art that include, for example, filtering or centrifuging, evaporation, and purification.
  • the method can include breaking open the host cells using ultrasound or a mechanical device, remove debris and extract the protein, after which the protein can be purified using, for example, electrophoresis.
  • the teachings include the use of a microbe, recombinant or non-recombinant, that has tolerance to lignin-derived compounds.
  • a microbe that is tolerant to lignin-derived compounds can be used industrially, for example, to express any enzyme, recombinant or non-recombinant, having a desired enzyme activity while directly in association with the lignin-derived compounds.
  • Such activities include, for example, beta etherase activity, C-alpha-dehydrogenase activity, glutathione lyase activity, or any other enzyme activity that would be useful in the
  • the activities can be wild-type or produce through methods known to one of skill, such as transfection or transformation, for example.
  • the teachings herein are also directed to the discovery and use of recombinant Azotobacter strains heterologously expressing novel beta-etherase enzymes for the hydrolysis of lignin oligomers.
  • Azotobacter vinelandii may possess the industrially relevant strain criteria desired for the teachings provided herein.
  • the criteria includes (i) growth on inexpensive and defined medium, (ii) resistance to inhibitors in hydrolysates of
  • Iignocellulose (iii) tolerance to acidic pH and higher temperatures, (iv) the co-fermentation of pentose and hexose sugars, (v) genetic tractability and availability of gene expression tools, (vi) rapid generation times, and (vii) successful growth performance in pilot scale
  • the teachings are also directed to a method of cleaving a beta-aryl ether bond, the comprising contacting a polypeptide taught herein with a lignin-derived compound having (i) a beta-aryl ether bond and (ii) a molecular weight ranging from about 180 Daltons to about 3000 Daltons; wherein, the contacting occurs in a solvent environment in which the lignin-derived compound is soluble.
  • the term "contacting” refers to placing an agent, such as a compound taught herein, with a target compound, and this placing can occur in situ or in vitro, for example.
  • the teachings are also directed to a method of cleaving a beta-aryl ether bond, the comprising contacting a polypeptide taught herein with a lignin-derived compound having (i) a beta-aryl ether bond and (ii) a molecular weight ranging from about 180 Daltons to about 3000 Daltons; wherein, the contacting occurs in a solvent environment in which the lignin-derived compound is soluble.
  • the lignin-derived compound has a molecular weight of about 180 Daltons to about 1000 Daltons.
  • the solvent environment comprises water.
  • the solvent environment comprises a polar organic solvent.
  • teachings are also directed to a system for bioprocessing lignin-derived
  • lignin-derived compounds having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; and, a solvent in which the lignin-derived compound is soluble;
  • system functions to cleave the beta-aryl ether bond by contacting the polypeptide with the lignin-derived compound in the solvent.
  • teachings are also directed to a recombinant polynucleotide comprising a nucleotide sequence that encodes a polypeptide taught herein.
  • teachings are also directed to a vector or plasmid comprising the polynucleotide, as well as a host cell transformed by the vector or plasmid to express the polypeptide.
  • the teachings are also directed to a method of cleaving a beta-aryl ether bond, the method comprising (i) culturing a host cell taught herein under conditions suitable to produce a polypeptide taught herein; (ii) recovering the polypeptide from the host cell culture; and, (iii) contacting the polypeptide of claim 1 with a lignin-derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; wherein, the contacting occurs in a solvent environment in which the lignin- derived compound is soluble.
  • the host cell can be E. Coli or an Azotobacter strain, such as Azotobacter vinelandii.
  • the lignin-derived compound can have a molecular weight of about 180 Daltons to about 1000 Daltons.
  • the teachings are also directed to a system for bioprocessing lignin-derived
  • the system comprising (i) a transformed host cell taught herein; (ii) a lignin- derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; and, (iii) a solvent in which the lignin-derived compound is soluble; wherein, the system functions to cleave the beta-aryl ether bond by contacting a polypeptide taught herein with the lignin-derived compound in the solvent.
  • a set of aromatic and nonaromatic compounds known to inhibit growth of E. coli and S. cerevisiae strains might be used to characterize the growth, tolerance and metabolic capability of Azotobacter vinelandii strain BAA1303, and A. chroococcum strain 4412 (EB Fred) X-50.
  • Metabolism of various aromatic and nonaromatic compounds by microbial strains might be determined as a function of cellular respiration by the reduction of soluble tetrazolium salts by actively metabolizing cells.
  • XTT (2,3-Bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5- carboxanilide inner salt, Sigma) is reduced to a soluble purple formazan compound by respiring cells.
  • E. coli might be used as the negative control strain in this study. Strains might be grown in rich medium to saturation, washed, and OD600nm of the cultures determined. Equal numbers of bacteria will be inoculated into wells of the 48-well growth asing concentrations of aromatic and non-aromatic compounds in the range of 0-500mM, will be added to the wells to a final volume of 0.8ml.
  • the cultures will be tested for growth upon exposure to the test compounds using the XTT assay kit (Sigma).
  • Culture samples will removed from the 48 well growth plate, and diluted appropriately in 96 well assay plates to which the XTT reagent will be added. Soluble formazan formed will be quantified by absorbance at 450nm. Increased absorbance at 450nm will be indicative of growth or survival, or metabolism of a particular test compound by the strains.
  • Table 3 lists some example compounds that can be used to test the tolerance of microbes on lignin-derived compounds.
  • microbial growth and metabolism studies on soluble lignin samples can also be performed actual industrial samples such as, for example, kraft lignins and biorefinery lignins.
  • This example describes a method for preparing recombinant host cells for the heterologous expression of known and putative beta-etherase encoding gene sequences in Escherichia coli (£. coli).
  • E. coli is used in this example as a surrogate enzyme production host organism for the enzyme discovery.
  • the construction of a novel industrial host microbe, A. vinelandii is described below.
  • ORFs open reading frames
  • the end sequences contained adaptors (Ndel and Xhol) for restriction digestion and cloning into the E. coli expression vector pET24b (Novagen). Internal Ndel and Xhol sites were excluded from the ORF sequences during design of the oligonucleotides. Assembled genes were cloned into a cloning vector (pGOV4), transformed into E. coli CH3 chemically competent cells, and DNA sequences determined from purified plasmid DNA.
  • pGOV4 cloning vector
  • LigE-1 from Accession No ABD26841 .1 , is listed herein as SEQ ID NO:101 for the protein and SEQ ID NO:102 for the gene.
  • SEQ ID NO:101 for the protein
  • SEQ ID NO:102 for the gene.
  • An "optimized" nucleic acid sequence was created to facilitate the transformation in E. co// ' and is listed herein as SEQ ID NO:978.
  • LigF from Accession No BAA2031 .1 (P30347.1 ), is listed herein as SEQ ID NO:513 for the protein and SEQ ID NO:514 for the gene.
  • SEQ ID NO:513 for the protein
  • SEQ ID NO:514 for the gene.
  • An "optimized" nucleic acid sequence was created to facilitate the transformation in E co// ' and is listed herein as SEQ ID NO:979.
  • LigF-1 from Accession No ABD26530.1 , is listed herein as SEQ ID NO:539 for the protein and SEQ ID NO:540 for the gene.
  • An "optimized" nucleic acid sequence was created to facilitate the transformation in E. co// ' and is listed herein as SEQ ID NO:980.
  • LigF-2 from Accession No ABD27301 .1 , is listed herein as SEQ ID NO:541 for the protein and SEQ ID NO:542 for the gene.
  • SEQ ID NO:541 for the protein
  • SEQ ID NO:542 for the gene.
  • An "optimized" nucleic acid sequence was created to facilitate the transformation in E. co// ' and is listed herein as SEQ ID NO:981 .
  • LigF-3 from Accession No ABD27309.1 , is listed herein as SEQ ID NO:545 for the protein and SEQ ID NO:546 for the gene.
  • SEQ ID NO:545 for the protein
  • SEQ ID NO:546 for the gene.
  • An "optimized" nucleic acid sequence was created to facilitate the transformation in E. co// ' and is listed herein as SEQ ID NO:982.
  • This example describes a method for gene expression in E coli, as well as beta- etherase biochemical assays. Expression of known and putative beta-etherase genes was performed using 5ml cultures of the recombinant E. coli strains described herein in Luria Broth medium by induction of gene expression using isopropylthiogalactoside (IPTG) to a final concentration of 0.1 mM. Following induction, and cell harvest, the cells were disrupted using either sonication or the BPER (Invitrogen) cell lysis system.
  • IPTG isopropylthiogalactoside
  • Clarified cell extracts were tested in the in vitro biochemical assay for beta- etherase activity on a fluorescent substrate, a model lignin dimer compound ⁇ -0-( ⁇ - methylumbelliferyl) acetovanillone (MUAV).
  • In vitro reactions were performed in a total volume of 200ul and contained: 25mM TrisHCI pH 7.5; 0.5mM dithiothreitol; 1 mM
  • UV/visible/fluorescent spectrophotometer UV/visible/fluorescent spectrophotometer.
  • the total protein concentrations of the cell lysates were determined using the BCA reagent system for protein quantification (Pierce).
  • Induction might be also performed using IPTG concentrations in the range of 0.01 -1 mM.
  • Cell disruption might be also performed using toluene permeabilization, French pressure techniques, or using multiple freeze/thaw cycles in conjunction with lysozyme.
  • Assay conditions might be varied to include TrisHCI at 10-150mM concentrations and in the pH range of 6.5-8.5; 0-2mM dithiothreitol; 0.05-2mM glutathione; 0.01 -5mM MUAV substrate; 22-42°C reaction temperatures.
  • the biochemical assay might be performed as a fixed time point assay with reaction times ranging from 5 minutes-12 hours, or performed continuously without quenching with glycine/NaOH buffer to extract enzyme kinetic parameters.
  • FIG. 4 illustrates unexpected results from biochemical activity assays for beta- etherase function for the S. paucimobilis positive control polypeptides, and the N. aromaticivorans putative beta-etherase polypeptide, according to some embodiments.
  • the much elevated beta-etherase activity exhibited by the putative ligEI gene product from N. aromaticivorans as compared to the S. paucimobilis ligE gene product was a completely unexpected result of the enzyme discovery program.
  • E. coli cell extracts expressing the N. aromaticovorans ligEI protein yielded a total activity of 529rfu/ug compared to 7rfu/ug for the S. paucimobilis ligE protein.
  • the newly discovered beta-etherase from N. aromaticovorans is approximately 75-fold more efficient than the previously described S. paucimobilis ligE beta-etherase enzyme.
  • the highly efficient novel beta-etherase is ideally suited to be a biocatalyst for conversion of lignin aryl ethers to monomers in biotechnological processes.
  • ABD26841 .1 (SEQ ID NO:101 ); ABD26530.1 (SEQ ID NO:539); ABD27301 .1 (SEQ ID NO:541 ); and ABD27309.1 (SEQ ID NO:545).
  • bioinformatic screen that was used to help identify putative enzymes is not a definitive predictor in itself of biochemical activities, particularly in view of (i) having only one known active enzyme for LigE in a different species, (ii) one known active enzyme for LigF, and (iii) the unexpected extent of such activities discovered.
  • the tests for function therefore had to be performed empirically on the N. aromaticivorans putative beta-etherase gene set.
  • This example describes the extended use of bioinformatics to identify a pool of putative enzymes in the discovery program.
  • the bioinformatic screen that was used to help identify putative enzymes initially was not a definitive predictor in itself of biochemical activities, particularly in view of (i) having only one known active enzyme for LigE in a different species, (ii) one known active enzyme for LigF, and (iii) the unexpected extent of such activities discovered. Having the additional known active enzymes provided more information that could be used to enhance the effectiveness of the bioinformatics in identifying the pool of putative enzymes for both LigE-type and LigF-type enzymes.
  • the N. aromaticivorans LigE1 and LigF2 polypeptide sequences were used as query sequences for the identification of functional domains using the conserveed Domain Database (CDD) in GenBank.
  • CDD Conserved Domain Database
  • the N. aromaticivorans LigE1 polypeptide is annotated as a glutathione S- transferase (GST)-like protein with similarity to the GST C family, and the beta-etherase LigE subfamily.
  • the LigE sub-family is composed of proteins similar to S. paucimobilis beta etherase, LigE, a GST-like protein that catalyzes the cleavage of the beta-aryl ether linkages present in low-moleculer weight lignins using reduced glutathione (GSH) as the hydrogen donor in the reaction.
  • the GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains.
  • Table 5 describes conserved domains and essential amino acid residues in the N. aromaticivorans LigE1 polypeptide (ABD26841 .1 ), according to some embodiments.
  • the three (3) conserved functional domains annotated in the N. aromaticivorans LigE1 polypeptide are: i) the dimer interface; ii) the N terminal domain; iii) the lignin substrate binding pocket or the H site.
  • Amino acid residues defining the functional domains in such embodiments are residues 98-221 in the N. aromaticivorans LigE1 polypeptide.
  • Table 5 also lists fifteen (15) amino acid residues as conserved and essential for catalytic activity (column 3 of Table 5), , according to some embodiments. These include: K100; A101 ; N104; P166; W107; Y184; Y187; R188; G191 ; G192; F195; V1 1 1 ; G1 12; M1 15; F1 16. While not intending to be bound by any theory or mechanism of action, these residues appear responsible for the high beta-etherase catalytic activity discovered for the N. aromaticivorans LigE1 polypeptide compared to the S. paucimobilis ligE polypeptide.
  • aromaticivorans LigE1 polypeptide might be altered conservatively, and singly or in combination with similar amino acid residues that would retain or improve the catalytic function of the N. aromaticivorans LigE1 polypeptide. Examples of such alternate residues that might be incorporated at the essential positions are also shown in column 4 of Table 5.
  • N. aromaticivorans LigF2 polypeptide is annotated as a glutathione S- transferase (GST)-like protein with similarity to the GST C family, catalyzing the conjugation of glutathione with a wide range of xenobiotic agents.
  • GST glutathione S- transferase
  • Table 6 describes conserved domains and essential amino acid residues in the N. aromaticivorans LigF2 polypeptide (ABD27301 .1 ), according to some embodiments.
  • the three (3) conserved functional domains annotated for the N. aromaticivorans LigF2 polypeptide are similar to those described for the N. aromaticivorans LigE polypeptide and comprise: i) the dimer interface; ii) the N terminal domain; iii) the substrate binding pocket or the H site.
  • amino acid residues defining the functional domains are residues 99-230 in the N. aromaticivorans LigF2 polypeptide.
  • Table 6 also lists sixteen (16) amino acid residues as conserved and essential for catalytic activity (column 3 of Table 6) of the N. aromaticivorans LigF2 polypeptide, according to some embodiments. These include: R100; Y101 ; K104; K176; D107; L194; 1197; N198; S201 ; M206; M1 1 1 ; N1 12; S1 15; M1 16; M206; H202. While not intending to be bound by any theory or mechanism of action, these 16 residues appear to be responsible for the high beta-etherase catalytic activity discovered for the N. aromaticivorans LigF2 polypeptide compared to the S. paucimobilis LigF polypeptide. [00182] In such embodiments, the essential amino acid residues of the N.
  • aromaticivorans LigF2 polypeptide might be altered conservatively, and singly or in combination with similar amino acid residues that would retain or improve the catalytic function of the N. aromaticivorans LigF2 polypeptide. Examples of such alternate residues that might be incorporated at the essential positions are shown in column 4 of Table 6.
  • PDOs protein disulfide oxidoreductases
  • TRX protein disulfide isomerase
  • tlpA protein disulfide isomerase
  • glutaredoxin glutaredoxin
  • NrdH redoxin bacterial Dsb proteins
  • TRX-like ferredoxins include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others.
  • Table 7 lists 3 subject sequences having high identities (>80%) to residues 19-54 of LigE-1 (SEQ ID NO:101 ). In some embodiments, these sequences are likely to be essential to catalytic functions similar to those discovered for the N. aromaticivorans ligEI polypeptide.
  • Table 8 provides the percent identities and similarities to N. aromaticovorans LigF2 query sequence residues 47-57.
  • Table 9 provides the percent identities and similarities to N. aromaticovorans LigF2 query sequence residues 63-76. [001991 Table 9.
  • the bioinformatics provides valuable information about protein structure that can assist in identifying test candidates.
  • the LigE1 has the 98-221 region, which is annotated in the databases as potentially responsible as component of binding and activity, dimerization, and for binding and catalysis in general. While not intending to be bound by any theory or mechanism of action, the variability in active site structures is reflected by the variability in substrate structures.
  • the 19-54 region which is annotated in the databases as a second region that is potentially responsible as component of the reductase function, and thus potentially responsible for catalysis in addition to the 98-221 region, while having more conservation between members.
  • Motif finding also known as profile analysis, constructs global multiple sequence alignments that attempt to align short conserved sequence motifs among the sequences in the query set. This can be done, for example, by first constructing a general global multiple sequence alignment, after which highly conserved regions are isolated, in a manner similar to what is taught herein, and used to construct a set of profile matrices.
  • the profile matrix for each conserved region is arranged like a scoring matrix but its frequency counts for each amino acid or nucleotide at each position are derived from the conserved region's character distribution rather than from a more general empirical distribution.
  • the profile matrices are then used to search other sequences for occurrences of the motif they characterize.
  • LigE-1 and LigF-2 were further examined by comparing their structures to other polypeptides of the LigE-type and LigF-type, respectively.
  • Table 10A shows conserved residues between the polypeptide sequences of LigE and LigE-1
  • Table 10B shows conserved residues between the polypeptide sequences of LigF and LigF-2.
  • LigE residues are from S. paucimobilis (BAA02032.1 ) and the LigE-1 residues are from N. aromaticivorans LigE1 (ABD26841 .1 ).
  • the numbering is done according to the S. paucimobilis sequence (BAA02032.1 ) in the PRALINE alignment file (gaps not included).
  • Table 10B Table 10B.
  • LigF residues are from S. paucimobilis (BAA02031 .1 ) and the LigF-2 residues are from N. aromaticivorans (ABD27301 .1 ). Numbering is according to the S. paucimobilis sequence (BAA02031 .1 ) in the PRALINE alignment file (gaps not included.
  • This example provides additional sequences for a second round of assays, the sequences containing the 3 conserved functional domains described herein for the GST C family of proteins, and belong to the beta-etherase LigE subfamily.
  • Table 1 1 lists nine (9) additional sequences having identities of 51 % -73% at the amino acid level that were identified in the SwissProt database using the S. paucimobilis LigE sequence (P27457.3) as the query.
  • the bioinformatics information suggests that these 9 sequences are excellent candidates for the next round of synthesis, cloning, expression and testing for the desired biochemical functions using the methods described herein.
  • FIG. 5 illustrates beta-aryl-ether compounds to be tested as substrates
  • MUAV native lignin structures
  • additional aryl-ether compounds such as those shown in FIG. 5 might be used to assess substrate specificities of the beta-etherases towards dimers and trimers of aromatic compounds containing the beta-aryl ether linkage and representative of native lignin structures.
  • Higher order oligomers of molecular weights ⁇ 2000 might be synthesized and tested as well.
  • the compounds might be obtained by custom organic synthesis, as for the fluorescent substrate MUAV.
  • FIG. 6 illustrates pathways of guaiacylglycerol ⁇ -guaiacyl ether (GGE)
  • GGE guaiacylglycerol- ⁇ -guaiacyl ether
  • the ligD gene product encodes a C alpha-dehydrogenase which oxidizes GGE to a-(2-methoxyphenoxy)-p- hydroxypropiovanillone (MPHPV); the ether bond of MPHPV is cleaved by the beta-etherase activities of the ligE and HgFgene products to yield the lignin monomer guaiacol, and oc- glutathionylhydroxypropiovanillone (GS-HPV), respectively.
  • MPHPV oc- glutathionylhydroxypropiovanillone
  • the HgG gene product encodes a glutathione (GSH)-eliminating glutathione S transferase (GST) which catalyzes the elimination of glutathione (GSH) from GS-HPV to yield the lignin hydroxypropiovanillone (HPV).
  • GSH glutathione
  • GST glutathione S transferase
  • LigE and LigF polypeptides might be sufficient to hydrolyze native lignin structures, it would be useful to discover novel C alpha dehydrogenases (S. paucimobilis LigD homologs) and glutathione (GSH)-eliminating glutathione S transferases (S. paucimobilis LigG homologs) for industrial applications.
  • the enzyme discovery programs might be conducted by methods similar to those described herein.
  • the detection of lignin substrates, intermediates, and products of biochemical reactions might be measured following filtration, and the extraction of substrates and products into ethyl acetate. Substrates and products might be separated using reverse phase HPLC conditions with a C18 column developed with a gradient solvent system of methanol and water, and detected at 230nm or 254nm.
  • Table 12 lists potential C alpha-dehydrogenase polypeptide sequences, the
  • LigD-type for use in conjunction with beta etherases including, but not limited to, LigE/F.
  • the sequences were identified using bioinformatic methods, such as those taught herein. These C alpha-dehydrogenases are classified in the CDD as short-chain
  • SDRs dehydrogenase/reductases
  • Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues.
  • Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns.
  • Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151 , human prostaglandin dehydrogenase (PGDH) numbering).
  • Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif.
  • Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase can have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN).
  • Fungal type ketoacyl reductases can have a TGXXXGX(1 -2)G NAD(P)-binding motif.
  • Table 13 lists potential LigG (glutathione-eliminating)-like enzyme sequences for use in conjunction with beta etherases including, but not limited to, LigE/F.
  • the sequences were identified using bioinformatic methods, such as those taught herein. These might be utilized in conjunction with C-alpha dehydrogenases, and/or with LigE/F-like beta-etherases.
  • the LigG-like proteins are annotated in the CDD as glutathione S-transferase (GST)-like proteins with similarity to the GST C family, the GST-N family, and the thioredoxin (TRX)- like superfamily of proteins containing a TRX fold.
  • GST glutathione S-transferase
  • TRX thioredoxin
  • This example describes the creation of a novel recombinant microbial system for the conversion of lignin oligomers to monomers.
  • Azotobacter vinelandii strain BAA-1303 DJ might be transformed with beta-etherase encoding genes from N. aromaticovorans with the objective of creating a lignin phenolics-tolerant A. vinelandii strain capable of converting lignin oligomers to monomers at high yields in industrial processes.
  • Table 14 lists additional A. vinelandii strains that might be used as host strains for beta- etherase gene expression, for example, by their strain designation and American Type
  • the heterologous production of beta etherases, Coc dehydrogenases, and other enzymes for the production of lignin monomers and aromatic products in A. vinelandii might be achieved using the expression plasmid system described herein.
  • the broad host range multicopy plasmid pKT230 (ATCC) encoding streptomycin resistance might be used for gene cloning.
  • Genes can be synthesized by methods describe above, and cloned into the Smal site of pKT230.
  • the nifH promoter from A. vinelandii strain BAA 1 303 DJ can be used to control gene expression.
  • A. vinelandii strain BAA 1303 DJ might be transformed with pKT230 derivatives using electroporation of electrocompetent cell (Eppendorf method), or by incubation of plasmid DNA with chemically competent cells prepared in TF medium (1 .9718g of MgS04, 0.0136 g of CaS04, 1 .1 g of CH3COONH4, 1 0 g of glucose, 0.25 g of KH2P04, and 0.55 g of K2HP04 per liter). Transformants might be selected by screening for resistance to streptomycin.
  • Gene expression might be induced by cell growth under nitrogen-free Burk's medium (0.2 g of MgS04, 0.1 g of CaS04, 0.5 g of yeast extract, 20 g of sucrose, 0.8 g of K2HP04, and 0.2 g of KH2P04, with trace amounts of FeCI3 and Na2Mo04, per liter).
  • A. vinelandii strain BAA 1303 DJ can be tested using methods known to one of skill, such as the methods provided herein. Biochemical activity assays for beta-etherase function, and for total protein might be performed as described herein.
  • EXAMPLE 9 28] This example describes the design and use of recombinant Azotobacter strains heterologously expressing enzymes for the production of high value aromatic compounds from lignin core structures. Table 15 lists a few examples of aromatic compounds that might be produced by the microbial platforms described herein.
  • Catechol might be produced from guaiacol using an A. vinelandii or A. chroococcum strain engineered with enzymes including beta-etherases and demethylases, or demethylase enzymes alone.
  • Azotobacter strains might be engineered to express the heterologous enzymes by the methods described herein.
  • FIG. 7 illustrates an example of a biochemical process for the production of catechol from lignin oligomers, according to some embodiments.
  • the biochemical processes leading to aromatic products such as catechol might be designed as 3 unit operations described below:
  • Biotransformation The biotransformation of the phenolic substrate stream might be carried out in a fed-batch bioprocess using Azotobacter strains engineered to specifically and optimally convert specific lignin-derived phenolic substrates to the final product, such as catechol. Corn steep liquor might be used the base medium used in the biotransformations.
  • the phenolic stream might be introduced in fed-batch mode, at concentrations that will be tolerated by the strains.
  • lignin-derived syringic acid might be converted to gallic acid via a 2-step biochemical conversion using aryl aldehyde oxidases and demethylases.
  • Lignin-derived vanillin might be converted to protocatechuic acid via a 2- step biochemical conversion using aryl aldehyde oxidases and demethylases.
  • the specific enzymes might be engineered into A. vinelandii or A. chroococcum strains, for example, and the process might be performed using unit operations similar to those described herein for the biochemical production of catechol.
  • FIG. 8 illustrates an example of a biochemical process for the production of vanillin from lignin oligomers, according to some embodiments.
  • Vanillin can be used as a flavoring agent, and as a precursor for pharmaceuticals such as methyldopa.
  • Synthetic vanillin for example, can be produced from petroleum-derived guaiacol by reaction with glyoxylic acid. Vanillin, however, can also be produced from lignin-derived ⁇ - hydroxypropiovanillone ( ⁇ -HPV) according to the process scheme indicated in FIG. 8.
  • a 2- step biochemical route to vanillin from ⁇ -HPV can be achieved using the enzymes 2,4- dihydroxyacetophenone oxidoreductase, and vanillin dehydrogenase or carboxylic acid reductases, engineered into A. vinelandii.
  • FIG. 9 illustrates an example of a biochemical process for the production of 2,4- diaminotoluene from lignin oligomers, according to some embodiments.
  • Toluene diisocyanate TDI
  • 2,4- diaminotoluene (2,4-DAT) is the key precursor to TDI.
  • Diaminotoluenes can be produced industrially by the sequential nitration of toluene with nitric acid, followed by the reduction of the dinitrotoluenes to the corresponding diaminotoluenes.
  • FIG. 10 illustrates process schemes for additional product targets that include ortho-cresol, salicylic acid, and aminosalicylic acid, for the production of valuable chemicals from lignin oligomers, according to some embodiments.
  • These chemicals as with the others, have traditionally been obtained from the problematic petrochemical processes.
  • a few of the process schemes for producing these chemicals using the teachings herein, based on guaiacol or 2-methoxytoluene, are shown schematically in FIG. 10.
  • Designed biochemical routes, combined with the remarkable phenolics-tolerance traits of Azotobacter strains are proposed for conversions of lignin structures to industrial and fine chemicals.
  • This example describes potential LigE-, LigF-, LigG-, and LigD-type polypeptides, and the genes encoding them.
  • the potential polypeptides were identified using
  • the query sequences in the initial pass for the LigE-type and LigF-type were Sphingomonas paucimobilis sequences, such as those discussed in Masai, E., et al.
  • the query sequences for the LigG-type and LigD-type were also provided.
  • Sphingomonas paucimobilis sequences such as those discussed in Masai. The following sequences were used in the initial pass for all queries:
  • LigE from Accession No BAA2032.1 , is listed herein as SEQ ID NO:1 for the protein and SEQ ID NO:2 for the gene.
  • LigF from Accession No BAA2031 .1 (P30347.1 ), is listed herein as SEQ ID No.
  • LigG from Accession No Q9Z339.2, is listed herein as SEQ ID NO:733 for the protein and SEQ ID NO:734 for the gene.
  • LigD from Accession No Q01 198.1 , is listed herein as SEQ ID NO:777 for the protein and SEQ ID NO:778 for the gene.
  • LigE-1 from Accession No ABD26841 .1 , is listed herein as SEQ ID NO:101 for the protein and SEQ ID NO:102 for the gene.
  • LigF-2 from Accession No ABD27301 .1 , is listed herein as SEQ ID NO:541 for the protein and SEQ ID NO:542 for the gene.
  • Table 16 lists SEQ ID NOs:1 -246, which are potential protein sequences of the LigE-type, as well as a respective gene sequence encoding the protein.
  • Table 17 lists SEQ ID NOs:247-576, which are potential protein sequences of the LigF-type, as well as a respective gene sequence encoding the protein.
  • Table 18 lists SEQ ID NOs:577-776, which are potential protein sequences of the LigG-type, as well as a respective gene sequence encoding the protein.
  • Table 19 lists SEQ ID NOs: 777-976, which are potential protein sequences of the LigD-type, as well as a respective gene sequence encoding the protein.
  • Bioinformatic methods such as those described herein, can be used to suggest an efficient order of experimentation to identify additional potential enzymes for use with the teachings provided herein.
  • mutations and amino acid substitutions can be used to test affects on enzyme activity to further understand the structure of the most active proteins with respect to the enzyme functions sought by teachings provided herein.
  • lignin beta-ether hydrolase [Mesorhizobium loti LIGE MAFF303099] >dbj
  • lignin degradation protein [Agrobacterium LIGE tumefaciens str. C58] >gb
  • terminal domain protein [Acidiphilium cryptum JF
  • beta-aryl ether cleaving enzyme beta-aryl ether cleaving enzyme
  • lignin LIGE degradation protein [Rhizobium etli CIAT 652]
  • beta etherase [Oligotropha carboxidovorans
  • glutathione S-transferase domain-containing LIGE protein [Methylobacterium nodulans ORS 2060] >gb
  • domain protein [Methylobacterium nodulans PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO: NO: NO:
  • lignin degradation protein [Agrobacterium vitis LIGE S4] >gb
  • glutathione S-transferase domain protein LIGE [Rhizobium leguminosarum bv. trifolii WSM1325] >gb
  • domain protein [Rhizobium leguminosarum bv.
  • lignin degradation protein [Agrobacterium sp. LIGE H13-3] >gb
  • beta-aryl ether cleaving enzyme beta-aryl ether cleaving enzyme
  • lignin LIGE degradation protein [Rhizobium etli CFN 42]
  • glutathione S-transferase-like protein LIGE Trichodesmium erythraeum IMS101
  • beta-etherase (beta-aryl ether cleaving LIGE enzyme) protein [Phaeobacter gallaeciensis
  • beta-etherase (beta-aryl ether cleaving LIGE enzyme) protein [Phaeobacter gallaeciensis
  • putative beta-etherase (beta-aryl ether cleaving LIGE enzyme) protein [Hoeflea phototrophica DFL-43] >gb
  • putative beta-etherase (beta-) protein [Hoeflea phototrophica DFL-43] >gb
  • glutathione S-transferase-like protein [alpha LIGE proteobacterium BAL199] >gb
  • lignin degradation protein [Achromobacter LIGE piechaudii ATCC 43553] >gb
  • Glutathione S-transferase domain protein [Afipia LIGE sp. 1 NLS2] >gb
  • Glutathione S-transferase domain protein [Afipia LIGE sp. 1 NLS2] >gb
  • Glutathione S-transferase domain protein [Afipia LIGE sp. 1 NLS2] >gb
  • Glutathione S-transferase [gamma LIGE proteobacterium IMCC1989] >gb
  • lignin degradation protein [Agrobacterium sp. LIGE ATCC 31749] >gb
  • lignin beta-ether hydrolase [Bradyrhizobiaceae LIGE bacterium SG-6C] >gb
  • lignin beta-ether hydrolase [Bradyrhizobiaceae LIGE bacterium SG-6C] >gb
  • Glutathione S-transferase domain-containing LIGE protein [Acidiphilium sp. PM] >gb
  • glutathione S-transferase domain-containing LIGE protein [Halomonas sp. TD01] >gb
  • Pc12g05530 [Penicillium chrysogenum LIGE Wisconsin 54-1255] >emb
  • glutathione S-transferase [Mesorhizobium ciceri LIGE biovar biserrulae WSM1271] >gb
  • DEHA2A00660p [Debaryomyces hansenii LIGE CBS767] >emb
  • terminal domain protein [Acidiphilium cryptum JF
  • GST putative glutathione S-transferase
  • PROTEIN GENE GENBANK DESCRIPTION TYPE SEQ ID SEQ ID ACCESSION NO: NO: NO:
  • glutathione S-transferase family protein LigG [Thiobacillus denitrificans ATCC 25259]
  • glutathione S-transferase family protein LigG [Maritimibacter alkaliphilus HTCC2654]
  • PROTEIN GENE GEN BANK DESCRIPTION TYPE SEQ ID SEQ ID ACCESSION NO: NO: NO:
  • omega-1 -like isoform 1 [Equus caballusl
  • PROTEIN GENE GENBANK DESCRIPTION TYPE SEQ ID SEQ ID ACCESSION NO:

Abstract

The teachings provided herein are generally directed to a method of converting lignin-derived compounds to valuable aromatic chemicals using an enzymatic, bioconversion process. The teachings provide a selection of (i) host cells that are tolerant to the toxic compounds present in lignin fractions; (ii) polypeptides that can be used as enzymes in the bioconversion of the lignin fractions to the aromatic chemical products; (iii) polynucleotides that can be used to transform the host cells to express the selection of polypeptides as enzymes in the bioconversion of the lignin fractions; and (iv) the transformants that express the enzymes.

Description

BIOPRODUCTION OF AROMATIC CHEMICALS FROM LIGNIN-DERIVED COMPOUNDS
RANJINI CHATTERJEE
KENNETH ZAHN KENNETH MITCHELL GARY LIU
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001 ] This application claims the benefit of U.S. Provisional Application Nos. 61/403,440, filed 9/15/2010; and 61 /455,709, filed 10/25/2010; each application of which is hereby incorporated herein by reference in it's entirety,
SEQUENCE LISTING
[0002] The instant application is filed with an ASCII compliant text file of a Sequence Listing.
The name of the attached file is ALIGP004US01_SEQLIST_AS-FILED.txt, and the file was created August 29, 201 1 , is 813 KB in size, and is hereby incorporated herein by reference in its entirety. Because the ASCII compliant text file serves as both the paper copy required by § 1 .821 (c) and the CRF required by § 1 .821 (e), the statement indicating that the paper copy and CRF copy of the sequence listing are identical is no longer necessary under 37 C.F.R. § 1 .821 (f), as per Federal Register /Vol. 74, No. 206 /Tuesday, October 27, 2009, Section I.
BACKGROUND OF THE INVENTION Field of the Invention
[0003] The teachings provided herein are generally directed to a method of converting lignin- derived compounds to valuable aromatic chemicals using an enzymatic, bioconversion process. Description of the Related Art
[0004] Currently, there is a worldwide, global dependence on petroleum as a deplete-able
feedstock for the manufacture of fuels and chemicals. The problems of using petroleum are so well-known and documented that they've become nearly a cliche to the world population. In short, petroleum-based processes are dirty and hazardous. Environmental effects associated with the use of petroleum are known to include, for example, air pollution, global warming, damage from extraction, oil spills, tarballs, and health hazards to humans, domestic animals, and wildlife.
[0005] Oil refineries, for example, are petroleum-based processes that primarily produce
gasoline. However, they are also used extensively to produce valuable and less well-known chemical products used in the manufacture of pharmaceuticals, agrochemicals, food ingredients, and plastics. A clean, green alternative to this market area would be appreciated worldwide.
[0006] Bioprocesses can present a clean, green alternative to the petroleum-based processes, a bioprocess being one that uses organisms, cells, organelles, or enzymes to carry out a commercial process. Biorefineries, for example, can produce, for example, chemicals, heat and power, as well as food, feed, fuel and industrial chemical products. Examples of biorefineries can include wet and dry corn mills, pulp and paper mills, and the biofuels industry. In leather tanning, hides are softened and hair is removed using proteases. In brewing, amylases are used in germinating barley. In cheese-making, rennin is used to coagulated the proteins in mil. The biofuels industry, for example, has been a point of focus recently, naturally focusing on fuel products to replace petroleum-based fuels and, as a result, has not developed other valuable chemical products that also rely on petroleum- based processes.
[0007] As such, biorefineries use enzymes to convert natural products to useful chemicals. A natural product, such as the wood that is used in a pulp and paper mill, contains cellulose, hemicelluloses, and lignin. A typical range of compositions for a hardwood may be about 40-44% cellulose, about 15-35% hemicelluloses, and about 18-25% lignin. Likewise, a typical range of compositions for a softwood may be about 40-44% cellulose, about 20-32% hemicelluloses, and about 25-35% lignin. Since all biofuels come from cellulosic
biorefineries, where the key raw material is glucose, derived from cellulose, lignin remains underutilized. Lignin is the single most abundant source of aromatic compounds in nature, and the use of lignin is currently limited to low value applications, such as combustion to generate process heat and energy for the biorefinery facilities. In the alternative, lignin is sold as a natural component of animal feeds or fertilizers. Interestingly, however, lignin is the only plant biomass component based on aromatic core structures, and such core structures are valuable in the production of industrial chemicals. One of skill will appreciate that, unfortunately, a major problem to such a use of lignin remains: the aromatic compounds present in the lignin fraction of a biorefinery include toxic compounds that inhibit the growth and survival of industrial microbes. For at least these reasons, processes for converting lignin fractions to industrial products using industrial microbes have not been successful.
[0008] In view of the above, one of skill will appreciate (i) a clean, green replacement for
petroleum-based processes in the production of valuable chemical products that include major markets such as, for example, pharmaceuticals, agrochemicals, food ingredients, and plastics; (ii) a profitable use of the abundant and renewable natural resource available in lignin, which is currently an industrial waste stream that is underutilized as an industrial feedstock; (iii) a selection of host cells that are tolerant to the toxic compounds present in lignin fractions in the feedstock; (iv) a selection of polypeptides that can be used as enzymes in the bioconversion of the lignin fractions to the valuable chemical products; (v) a selection of polynucleotides that can be used to transform host cells to express the selection of polypeptides in the bioconversion of the lignin fractions to the valuable chemical products; (vi) systems that include transformants that express the enzymes, where the transformants can be used to (a) express the enzymes while in direct contact with the lignin fractions or (b) express the enzymes for extraction from the cells, after which the extracted enzymes are used directly in contact with the lignin fractions; and (vii) a clean-and-green method of producing valuable chemical products at higher profits than petroleum-based processes.
SUMMARY
[0009] This invention is generally directed to a recombinant method of producing enzymes for use in the bioconversion of lignin-derived compounds to valuable aromatic chemicals. In some embodiments, the teachings are directed to an isolated recombinant polypeptide, comprising an amino acid sequence having at least 95% identity to SEQ ID NO:101 . The sequence can conserve residues T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, G54, K100, A101 , N104, V1 1 1 , G1 12, M1 15, F1 16, P166, W107, Y184, Y187, R188, G191 , G192, and F195.
[0010] In some embodiments, the teachings are directed to an isolated recombinant
polypeptide, comprising SEQ ID NO:101 ; or conservative substitutions thereof outside of the conserved residues. The conserved residues can include T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, G54; K100, A101 , N104, V1 1 1 , G1 12, M1 15, F1 16, P166, W107, Y184, Y187, R188, G191 , G192, and F195.
[001 1 ] In some embodiments, the teachings are directed to an isolated recombinant glutathione S-transferase enzyme, comprising an amino acid sequence having at least 95% identity to SEQ ID NO:101 . The amino acid sequence can conserve residues T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, G54; K100, A101 , N104, V1 1 1 , G1 12, M1 15, F1 16, P166, W107, Y184, Y187, R188, G191 , G192, and F195; wherein, the amino acid sequence functions to cleave a beta-aryl ether.
[0012] In some embodiments, the teachings are directed to an isolated recombinant glutathione S-transferase enzyme, comprising an amino acid sequence having at least 95% identity to SEQ ID NO:101 ; wherein, the amino acid sequence functions to cleave a beta-aryl ether.
[0013] In some embodiments, the teachings are directed to an isolated recombinant
polypeptide, comprising (i) a length ranging from about 279 to about 281 amino acids; (ii) a first amino acid region consisting of residues 19-54 from SEQ ID NO:101 , or conservative substitutions thereof outside of conserved residues T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, and G54; wherein, the first amino acid region can be located in the recombinant polypeptide from about residue 14 to about residue 59; and, (iii) a second amino acid region consisting of residues 98-221 from SEQ ID NO:101 , or conservative substitutions thereof outside of conserved residues K100, A101 , N104, V1 1 1 , G1 12, M1 15, F1 16, P166, W107, Y184, Y187, R188, G191 , G192, and F195; wherein, the second amino acid region is located in the recombinant polypeptide from about residue 93 to about residue 226.
[0014] In some embodiments, the teachings are directed to an isolated recombinant glutathione S-transferase enzyme, comprising (i) a length ranging from about 279 to about 281 amino acids; (ii) a first amino acid region having at least 95% identity to residues 19-54 from SEQ ID NO:101 while conserving residues T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, and G54; wherein, the first amino acid region is located in the recombinant polypeptide from about residue 14 to about residue 59; and, (iii) a second amino acid region having at least 95% identity to residues 98-221 from SEQ ID NO:101 while conserving residues K100, A101 , N104, V1 1 1 , G1 12, M1 15, F1 16, P166, W107, Y184, Y187, R188, G191 , G192, and F195; wherein, the second amino acid region can be located in the recombinant polypeptide from about residue 93 to about residue 226; and, the recombinant glutathione S-transferase enzyme can function to cleave a beta-aryl ether.
[0015] In some embodiments, the teachings are directed to an isolated recombinant glutathione S-transferase enzyme, comprising an amino acid sequence having at least 95% identity to SEQ ID NO:541 ; wherein, the amino acid sequence functions to cleave a beta-aryl ether.
[0016] In some embodiments, the teachings are directed to an isolated recombinant
polypeptide, comprising (i) a length ranging from about 256 to about 260 amino acids; (ii) a first amino acid region consisting of residues 47-57 from SEQ ID NO:541 , or conservative substitutions thereof outside of conserved residues A47, I48, N49, P50, G52, V54, P55, V56, L57; wherein, the first amino acid region is located in the recombinant polypeptide from about residue 45 to about residue 57; (iii) a second amino acid region consisting of 63-76 from SEQ ID NO:541 ; and, (iv) a third amino acid region consisting of residues 99-230 from SEQ ID NO:541 , or conservative substitutions thereof outside of conserved residues R100, Y101 , K104, D107, M1 1 1 , N1 12, S1 15, M1 16, K176, L194, 1197, N198, S201 , H202, and M206; wherein, the second amino acid region is located in the recombinant polypeptide from about residue 94 to about residue 235.
[0017] In some embodiments, the teachings are directed to an isolated recombinant glutathione S-transferase enzyme, comprising (i) a length ranging from about 279 to about 281 amino acids; (ii) a first amino acid region having at least 95% identity to 47-57 from SEQ ID NO:541 , or conservative substitutions thereof outside of conserved residues A47, I48, N49, P50, G52, V54, P55, V56, L57; wherein, the first amino acid region can be located in the recombinant polypeptide from about residue 45 to about residue 57; (iii) a second amino acid region consisting of 63-76 from SEQ ID NO:541 ; and, (iv) a third amino acid region having at least 95% identity to residues 99-230 from SEQ ID NO:541 , or conservative substitutions thereof outside of conserved residues R100, Y101 , K104, D107, M1 1 1 , N1 12, S1 15, M1 16, K176, L194, 1197, N198, S201 , H202, and M206; wherein, the second amino acid region can be located in the recombinant polypeptide from about residue 94 to about residue 235; wherein, the recombinant glutathione S-transferase enzyme functions to cleave a beta-aryl ether.
[0018] In some embodiments, an amino acid substitution outside of the conserved residues can be a conservative substitution. And, in many embodiments, the amino acid sequence can function to cleave a beta-aryl ether.
[0019] The teachings are also directed to a method of cleaving a beta-aryl ether bond, the
comprising contacting a polypeptide taught herein with a lignin-derived compound having (i) a beta-aryl ether bond and (ii) a molecular weight ranging from about 180 Daltons to about 3000 Daltons; wherein, the contacting occurs in a solvent environment in which the lignin- derived compound is soluble.
[0020] In some embodiments, the lignin-derived compound has a molecular weight of about 180 Daltons to about 1000 Daltons. In some embodiments, the solvent environment comprises water. And, in some embodiments, the solvent environment comprises a polar organic solvent.
[0021 ] The teachings are also directed to a system for bioprocessing lignin-derived compounds, the system comprising a polypeptide taught herein, a lignin-derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; and, a solvent in which the lignin-derived compound is soluble; wherein, the system functions to cleave the beta-aryl ether bond by contacting the polypeptide with the lignin- derived compound in the solvent.
[0022] The teachings are also directed to a recombinant polynucleotide comprising a nucleotide sequence that encodes a polypeptide taught herein. Likewise, the teachings are also directed to a vector or plasmid comprising the polynucleotide, as well as a host cell transformed by the vector or plasmid to express the polypeptide.
[0023] The teachings are also directed to a method of cleaving a beta-aryl ether bond, the
method comprising (i) culturing a host cell taught herein under conditions suitable to produce a polypeptide taught herein; (ii) recovering the polypeptide from the host cell culture; and, (iii) contacting the polypeptide of claim 1 with a lignin-derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; wherein, the contacting occurs in a solvent environment in which the lignin- derived compound is soluble.
[0024] In some embodiments, the host cell can be E. Coli or an Azotobacter strain, such as Azotobacter vinelandii. And, in some embodiments, the lignin-derived compound can have a molecular weight of about 180 Daltons to about 1000 Daltons.
[0025] The teachings are also directed to a system for bioprocessing lignin-derived compounds, the system comprising (i) a transformed host cell taught herein; (ii) a lignin-derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; and, (iii) a solvent in which the lignin-derived compound is soluble; wherein, the system functions to cleave the beta-aryl ether bond by contacting a polypeptide taught herein with the lignin-derived compound in the solvent.
BRIEF DESCRIPTION OF THE DRAWINGS
[0026] FIGs. 1 A and 1 B illustrate general concepts of the biorefinery and discovery processes discussed herein, according to some embodiments.
[0027] FIG. 2 illustrates the structures of some building block chemicals that can be produced using bioconversions, according to some embodiments.
[0028] FIG. 3 is an example of a beta-etherase catalyzed hydrolysis of a model lignin dimer, a- O-(B-methylumbelliferyl) acetovanillone (MUAV), according to some embodiments.
[0029] FIG. 4 illustrates unexpected results from biochemical activity assays for beta-etherase function for the S. paucimobilis positive control polypeptides, and the N. aromaticivorans putative beta-etherase polypeptide, according to some embodiments.
[0030] FIG. 5 illustrates beta-aryl-ether compounds to be tested as substrates representing native lignin structures, according to some embodiments.
[0031 ] FIG. 6 illustrates pathways of guaiacylglycerol^-guaiacyl ether (GGE) metabolism by S. paucimobilis, according to some embodiments.
[0032] FIG. 7 illustrates an example of a biochemical process for the production of catechol from lignin oligomers, according to some embodiments.
[0033] FIG. 8 illustrates an example of a biochemical process for the production of vanillin from lignin oligomers, according to some embodiments. [0034] FIG. 9 illustrates an example of a biochemical process for the production of 2,4- diaminotoluene from lignin oligomers, according to some embodiments.
[0035] FIG. 10 illustrates process schemes for additional product targets that include ortho- cresol, salicylic acid, and aminosalicylic acid, for the production of valuable chemicals from lignin oligomers, according to some embodiments.
DETAILED DESCRIPTION OF THE INVENTION
[0036] This invention is generally directed to a recombinant method of producing enzymes for use in the bioconversion of lignin-derived compounds to valuable aromatic chemicals.
Currently, the art is limited in it's ability to control the degradation of lignin to produce useful products, as it's limited in it's knowledge of enzymes that are capable of selectively converting lignin into desired aromatic compounds. Generally, the art knows two basic things: (1 ) lignin is complex; and (2) bacterial lignin degradation systems are therefore at least as complex as lignin itself. Accordingly, and for at least these reasons, the teachings provided herein offer a valuable, unexpected, and surprising set of systems, methods, and compositions of matter that will be useful in the production of industrially useful aromatic chemicals.
[0037] FIGs. 1 A and 1 B illustrate general concepts of the biorefinery and discovery processes discussed herein, according to some embodiments. FIG. 1 A shows a generalized example of a use of recombinant microbial strains in biotransformations for the production of aromatic chemicals from lignin-derived compounds. Biorefinery process 100 converts a soluble biorefinery lignin 105 through a series of biotransformations using a transformed host cell. The biorefinery lignin 105 is a feedstock comprising a lignin-derived compound which can be, for example, a combination of lignin-derived monomers and oligomers.
"Biotransformation 1 " 107 can be used to selectively cleave a bond on or between monomers to create additional lignin monomers 1 10. "Biotransformation 2" 1 12 can be used to selectively cleave an additional bond on or between monomers to create mono-aromatic commercial products 1 15. FIG. 1 B shows a discovery process 120, which includes selecting a host cell strain that is tolerant to toxic lignin-derived compounds. The strain acquisition 125 includes growth of the strain, sample preparation, and storage. A set of bacterial strains are obtained for testing strain tolerance to soluble biorefinery lignin samples. [0038] In some embodiments, the strains can be selected for (i) having well-characterized aromatic and xenobiotic metabolisms; (ii) annotated genome sequences; and (iii) prior use in fermentation processes at pilot or larger scales. Examples of strains can include, but are not limited to, Azotobacter vinelandii (ATCC BAA-1303 DJ), Azotobacter chroococcum (ATCC 4412 (EB Fred) X-50), Pseudomonas putida (ATCC BAA-477 Pf-5), Pseudomonas fluorescens (ATCC 29837 NCTC 1 100). Stains can be streaked on relevant rich media plates as described by the accompanying ATCC literature for revival. Individual colonies (5 each) can be picked and cultured on relevant liquid media to saturation. Culture samples prepared in a final glycerol concentration of 12.5% can be flash-frozen and stored at -80°C.
[0039] The model substrate synthesis 150 for use in the biochemical screening for selective activity can be outsourced through a contract research organization (CRO). The enzyme discovery effort can initially be focused on identifying potential beta-etherase candidate genes identified through bioinformatic methods. The identification of candidates having beta-etherase activity is the 1 st step towards generating lignin monomers from lignin oligomers present in soluble lignin streams. The fluorescent substrate α-0-(β- methylumbelliferyl) acetovanillone (MUAV), for example, can be used in in vitro assays to identify beta-etherase function (Acme Biosciences, Mt. View, CA). The formation of 4 methylumbelliferone (4MU) upon hydrolysis of the aryl ether bond can be monitored by fluorescence, for example, at Aex=365nm and Aem=450nm (or 460nm).
[0040] The gene synthesis, cloning, and transformation step 145 can include combining
bioinformatic methods with known information about enzymes showing a desired, selective enzyme activity. For example, bioinformatics can produce a putative beta-etherase sequence that shares a significant homology to the S. paucimobilis ligE and ligF beta- etherase sequences. See Masai, E., et al. Journal of Bacteriology (3):1768- 1775(2003)("Masai"), which is hereby incorporated herein in it's entirety by reference. The S. paucimobilis sequences can be used as positive controls for biochemical assays to show relative activities in an enzyme discovery strategy.
[0041 ] The gene synthesis, cloning, and transformation step 145 can be performed using any method known to one of skill. For example, all genes can be synthesized directly as open reading frames (ORFs) from oligonucleotides by using standard PCR-based assembly methods, and using the E. coli codon bias. The end sequences can contain adaptors (BamHI and Hind III) for restriction digestion and cloning into the E. coli expression vector pET24a (Novagen). Internal BamHI and Hind 111 sites can be excluded from the ORF sequences during design of the oligonucleotides. Assembled genes can be cloned into the proprietary cloning vector (pGOV4), transformed into E. coli CH3 chemically competent cells, and DNA sequences determined (Tocore Inc.) from purified plasmid DNA. After sequence verification, restriction digestion can be used to excise each ORF fragment from the cloning vector, and the sequence can be sub-cloned into pET24a. The entire set of ligE and ligF bearing plasmids can then be transformed into E. coli BL21 (DE3) which can serve as the host strain for beta-etherase expression and biochemical testing.
[0042] The enzyme screening 155 is done to identify novel etherases 160. The fluorescent substrate MUAV can be used to screen for and identify beta-etherase activity from the recombinant E. coli clones. Expression of the beta-etherase genes can be done in 5ml or 25ml samples of the recombinant E. coli strains in LB medium using induction with IPTG. Following induction, and cell harvest, cell pellets can be be lysed using the BPER
(Invitrogen) cell lysis system. Cell extracts can be tested in the in vitro biochemical assay for beta-etherase activity on the fluorescent substrate MUAV. The formation of 4 methylumbelliferone (4MU) upon hydrolysis of the aryl ether bond in MUAV can be monitored by fluorescence at Aex=365nm and Aem=460nm, and can provide quantitative measurement of beta-etherase function. Cell extracts of E. coli transformed with the S. paucimobilis ligE and ligF genes can be the assay positive controls. Test or unknown samples can include, for example, E. coli strains expressing putative beta-etherase genes from N. aromaticovorans.
[0043] The lignin stream acquisition 130 includes a waste lignin stream from a biorefinery for testing. A preliminary characterization of one source of such lignin has shown an aromatic monomer concentration of less than 1 g/L and an oligomer concentration of ~10g/L.
Oligomers appear to be associated with carbohydrates in 10:1 ratio for sugar:phenolics. Some information exists on compounds in the liquid stream, including benzoic acid, vanillin, syringic acid and ferulics, which are routinely quantified in soluble samples. An average molecular weight of -280 has been established for the monomers; and the oligomeric components remain to be characterized.
[0044] The strain tolerance testing 135 Strain tolerance will be determined by cell growth upon exposure to biorefinery lignin. Tolerance to the phenolic compounds in biorefinery lignin waste stream will be critically important to the bioprocess efficiency and high level production of aromatic chemicals by microbial systems. Cell growth will be quantified as a function of respiration by the reduction of soluble tetrazolium salts. XTT (2,3-Bis(2-methoxy- 4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide inner salt, Sigma) is reduced to a soluble purple formazan compound by respiring cells. The formazan product will be detected and quantified by absorbance at 450nm.
[0045] Strain tolerance testing 135 on soluble lignin can be done in liquid format in 48 well plates, for example. Each strain can be tested in replicates of 8, for example, and E. coli can be used as a negative control strain. Strains can first be grown in rich medium to saturation, washed, and OD600nm of the cultures determined. Equal numbers of bacteria can be inoculated into wells of the 48-well growth plate containing minimal medium excluding a carbon source. Increasing concentrations of soluble lignin fractions, in addition to a minus-lignin positive control, can be added to the wells containing each species to a final volume of 0.8ml. A benzoic acid content analysis of the lignin fractions can be used as an internal indicator of the phenolic content of lignin wastes of different origin. Following incubation for 24-48 hours with shaking at 30°C, the cultures can be tested for growth upon exposure to the lignin fraction using an XTT assay kit. Culture samples can be removed from the 48 well growth plate and diluted appropriately in 96 well assay plates to which the XTT reagent can be be added. The soluble formazan produced will be quantified by absorbance at 450nm. Bacterial strains exhibiting the highest level of growth, and therefore tolerance, can be candidates for further development as host strains for lignin conversions.
[0046] The strain demonstrated to have the best tolerance characteristics can be transformed with the beta-etherase gene identified as showing the highest biochemical activity.
Restriction digestion can be used to excise the ORF fragment from the cloning vector, and the sequence can be sub-cloned into the shuttle vector pMMB206. Constructs cloned in the shuttle vector can be transformed into Azotobacter or Pseudomonas strains by
electroporation, or chemical transformation. The recombinant, lignin tolerant host strain can be re-tested for beta-etherase expression and activity using any methods known to one of skill, such as those described herein, adapted to the particular host strain being used.
Feedstock from biorefinery processes
[0047] An example of a starting material might be pretreated lignocellulosic biomass. In some embodiments, the lignocellulose biomass material might include grasses, corn stover, rice hull, agricultural residues, softwoods and hardwoods. In some embodiments, the lignin- derived compounds might be derived from hardwood species such as poplar from the Upper Peninsula region of Michigan, or hardwoods such as poplar, lolloby pine, and eucalyptus from Virginia and Georgia areas, or mixed hardwoods including maple and oak species from upstate New York.
[0048] In some embodiments, the pretreatment methods might encompass a range of physical, chemical and biological based processes. Examples of pretreatment methods used to generate the feedstock for Aligna processes might include physical pretreatment, solvent fractionation, chemical pretreatment, biological pretreatment, ionic liquids pretreatment, supercritical fluids pretreatment, or a combination thereof, for example, which can be applied in stages.
[0049] Physical pretreatment methods used to reduce the lignocellulose biomass particle size reduction might utilize mechanical stress methods of dry, wet vibratory and compression- based ball milling procedures. Solvent fractionation methods include organosolve processes, phosphoric acid fractionation processes, and methods using ionic liquids to pretreat the lignocellulose biomass to differentially solubilize and partition various components of the biomass. In some embodiments, organosolve methods might be performed using alcohol, including ethanol, with an acid catalyst at temperature ranges from about 90 to about 20°C, and from about 155 to about 220°C with residence time of about 25 minutes to about 100 minutes. Catalyst concentrations can vary from about 0.83% to about 1 .67% and alcohol concentrations can vary from about 25% to about 74% (v/v). In some embodiments, phosphoric acid fractionations of lignocellulose biomass might be performed using a series of different extractions using phosphoric acid, acetone, and water at temperature of around 50°C. In some embodiments, ionic liquid pretreatment of
lignocellulose biomass might include use of ionic liquids containing anions like chloride, formate, acetate, or alkylphosphonate, with biomass:ionic liquids ratios of approximately 1 :10 (w/w). The pretreatment might be performed at temperatures ranging from about 100°C to about 150°C. Other ionic liquid compounds that might be used include 1 -butyl-3- methyl-imidazolium chloride and 1 -ethyl-3-methylimidazolium chloride.
[0050] Chemical pretreatments of lignocellulose biomass material might be performed using technologies that include acidic, alkaline and oxidative treatments. In some embodiments, acidic pretreatment methods of lignocellulose biomass such as those described below might be applied. Dilute acid pretreatments using sulfuric acid at concentrations in the
approximate range of about 0.05% to about 5%, and temperatures in the range of about 160°C to about 220°C. Steam explosion, with or without the use of catalysts such as sulfuric acid, nitric acid, carbonic acid, succinic acid, fumaric acid, maleic acid, citric acid, sulfur dioxide, sodium hydroxide, ammonia, before steam explosion, at temperatures between about 160°C to about 290°C. Liquid hot water treatment at pressure >5MPa at temperatures ranging from about 160°C to about 230°C, and pH range between about 4 and about 7. And, in some embodiments, alkaline pretreatment methods using catalysts such as calcium oxide, ammonia, and sodium hydroxide might be used. The ammonia fiber expansion (AFEX) method might be applied in which concentrated ammonia at about 0.3kg to about 2kg of ammonia per kg of dry weight biomass is used at about 60°C to about 140°C in a high pressure reactor, and cooked for 5-45 minutes before rapid pressure release. The ammonia recycle percolation (ARP) method might be used in flow through mode by percolating ammoniacal solutions at 5-15% concentrations at high temperatures and pressures.
Oxidative pretreatment methods such as alkaline wet oxidation might be used with sodium carbonate at a temperature ranging from about 170°C to about 220°C in a high pressure reactor using pressurized air/oxygen mixtures or hydrogen peroxide as the oxidants.
[0051 ] Biological pretreatment methods using white rot basidomycetes and certain
actinomycetes might be applied. One type of product stream from such pretreatment methods might be soluble lignin, and might contain lignin-derived monomers and oligomers in the range of about 1 g/L to about 10g/L, and xylans. The lignin-derived monomers might include compounds such as gallic acid, hydroxybenzoate, ferulic acid, hydroxymethyl furfural, hydroxymethyl furfural alcohol, vanillin, homovanillin, syringic acid, syringaldehyde, and furfural alcohol.
[0052] Supercritical fluid pretreatment methods might be used to process the biomass.
Examples of supercritical fluids for use in processing biomass include ethanol, acetone, water, and carbon dioxide at a temperature and pressures above the critical points for ethanol and carbon dioxide but at a temperature and/or pressure below that of the critical point for water.
[0053] Combinations of steam pretreatment and biological pretreatment methods might be applied. For example, a biomass steam can be pretreated at 195°C for 10 min at controlled pH, followed by enzymatic treatment using commercial cellulases and xylanases at dosings of 100mg protein/g total solid, and with incubation at 50°C at pH 5.0 with agitation of 500 rpm.
[0054] In some embodiments, combinations of hydrothermal, organosolve, and biological
pretreatment methods might be used. One example of such a combination is a 3 stage process: Stage 1 . Use heat in an aqueous medium at a predetermined pH, temperature and pressure for the hydrothermal process;
Stage 2. Use at least one organic solvent from those described in 6-6c in water for the organosolve step;
Stage 3. Use yeast, white rot basidomycetes, actinomycetes, and cellulases and xylanases in native or recombinant forms for the biological pretreatment step.
[0055] Soluble lignin fractions derived using organosolve methods might produce soluble lignins in the molecular weight range of 188-1000, soluble in various polar solvents. Without intending to be bound by any theory or mechanism of action, organosolve processes are generally believed to maintain the lignin beta-aryl ether linkage.
[0056] Lignin streams from steam exploded lignocellulosic biomass might be used. Steam
explosion might be performed, for example, using high pressure steam in the range of about 200 psi to about 500psi, and at temperatures ranging from about 180°C to about 230°C for about 1 minute to about 20 minutes in batch or continuous reactors. The lignin might be extracted from the steam-exploded material with alkali washing or extraction using organic solvents. Steam exploded lignins can exhibit properties similar to those described form organosolve lignins, retaining native bond structures and containing about 3 to about 12 aromatic units per oligomer unit.
[0057] Supercritical fluid pretreatment can produce soluble lignin fractions that can be used with the teachings provided herein. Such processes typically yield monomers and lignin oligomers having a molecular weight of about <1000 Daltons.
[0058] Biological pretreatment can produce soluble lignin fractions that can be used with the teachings provided herein. Such lignin streams might contain lignin monomers and oligomers in the range of about 1 g/L to about 10 g/L and have a molecular weight of about <1000 Daltons, and xylans. The lignin-derived monomers might include compounds such as gallic acid, hydroxybenzoate, ferulic acid, hydroxymethyl furfural, hydroxymethyl furfural alcohol, vanillin, homovanillin, syringic acid, syringaldehyde, and furfural alcohol.
Feedstock from wood pulping processes
[0059] Wood pulping processes produce a variety of lignin types, the type of lignin dependent on the type of process used. Chemical pulping processes include, for example, Kraft and sulfite pulping. [0060] In some embodiments, the lignin-derived compound can be derived from a spent pulping liquor or "black liquor" from Kraft pulping processes. Kraft lignin might be derived from batch or continuous processes using, for example, reaction temperatures in the range of about 150°C to about 200°C and reaction times of approximately 2 hours. Any range of molecular weights of lignin may be obtained, and the useful fraction may range, in some embodiments, from about 200 Daltons to about 4000 Daltons. A Kraft lignin having a molecular weight ranging from about 1000 Daltons to about 3000 Daltons might be used in a bioconversion.
[0061 ] In some embodiments, lignin from a sulfite pulping process might be used. A sulfite pulping process can include, for example, a chemical sulfonation using aqueous sulfur dioxide, bisulfite and monosulfite at a pH ranging from about 2 to about 12. The sulfonated lignin might be recovered by precipitation with excess lime as lignosulfonates. Alternatively, formaldehyde-based methylation of the lignin aromatics followed by sulfonation might be performed. Any range of molecular weights of lignin may be obtained, and the useful fraction may range, in some embodiments, from about 200 Daltons to about 4000 Daltons. A sulfite lignin having a molecular weight ranging from about 1000 Daltons to about 3000 Daltons might be used in a bioconversion.
Characterization of lignin-derived compounds for use in bioconversion
[0062] Optimization of a system for a particular feedstock should include an understanding of the composition of the particular feedstock. For example, one of skill will appreciate that the composition of a native lignin can be significantly different than the composition of the lignin- derived compounds in a given lignin faction that is used for a feedstock. Accordingly, and understanding of the composition of the feedstock will assist in optimizing the conversion of the lignin-derived compounds to the valuable aromatic compounds. Any method known to one of skill can be used to characterize the compositions of the feedstock. For example, one of skill may use wet chemistry techniques, such as thioacidolysis and nitrobenzene oxidation, coupled with gas chromatography, which have been used traditionally, or spectroscopic techniques such as NMR and FTIR. Thioacidolysis, for example, cleaves the β-Ο-4 linkages in lignin, giving rise to monomers and dimers which are then used to calculate the S and G content. Similar information can be obtained using nitrobenzene oxidation, but the ratios are thought to be less accurate. In some embodiments, the content of S, G, and H, as well as their relative ratios can be used to characterize feedstock compositions for purposes of determining a bioconversion system design. [0063] It is widely accepted that the biosynthesis of lignin stems from the polymerization of three types of phenylpropane units, also referred to as monolignols. These units are coniferyl, sinapyl, and p-coumaryl alcohol. The three structures are as follows:
Figure imgf000018_0001
coniferyl alcohol (G); and,
Figure imgf000018_0002
sinapyl alcohol (S).
[0064] Tables 1 A and 1 B summarize distributions of p-coumaryl alcohol or p-hydroxyl phenol (H), coniferyl alcohol or guaiacyl (G), and sinapyl alcohol or syringyl (S) lignin in several sources of biomass. Table 1 A compares percent lignin in the biomass to the G:S:H.
[0065] Table 1 A.
G : S : H
Wheat Straw 16-21 45 46 9
Rice Straw 6 45 40 15
Rye Straw 18 43 53 I
Hemp 8-13 51 40 9
Tall Fescue:
Stems 7-10 55 42 3 liitemodes 1 1 48 50 2
Flax 21-34 67 29 4 lute 15-26 36 62 2 Sisal 7-14 22 76 2
Curaua Leaf fiber 7 29 4 1 30 Banana. Plant Leaf 43 50 7 Piassava Fiber
(Flam Tree) 45 4G 9 51 Abaca 7 > 19 55 26
Loblolly Fine 29 56 2 12
29 87 0 13
Compress ion. 60 40 Spruce (Picea Abies) 94 1 5
MWL 98 2 0 Eucalyptus globus 14 84 2 Eucalyptus grandls 27 69 4 Birc endula 29 69 2 Beech 56 40 4
4B 49 3
Table 1 A compares location of a sample in the biomass, species, and environmental stress to the G:S:H.
Table 1 B.
White
Figure imgf000020_0001
I S t H tiga Salte
Carp nus betmte MWL 19 80 1 Eycf ypMa c d l¾li¾ MWL 35 5f 6 Bt a sp, M WL 23 57 2i l¾jps yivafea toft
Eu- aly tas g!d!a s toft lignin 22 13 6
Ldki Fiiiss Jn eiill*
* Hernial 95 5
* Wind Opposite 96 4
» Wind C¾m tf lcir. 89 1 1
* Bent Cl Of te m 4
* Bent: Conspreis on i2
[0066] In general, the relative amounts of G, S, and H in lignin can be a good indicator of its overall composition and response to a treatment, such as the bioconversions taught herein In poplar species, for example, differences can be seen based on the measurement technique as well as species, but in general the S/G ratio ranges from 1 .3 to 2.2. This is similar to the hardwood eucalyptus, but higher than herbaceous biomass switchgrass and Miscanthus. This is to be expected given the higher H contents in grass lignin. An optimized nitrobenzene oxidation method has shown S/G ratios of 13 poplar samples from two different sites and obtained values ranging from 1 .01 to 1 .68. Further, a linear correlation (R2 = 0.85) has been found in poplar between decreasing lignin content and increasing S/G ratios. The correlation was stronger (R2 = 0.93) in samples from a single site suggesting a dependency on geographic location.
[0067] Higher throughput methods can be used for rapid screening of feedstocks. Examples of such methods can include, but are not limited to, near-infrared (NIR), reflectance
spectroscopy, pyrolysis molecular beam mass spectrometry (pyMBMS), Fourier transform infrared spectroscopy, a modified thioacidolysis technique, and whole cell NMR after dissolution in ionic liquids. Information on some structural characteristics of lignin, such as S/G ratios, can be rapidly obtained using these methods. The average S:G:H ratio of 104 poplar lignin samples, for example, was determined using the modified thioacidolysis technique, and was found to be 68:32:0.02. In some embodiments, the S, G, and H components in the ratio can be expressed as mass percent. In some embodiments, the S, G, and H components in the ratio can be expressed as any relative unit, or unitless. Any comparison can be used, if the amount of each component directly correlates with the other respective components in the composition. The ratios can be expressed in relative whole numbers or fractions as S:G:H, or any other order or combination of components, S/G, G/S, and the like. In some embodiments, the S/G ratio is used. In some embodiments, the S/G ratio can range from about 0.20 to about 20.0, from about 0.3 to about 18.0, from about 0.4 to about 15.0, from about 0.5 to about 15.0, from about 0.6 to about 12.0, from about 0.7 to about 10.0, from about 0.8 to about 8.0, from about 0.9 to about 9.0, from about 1 .0 to about 7.0, or any range therein. In some embodiments, the S/G ratio can be about 0.2, about 0.4, about 0.6, about 0.8, about 1 .0, about 1 .2, about 1 .4, about 1 .6, about 1 .8, about 2.0, about 2.2, about 2.4, about 2.6, about 2.8, about 3.0, about 3.2, about 3.4, about 3.6, about 3.8, about 4.0, about 4.2, about 4.4, about 4.6, about 4.8, about 5.0, about 5.2, about 5.4, about 5.6, about 5.8, about 6.0, about 6.2, about 6.4, about 6.6, about 6.8, about 7.0, about 7.2, about 7.4, about 7.6, about 7.8, about 8.0, about 8.2, about 8.4, about 8.6, about 8.8, about 9.0, about 9.2, about 9.4, about 9.6, about 9.8, about 10.0, and any ratio in-between on 0.1 increments, and any range of ratios therein.
Fractionation of liqnin-derived compounds for use in bioconversion
[0068] Soluble lignin streams derived from biorefinery or Kraft processes might be used directly in microbial conversions without additional purification or, they might be further purified by one or more of the separation or fractionation techniques prior to microbial conversions. [0069] In some embodiments, membrane filtration might be applied to achieve a starting concentration of lignin monomers and oligomers in the 1 -60% (w/v) concentration range, and molecular weights ranging from about 180 Daltons to about 2000 Daltons, from about 200 Daltons to about 4000 Daltons, from about 250 Daltons to about 2500 Daltons, from about 180 Daltons to about 3500 Daltons, from about 300 Daltons to about 3000 Daltons, or any range therein.
[0070] In some embodiments, soluble lignin streams might be partially purified by
chromatography using, for example, HP-20 resin. The lignin monomers and oligomers can bind to the resin while highly polar impurities or inorganics that might be toxic to
microorganisms can remain un-bound. Subsequent elution, for example, with a methanol- water solvent system, can provide fractions of higher purity that are enriched in lignin monomers and oligomers.
Chemical products
[0071 ] A purpose of the present teaching includes the discovery of novel biochemical
conversions that create valuable commercial products from various lignin core structures. Such commercial products include monomeric aromatic chemicals that can serve as building block chemicals. One of skill will appreciate that a vast number of aromatic chemicals can be produced using the principles provided by the teachings set-forth herein, and that a comprehensive teaching of every possible chemical that can be produced would be beyond the scope and purpose of this teaching.
[0072] FIGs. 2A and 2B illustrate (i) the structures of some building block chemicals that can be produced using bioconversions, and (ii) an example enzyme system from a Sphingomonaas paucimobilis gene cluster, according to some embodiments. FIG. 2A shows that examples of some monomeric aromatic structures that can serve as building block chemicals derived from lignin include, but are not limited to, guaiacol, β-hydroxypropiovanillone, 4-hydroxy-3 methoxy mandelic acid, coniferaldehyde, ferulic acid, eugenol, propylguaicol, and 4- acetylguaiacol. It should be appreciated that each of these structures can be produced using the teachings provided herein. FIG. 2B(i) shows the organization of the LigDFEG gene cluster in a Sphingomonaas paucimobilis strain. FIG. 2B(ii) shows deduced functions of the gene products believed to be involved in a β-aryl ether bond cleavage in a model lignin structure, guaiacylglycerol^-guaiacyl ether (GGE). The vertical bars above the restriction map indicate the positions of the gene insertions of LigD, LigF, LigE, and LigG. LigD shoed Ca-dehydrogenase activity, LigF and LigE showed β-etherase activity, and LigG showed glutathione lyase activity. FIG. 2 LEGEND (Abbreviations): restriction enzymes Ap (Apal), Bs (BstXI), E (EcoRI), Ec (Eco47lll), Ml (Mlul), P (Pstl), RV (EcoRV), S, (Sail), Sc (Sacl). Sell (Sacll), St (Stul), Sm (Smal), Tt (Tthllll), and X (Xhol); chemicals GGE
(guaiacylglycerol^-guaiacyl ether), GSH (glutathione), GSSG (glutathione disulfide), and asterisks are asymmetric carbons.
[0073] Commercial products that can be obtained from a bioconversion of lignin-derived
compounds, as taught herein, include mono-aromatic chemicals. Examples of such chemicals include, but are not limited to, caprolactam, cumene, styrene, mononitro- and dinitrotoluenes and their derivatives, 2,4-diaminotoluene, 2,4-dinitrotoluene, terephthalic acid, catechol, vanillin, salicylic acid, aminosalicylic acid, cresol and isomers, alkylphenols, chlorinated phenols, nitrophenols, polyhydric phenols, nitrobenzene, aniline and secondary and tertiary aniline bases, benzothiazole and derivatives, alkylbenzene and alkylbenzene sulfonates, 4,4-diphenylmethane diisocyanate (MDI), chlorobenzenes and
dichlorobenzenes, nitrochlorobenzenes, sulfonic acid derivatives of toluene, pseudocumene, mesitylene, nitrocumene, cumenesulfonic acid.
Enzyme discovery
[0074] The teachings herein are also directed to the discovery of novel enzymes. In some
embodiments, the enzymes are beta-etherase enzymes.
[0075] Lignin is the only plant biomass constituent based on aromatic core structures, and is comprised of branched phenylpropenyl (C9) units. The guaiacol and syringol building blocks of lignin are linked through carbon-carbon (C-C) and carbon-oxygen (C-O, ether) bonds. The native structure of lignin suggests its key application as a chemical feedstock for aromatic chemicals. The production of such chemical structures necessitates
depolymerization and rupture of C-C and C-0 bonds. An abundant chemical linkage in lignin is the beta-aryl ether linkage, which comprises 50% to 70% of the bond type in lignin. The efficient scission of the beta-aryl ether bond would generate the monomeric building blocks of lignin, and provide the chemical feedstock for subsequent conversion to a range of industrial products.
[0076] The beta-etherase enzyme system has multiple advantages for conversions of lignin oligomers to monomers over the laccase enzyme systems. The beta-etherase enzyme system would achieve highly selective reductive bond scission catalysis for efficient and high yield conversions of lignin oligomers to monomers without the formation of side products, degradation of the aromatic core structures of lignin, or the use of electron transfer mediators required with use of the oxidative and radical chemistry-based laccase enzyme systems.
[0077] FIG. 3 is an example of a beta-etherase catalyzed hydrolysis of a model lignin dimer, a- O-(B-methylumbelliferyl) acetovanillone (MUAV), according to some embodiments. The scission of the beta-aryl ether bond in model compounds of lignin by beta-etherases from the microbe Sphingmonas paucimobilis has been described. However, the available information is limited, and there is no precedent in the literature for the use of S.
paucimobilis as an industrial microbe for commercial scale processes. The discovery of new beta-etherase enzymes, and the heterologous expression of these new enzymes in
Azotobacter strains will provide the art with valuable industrial strains that particulary well- suited for lignin conversion processes.
[0078] One of skill will recognize the chemical nomenclature used herein as standard to the art.
For example, the amino acids used herein can be identified by at least the following conventional three-letter abbreviations in Table 2:
[0079] Table 2.
Alanine A Ala Leucine L Leu
Arginine R Arg Lysine K Lys
Asparagine N Asn Methionine M Met
Aspartic acid D Asp Phenylalanine F Phe
Cysteine C Cys Proline P Pro
Glutamic acid E Glu Serine S Ser
Glutamine Q Gin Threonine T Thr
Glycine G Gly Tryptophan w Trp
Histidine H His Tyrosine Y Tyr
Isoleucine 1 lie Valine V Val
Ornithine O Orn Other Xaa
[0080] The single letter identifier is provided for ease of reference, but any format can be used.
The three-letter abbreviations are generally accepted in the peptide art, recommended by the lUPAC-IUB commission in biochemical nomenclature, and are provided to comply with WIPO Standard ST.25. Furthermore, the peptide sequences are taught according to the generally accepted convention of placing the N-terminus on the left and the C-terminus on the right of the sequence listing to again comply with WIPO Standard ST.25.
The Recombinant Polypeptides [0081 ] The teachings herein are based on discovery of novel and non-obvious proteins, DNAs, and host cell systems that can function in the conversion of lignin-derived compounds into valuable aromatic compounds. The systems can include natural, wild-type components or recombinant components, the recombinant components being isolatable from what occurs in nature.
[0082] The term "isolated" means altered "by the hand of man" from its natural state; i.e., if it occurs in nature, it has been changed or removed from its original environment, or both. For example, a naturally occurring polynucleotide or a polypeptide naturally present in a living animal in its natural state is not "isolated," but the same polynucleotide or polypeptide separated from the coexisting materials of its natural state is "isolated", as the term is used herein. For example, with respect to polynucleotides, the term isolated means that it is separated from the chromosome and cell in which it naturally occurs. However, a nucleic acid molecule contained in a clone that is a member of a mixed clone library (e.g., a genomic or cDNA library) and that has not been isolated from other clones of the library (e.g., in the form of a homogeneous solution containing the clone without other members of the library) or a chromosome isolated or removed from a cell or a cell lysate (e.g., a
"chromosome spread", as in a karyotype), is not "isolated" for the purposes of the teachings herein. Moreover, a lone nucleic acid molecule contained in a preparation of mechanically or enzymatically cleaved genomic DNA, where the isolation of the nucleic molecule was not the goal, is also not "isolated" for the purposes of the teachings herein. As part of, or following, an intentional isolation, polynucleotides can be joined to other polynucleotides, for mutagenesis, to form fusion proteins, and for propagation or expression in a host, for instance. Isolated polynucleotides, alone or joined to other polynucleotides such as vectors, can be introduced into host cells, in culture or in whole organisms, after which such DNAs still would be isolated, as the term is used herein, because they would not be in their naturally occurring form or environment. Similarly, the isolated polynucleotides and polypeptides may occur in a composition, such as a media formulation, solutions for introduction of polynucleotides or polypeptides, for example, into cells, compositions or solutions for chemical or enzymatic reactions, for instance, which are not naturally occurring compositions, and, therein remain "isolated" polynucleotides or polypeptides within the meaning of that term as it is used herein.
[0083] A "vector," such as an expression vector, is used to transfer or transmit the DNA of
interest into a prokaryotic or eukaryotic host cell, such as a bacteria, yeast, or a higher eukaryotic cell. Vectors can be recombinantly designed to contain a polynucleotide encoding a desired polypeptide. These vectors can include a tag, a cleavage site, or a combination of these elements to facilitate, for example, the process of producing, isolating, and purifying a polypeptide. The DNA of interest can be inserted as the expression component of a vector. Examples of vectors include plasmids, cosmids, viruses, and bacteriophages. If the vector is a virus or bacteriophage, the term vector can include the viral/bacteriophage coat. The term "expression vector" is usually used to describe a DNA construct containing gene encoding an expression product of interest, usually a protein, that is expressed by the machinery of the host cell. This type of vector is frequently a plasmid, but the other forms of expression vectors, such as bacteriophage vectors and viral vectors (e.g., adenoviruses, replication defective retroviruses, and adeno-associated viruses), can be used.
[0084] In some embodiments, the polypeptides taught herein can be natural or wildtype,
isolated and/or recombinant. In some embodiments, the polynucleotides can be natural or wildtype, isolated and/or recombinant. In some embodiments, the teachings are directed to a vector than can include such a polynucleotide or a host cell transformed by such a vector.
[0085] In some embodiments, the polypeptide can be an isolated recombinant polypeptide, comprising an amino acid sequence having at least 95% identity to SEQ ID NO:101 . The sequence can conserve residues T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, G54, K100, A101 , N104, V1 1 1 , G1 12, M1 15, F1 16, P166, W107, Y184, Y187, R188, G191 , G192, and F195.
[0086] In some embodiments, the polypeptide can be an isolated recombinant polypeptide, comprising SEQ ID NO:101 ; or conservative substitutions thereof outside of the conserved residues. The conserved residues can include T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, G54; K100, A101 , N104, V1 1 1 , G1 12, M1 15, F1 16, P166, W107, Y184, Y187, R188, G191 , G192, and F195.
[0087] In some embodiments, the polypeptide can be an isolated recombinant glutathione S- transferase enzyme, comprising an amino acid sequence having at least 95% identity to SEQ ID NO:101 . The amino acid sequence can conserve residues T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, G54; K100, A101 , N104, V1 1 1 , G1 12, M1 15, F1 16, P166, W107, Y184, Y187, R188, G191 , G192, and F195; wherein, the amino acid sequence functions to cleave a beta-aryl ether.
[0088] In some embodiments, the polypeptide can be an isolated recombinant glutathione S- transferase enzyme, comprising an amino acid sequence having at least 95% identity to SEQ ID NO:101 ; wherein, the amino acid sequence functions to cleave a beta-aryl ether.
[0089] In some embodiments, the polypeptide can be an isolated recombinant polypeptide, comprising (i) a length ranging from about 279 to about 281 amino acids; (ii) a first amino acid region consisting of residues 19-54 from SEQ ID NO:101 , or conservative substitutions thereof outside of conserved residues T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, and G54; wherein, the first amino acid region can be located in the recombinant polypeptide from about residue 14 to about residue 59; and, (iii) a second amino acid region consisting of residues 98-221 from SEQ ID NO:101 , or conservative substitutions thereof outside of conserved residues K100, A101 , N104, V1 1 1 , G1 12, M1 15, F1 16, P166, W107, Y184, Y187, R188, G191 , G192, and F195; wherein, the second amino acid region is located in the recombinant polypeptide from about residue 93 to about residue 226.
[0090] In some embodiments, the polypeptide can be an isolated recombinant glutathione S- transferase enzyme, comprising (i) a length ranging from about 279 to about 281 amino acids; (ii) a first amino acid region having at least 95% identity to residues 19-54 from SEQ ID NO:101 while conserving residues T19, I20, S21 , P22, V24, W25, T27, K28, Y29, A30, H33, K34, G35, F36, D39, I40, V41 , P42, G43, G44, F45, G47, I48, E50, R51 , T52, G53, and G54; wherein, the first amino acid region is located in the recombinant polypeptide from about residue 14 to about residue 59; and, (iii) a second amino acid region having at least 95% identity to residues 98-221 from SEQ ID NO:101 while conserving residues K100, A101 , N104, V1 1 1 , G1 12, M1 15, F1 16, P166, W107, Y184, Y187, R188, G191 , G192, and F195; wherein, the second amino acid region can be located in the recombinant polypeptide from about residue 93 to about residue 226; and, the recombinant glutathione S-transferase enzyme can function to cleave a beta-aryl ether.
[0091 ] In some embodiments, the polypeptide can be an isolated recombinant glutathione S- transferase enzyme, comprising an amino acid sequence having at least 95% identity to SEQ ID NO:541 ; wherein, the amino acid sequence functions to cleave a beta-aryl ether. [0092] In some embodiments, the polypeptide can be an isolated recombinant polypeptide, comprising (i) a length ranging from about 256 to about 260 amino acids; (ii) a first amino acid region consisting of residues 47-57 from SEQ ID NO:541 , or conservative substitutions thereof outside of conserved residues A47, I48, N49, P50, G52, V54, P55, V56, L57;
wherein, the first amino acid region is located in the recombinant polypeptide from about residue 45 to about residue 57; (iii) a second amino acid region consisting of 63-76 from SEQ ID NO:541 ; and, (iv) a third amino acid region consisting of residues 99-230 from SEQ ID NO:541 , or conservative substitutions thereof outside of conserved residues R100, Y101 , K104, D107, M1 1 1 , N1 12, S1 15, M1 16, K176, L194, 1197, N198, S201 , H202, and M206; wherein, the second amino acid region is located in the recombinant polypeptide from about residue 94 to about residue 235.
[0093] In some embodiments, the polypeptide can be an isolated recombinant glutathione S- transferase enzyme, comprising (i) a length ranging from about 279 to about 281 amino acids; (ii) a first amino acid region having at least 95% identity to 47-57 from SEQ ID NO:541 , or conservative substitutions thereof outside of conserved residues A47, I48, N49, P50, G52, V54, P55, V56, L57; wherein, the first amino acid region can be located in the recombinant polypeptide from about residue 45 to about residue 57; (iii) a second amino acid region consisting of 63-76 from SEQ ID NO:541 ; and, (iv) a third amino acid region having at least 95% identity to residues 99-230 from SEQ ID NO:541 , or conservative substitutions thereof outside of conserved residues R100, Y101 , K104, D107, M1 1 1 , N1 12, S1 15, M1 16, K176, L194, 1197, N198, S201 , H202, and M206; wherein, the second amino acid region can be located in the recombinant polypeptide from about residue 94 to about residue 235; wherein, the recombinant glutathione S-transferase enzyme functions to cleave a beta-aryl ether.
[0094] In some embodiments, an amino acid substitution outside of the conserved residues can be a conservative substitution. And, in many embodiments, the amino acid sequence can function to cleave a beta-aryl ether.
Methods of Preparing the Recombinant SDF-1 Polynucleotide and Polypeptides
[0095] The teachings include a method of preparing the polypeptides described herein,
comprising culturing a host cell under conditions suitable to produce the desired
polypeptide; and recovering the polypeptide from the host cell culture; wherein, the host cell comprises an exogenously-derived polynucleotide encoding the desired polypeptide. In some embodiments, the host cell is E. Coli. In some embodiments, the host cell can be an Azotobacter strain such as, for example, Azotobacter vinelandii.
[0096] Initially, a double-stranded DNA fragment encoding the primary amino acid sequence of recombinant polypeptide can be designed. This DNA fragment can be manipulated to facilitate synthesis, cloning, expression or biochemical manipulation of the expression products. The synthetic gene can be ligated to a suitable cloning vector and then the nucleotide sequence of the cloned gene can be determined and confirmed. The gene can be then amplified using designed primers having specific restriction enzyme sequences introduced at both sides of insert gene, and the gene can be subcloned into a suitable subclone/expression vector. The expression vector bearing the synthetic gene for the mutant can be inserted into a suitable expression host. Thereafter the expression host can be maintained under conditions suitable for production of the gene product and, in some embodiments, the protein can be (i) isolated and purified from the cells expressing the gene or (ii) used directly in a reaction environment that includes the host cell.
[0097] The nucleic acid (e.g., cDNA or genomic DNA) may be inserted into a replicable vector for cloning (amplification of the DNA) for expression. Various vectors are publicly available. In general, DNA can be inserted into an appropriate restriction endonuclease site(s) using techniques known in the art, for example. Vector components generally include, but are not limited to, one or more of a signal sequence, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence.
[0098] The signal sequence may be a prokaryotic signal sequence selected, for example, from the group of the alkaline phosphatase, penicillinase, Ipp, or heat-stable enterotoxin II leaders. For yeast secretion the signal sequence may be, e.g., the yeast invertase leader, alpha factor leader (including Saccharomyces and Kluyveromyces alpha-factor leaders, the latter described in U.S. Pat. No. 5,010,182), or acid phosphatase leader, the C. albicans glucoamylase leader (EP 362,179), or the signal described in WO 90/13646, for example. In mammalian cell expression, mammalian signal sequences may be used to direct secretion of the protein, such as signal sequences from secreted polypeptides of the same or related species, as well as viral secretory leaders.
[0099] Both expression and cloning vectors contain a nucleic acid sequence that enables the vector to replicate in one or more selected host cells. Such sequences are well known for a variety of bacteria, yeast, and viruses. The origin of replication from a plasmid, e.g.
pBR322, for example, is suitable for most Gram-negative bacteria, and the 2 μ plasmid origin is suitable for yeast, and various viral origins (SV40, polyoma, adenovirus, VSV or BPV) are useful for cloning vectors in mammalian cells.
[00100] Expression and cloning vectors will typically contain a selection gene, also
termed a selectable marker. Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e g., ampicillin, neomycin, methotrexate, or tetracycline, (b) complement auxotrophic deficiencies, or (c) supply critical nutrients not available from complex media, e.g., the gene encoding D-alanine racemase for Bacilli.
[00101 ] An example of suitable selectable markers for mammalian cells are those that enable the identification of cells competent to take the encoding nucleic acid, such as DHFR or thymidine kinase. An appropriate host cell when wild-type DHFR is employed is the CHO cell line deficient in DHFR activity, prepared and propagated as described by Urlaub et al., Proc. Natl. Acad. Sci. USA, 77:4216 (1980). A suitable selection gene for use in yeast is the trpl gene present in the yeast plasmid YRp7 (Stinchcomb et al., Nature, 282:39 (1979); Kingsman et al., Gene, 7:141 (1979); Tschemper et al., Gene, 10:157 (1980)). The trpl gene provides a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan, for example, ATCC No. 44076 or PEP4-1 (Jones, Genetics, 85:12 (1977)).
[00102] Expression and cloning vectors usually contain a promoter operably linked to the encoding nucleic acid sequence to direct mRNA synthesis. Promoters recognized by a variety of potential host cells are well known. Promoters suitable for use with prokaryotic hosts include the .beta.-lactamase and lactose promoter systems (Chang et al., Nature, 275:615 (1978); Goeddel et al., Nature, 281 :544 (1979)), alkaline phosphatase, a tryptophan (trp) promoter system (Goeddel, Nucleic Acids Res., 8:4057 (1980); EP 36,776), and hybrid promoters such as the tac promoter (deBoer et al., Proc. Natl. Acad. Sci. USA, 80:21 25 (1983)). Promoters for use in bacterial systems also will contain a Shine-Dalgarno sequence operably linked to the encoding DNA.
[00103] Other yeast promoters, which are inducible promoters having the additional advantage of transcription controlled by growth conditions, are the promoter regions for alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degradative enzymes associated with nitrogen metabolism, metallothionein, glyceraldehyde-3-phosphate dehydrogenase, and enzymes responsible for maltose and galactose utilization. Suitable vectors and promoters for use in yeast expression are known in the art, e.g. see EP 73,657 for a further discussion. [00104] PR087299 transcription from vectors in mammalian host cells is controlled, for example, by promoters obtained from the genomes of viruses such as polyoma virus, fowlpox virus (UK 2,21 1 ,504), adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), from heterologous mammalian promoters, e.g., the actin promoter or an
immunoglobulin promoter, and from heat-shock promoters, provided such promoters are compatible with the host cell systems.
[00105] Transcription of the encoding DNA by higher eukaryotes may be increased by inserting an enhancer sequence into the vector. Enhancers are cis-acting elements of DNA, usually about from 10 to 300 bp, that act on a promoter to increase its transcription. Many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, a- fetoprotein, and insulin). Typically, however, one will use an enhancer from a eukaryotic cell virus. Examples include the SV40 enhancer on the late side of the replication origin, the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers. The enhancer may be spliced into the vector at a position 5' or 3' to the coding sequence but is preferably located at a site 5' from the promoter.
[00106] Expression vectors used in eukaryotic host cells (yeast, fungi, insect, plant,
animal, human, or nucleated cells from other multicellular organisms) will also contain sequences necessary for the termination of transcription and for stabilizing the mRNA.
Such sequences are commonly available from the 5' and, occasionally 3', untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of the mRNA encoding the mutants.
[00107] In some embodiments, the expression control sequence can be selected from a group consisting of a lac system, T7 expression system, major operator and promoter regions of pBR322 origin, and other prokaryotic control regions. Still other methods, vectors, and host cells suitable for adaptation to the synthesis of the mutants in recombinant vertebrate cell culture are described in Gething et al., Nature, 293:620 625 (1981 ); Mantei et al., Nature, 281 :40 46 (1979); EP 1 17,060; and EP 1 17,058.
[00108] Mutants can be expressed as a fusion protein. In some embodiments, the
methods involve adding a number of amino acids to the protein, and in some embodiments, to the amino terminus of the protein. Extra amino acids can serve as affinity tags or cleavage sites, for example. Fusion proteins can be designed to: (1 ) assist in purification by acting as a temporary ligand for affinity purification, (2) produce a precise recombinant by removing extra amino acids using a cleavage site between the target gene and affinity tag, (3) increase the solubility of the product, and/or (4) increase expression of the product. A proteolytic cleavage site can be included at the junction of the fusion region and the protein of interest to enable further purification of the product - separation of the recombinant protein from the fusion protein following affinity purification of the fusion protein. Such enzymes, and their cognate recognition sequences, can include Factor Xa, thrombin and enterokinase, cyanogen bromide, trypsin, or chymotrypsin, for example. Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith, D. B. and Johnson, K. S. Gene 67:31 -40 (1988)), pMAL (New England Biolabs, Beverly, Mass.), pRIT5 (Pharmacia, Piscataway, N.J.), and pET (Strategen), which can fuse glutathione S-transferase (GST), maltose E binding protein, protein A, or a six-histidine sequence, respectively, to a target recombinant protein.
[00109] Synthetic DNAs containing the sequences of nucleotides, tags and cleavage sites can be designed and provided as a modified coding for recombinant polypeptide mutants. In some embodiments, a polypeptide can be a fusion polypeptide having an affinity tag, and the recovering step includes (1 ) capturing and purifying the fusion polypeptide, and (2) removing the affinity tag for high yield production of the desired polypeptide or an amino acid sequence that is at least 95% homologous to a desired polypeptide. DNA encoding the mutants may be obtained from a cDNA library prepared from tissue possessing the mRNA for the mutants. As such, the DNA can be conveniently obtained from a cDNA library. The encoding gene for the mutants may also be obtained from a genomic library or by known synthetic procedures (e.g., automated nucleic acid synthesis).
[001 10] Libraries can be screened with probes designed to identify the gene of interest or the protein encoded by it. Screening the cDNA or genomic library with the selected probe may be conducted using standard hybridization procedures, such as described in Sambrook et al., Molecular Cloning: A Laboratory Manual (New York: Cold Spring Harbor Laboratory Press, 1989), which is herein incorporated by reference. An alternative means to isolate the gene encoding recombinant polypeptide mutants is to use PCR methodology [Sambrook et al., supra; Dieffenbach et al., PCR Primer: A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1995)]. [001 1 1 ] Nucleic acids having a desired protein coding sequence may be obtained by screening selected cDNA or genomic libraries using a deduced amino acid sequence and, if necessary, a conventional primer extension procedure as described in Sambrook et al., supra, to detect precursors and processing intermediates of mRNA that may not have been reverse-transcribed into cDNA.
[001 12] The selection of expression vectors, control sequences, transformation methods, and the like, are dependent on the type of host cell used to express the gene. Following entry into a cell, all or part of the vector DNA, including the insert DNA, may be incorporated into the host cell chromosome, or the vector may be maintained extrachromosomally.
Those vectors that are maintained extrachromosomally are frequently capable of autonomous replication in the host cell. Other vectors are integrated into the genome of a host cell upon and are replicated along with the host genome.
[001 13] Host cells are transfected or transformed with the expression or cloning vectors described herein to produce the mutants. The cells are cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences. The culture conditions, such as media, temperature, pH and the like, can be selected by the skilled artisan without undue experimentation. In general, principles, protocols, and practical techniques for maximizing the productivity of cell cultures can be found in Mammalian Cell Biotechnology: a Practical Approach, M. Butler, ed. (IRL Press, 1991 ) and Sambrook et al., supra, each of which are incorporated by reference.
[001 14] The host cells can be prokaryotic or eukaryotic and, suitable host cells for cloning or expressing the DNA in the vectors herein can include prokaryote, yeast, or higher eukaryote cells. Methods of eukaryotic cell transfection and prokaryotic cell transformation are known to the ordinarily skilled artisan, for example, CaCI2, CaP04, liposome-mediated and electroporation. Depending on the host cell used, transformation is performed using standard techniques appropriate to such cells. The calcium treatment employing calcium chloride, as described in Sambrook et al., supra, or electroporation is generally used for prokaryotes. Infection with Agrobacterium tumefaciens is used for transformation of certain plant cells, as described by Shaw et al., Gene, 23:315 (1983) and WO 89/05859 published 29 Jun. 1989. For mammalian cells without such cell walls, the calcium phosphate precipitation method of Graham and van der Eb, Virology, 52:456 457 (1978) can be employed. General aspects of mammalian cell host system transfections have been described in U.S. Pat. No. 4,399,216. Transformations into yeast are typically carried out according to the method of Van Solingen et al., J. Bact., 130:946 (1977) and Hsiao et al., Proc. Natl. Acad. Sci. (USA), 76:3829 (1979). However, other methods for introducing DNA into cells, such as by nuclear microinjection, electroporation, bacterial protoplast fusion with intact cells, or polycations, e.g., polybrene, polyornithine, may also be used. For various techniques for transforming mammalian cells, see Keown et al., Methods in Enzymology, 185:527 537 (1990) and Mansour et al., Nature, 336:348 352 (1988).
[001 15] Suitable host cells for cloning or expressing the DNA in the vectors herein
include prokaryote, yeast, or higher eukaryote cells. Suitable prokaryotes include, but are not limited to, eubacteria, such as Gram-negative or Gram-positive organisms, for example, Enterobacteriaceae such as E. coli. Various E. coli strains are publicly available, such as E. coli K12 strain MM294 (ATCC 31 ,446); E. coli X1776 (ATCC 31 ,537); E. coli strain W31 10 (ATCC 27,325) and K5 772 (ATCC 53,635). Other suitable prokaryotic host cells include Enterobacteriaceae such as Escherichia, e.g., E. coli, Enterobacter, Erwinia, Klebsiella, Proteus, Salmonella, e.g., Salmonella typhimunrium, Serratia, e.g., Serratia marcescans, and Shigella, as well as Bacilli such as B. subtilis and B. licheniformis (e.g., B. licheniformis 41 P disclosed in DD 266,710 published 12 Apr. 1989), Pseudomonas such as P.
aeruginosa, and Streptomyces. These examples are illustrative rather than limiting, and merely supplement the remainder of the teachings herein. Strain W31 10 is one particularly preferred host or parent host because it is a common host strain for recombinant DNA product fermentations. Preferably, the host cell secretes minimal amounts of proteolytic enzymes. For example, strain W31 10 may be modified to effect a genetic mutation in the genes encoding proteins endogenous to the host, with examples of such hosts including E. coli W31 10 strain 1 A2, which has the complete genotype tonA; E. coli W31 10 strain 9E4, which has the complete genotype tonA ptr3; E. coli W31 10 strain 27C7 (ATCC 55,244), which has the complete genotype tonA ptr3 phoA E15 (argF-lac)169 degP ompT kanr ; E. coli W31 10 strain 37D6, which has the complete genotype tonA ptr3 phoA E15 (argF- lac)169 degP ompT rbs7 ilvC kanr ; E. coli W31 10 strain 40B4, which is 37D6 with a non- kanamycin resistant degP deletion mutation; and an E. coli strain having mutant periplasmic protease as disclosed in U.S. Pat. No. 4,946,783. Alternatively, in vitro methods of cloning, e.g., PCR or other nucleic acid polymerase reactions, are suitable.
[001 16] In addition to prokaryotes, eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for the mutants. Saccharomyces cerevisiae is a commonly used lower eukaryotic host microorganism. Others include
Schizosaccharomyces pombe (Beach and Nurse, Nature, 290: 140 (1981 ); EP 139,383 published 2 May 1985); Kluyveromyces hosts (U.S. Pat. No. 4,943,529; Fleer et al., Bio/Technology, 9:968 975 (1991 )) such as, e.g., K. lactis (MW98-8C, CBS683, CBS4574; Louvencourt et al., J. Bacteriol., 154(2):737 742 (1983)), K. fragilis (ATCC 12,424), K.
bulgaricus (ATCC 16,045), K. wickeramii (ATCC 24,178), K. waltii (ATCC 56,500), K.
drosophilarum (ATCC 36,906; Van den Berg et al., Bio/Technology, 8:135 (1990)), K.
thermotolerans, and K. marxianus; yarrowia (EP 402,226); Pichia pastoris (EP 183,070; Sreekrishna et al., J. Basic Microbiol., 28:265 278 [1988]); Candida; Trichoderma reesia (EP 244,234); Neurospora crassa (Case et al., Proc. Natl. Acad. Sci. USA, 76:5259 5263 (1979)); Schwanniomyces such as Schwanniomyces occidentalis (EP 394,538); and filamentous fungi such as, e.g., Neurospora, Penicillium, Tolypocladium (WO 91 /00357), and Aspergillus hosts such as A. nidulans (Ballance et al., Biochem. Biophys. Res.
Commun., 1 12:284 289 (1983); Tilburn et al., Gene, 26:205 221 (1983); Yelton et al., Proc. Natl. Acad. Sci. USA, 81 : 1470 1474 (1984)) and A. niger (Kelly and Hynes, EMBO J., 4:475 479 (1985)) Methylotropic yeasts are suitable herein and include, but are not limited to, yeast capable of growth on methanol selected from the genera consisting of Hansenula, Candida, Kloeckera, Pichia, Saccharomyces, Torulopsis, and Rhodotorula. A list of specific species that are exemplary of this class of yeasts may be found in C. Anthony, The
Biochemistry of Methylotrophs, 269 (1982).
17] Suitable host cells for the expression of glycosylated mutants can be derived from multicellular organisms. Invertebrate cells include insect cells such as Drosophila S2 and Spodoptera Sf9, as well as plant cells. Useful mammalian host cell lines include Chinese hamster ovary (CHO) and COS cells. More specific examples include monkey kidney CVI line transformed by SV40 (COS-7, ATCC CRL 1651 ); human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture, Graham et al., J. Gen Virol., 36:59 (1977)); Chinese hamster ovary cells/-DHFR (CHO, Urlaub and Chasin, Proc. Natl. Acad. Sci. USA, 77:4216 (1980)); mouse Sertoli cells (TM4, Mather, Biol. Reprod., 23:243 251 (1980)); human lung cells (W138, ATCC CCL 75); human liver cells (Hep G2, HB 8065); and mouse mammary tumor (MMT 060562, ATCC CCL5 1 ). One of skill can readily choose the appropriate host cell, at least for extracellular protein harvesting embodiments, without undue experimentation. [001 18] In some embodiments, a nucleotide sequence will be hybridizable, under moderately stringent conditions, to a nucleic acid having a nucleotide sequence comprising or complementary to the desired nucleotide sequences. In some embodiments, an isolated nucleotide sequence will be hybridizable, under stringent conditions, to a nucleic acid having a nucleotide sequence comprising or complementary to the desired nucleotide sequences. A nucleic acid molecule can be "hybridizable" to another nucleic acid molecule when a single-stranded form of the nucleic acid molecule can anneal to the other nucleic acid molecule under the appropriate conditions of temperature and ionic strength (see Sambrook et al., supra,). The conditions of temperature and ionic strength determine the "stringency" of-the hybridization. "Hybridization" requires that two nucleic acids contain complementary sequences. However, depending on the stringency of the hybridization, mismatches between bases may occur. The appropriate stringency for hybridizing nucleic acids depends on the length of the nucleic acids and the degree of complementation. Such variables are well known in the art. More specifically, the greater the degree of similarity or homology between two nucleotide sequences, the greater the value of Tm for hybrids of nucleic acids having those sequences. For hybrids of greater than 100 nucleotides in length, equations for calculating Tm have been derived (see Sambrook et al., supra). For hybridization with shorter nucleic acids, the position of mismatches becomes more important, and the length of the oligonucleotide determines its specificity (see Sambrook et al., supra).
[001 19] In some embodiments, the polynucleotides and polypeptides have at least 55, 60, 65, 70, 75, 80, 85, 90, 91 , 92, 93, 94, 95, 96, 97, 98, or 99 percent homology to a desired polynucleotide or polypeptide. In some embodiments, the polynucleotides and polypeptides have at least 55, 60, 65, 70, 75, 80, 85, 90, 91 , 92, 93, 94, 95, 96, 97, 98, or 99 percent identity to a desired polynucleotide or polypeptide. And, in some embodiments, the polynucleotides and polypeptides have at least 55, 60, 65, 70, 75, 80, 85, 90, 91 , 92, 93, 94, 95, 96, 97, 98, or 99 percent similarity to a desired polynucleotide or polypeptide. As described above, degenerate forms of the desired polynucleotide are also acceptable. In some embodiments, a polypeptide can be 90, 91 , 92, 93, 94, 95, 96, 97, 98, or 99 homologous, identical, or similar to a desired polypeptide as long as it shares the same function as the desired polypeptide, and the extent of the function can be less or more than that of the desired polypeptide. In some embodiments, for example, a polypeptide can have a function that is 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any 0.1 % increment in-between, that of the desired polypeptide. And, in some embodiments, for example, a polypeptide can have a function that is 1 10%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 300%, 400%, 500%, or more, or any 1 % increment in-between, that of the desired polypeptide. In some embodiments the "function" is an enzymatic activity, measurable by any method known to one of skill such as, for example, a method used in the teachings herein. The "desired polypeptide" or "desired polynucleotide" can be referred to as a "reference polypeptide" or "reference polynucleotide", or the like, in some embodiments as a control for comparison of a polypeptide of interest, which may be considered a "test polypeptide" or "test polynucleotide" or the like. In any event, the comparison is that of one set of bases or amino acids against another set for purposes of measuring homology, identity, or similarity. The ability to hybridize is, of course, another way of comparing nucleotide sequences.
[00120] The terms "homology" and "homologous" can be used interchangeably in some embodiments. The terms can refer to nucleic acid sequence matching and the degree to which changes in the nucleotide bases between polynucleotide sequences affects the gene expression. These terms also refer to modifications, such as deletion or insertion of one or more nucleotides, and the effects of those modifications on the functional properties of the resulting polynucleotide relative to the unmodified polynucleotide. Likewise the terms refer to polypeptide sequence matching and the degree to which changes in the polypeptide sequences, such as those seen when comparing the modified polypeptides to the unmodified polypeptide, affect the function of the polypeptide. It should appreciated to one of skill that the polypeptides, such as the mutants taught herein, can be produced from two non-homologous polynucleotide sequences within the limits of degeneracy.
[00121 ] The terms "similarity" and "identity" are known in the art. The term "identity" can be used to refer to a sequence comparison based on identical matches between
correspondingly identical positions in the sequences being compared. The term "similarity" can be used to refer to a comparison between amino acid sequences, and takes into account not only identical amino acids in corresponding positions, but also functionally similar amino acids in corresponding positions. Thus similarity between polypeptide sequences indicates functional similarity, in addition to sequence similarity. Levels of identity between gene sequences and levels of identity or similarity between amino acid sequences can be calculated using known methods. For example, publicly available computer based methods for determining identity and similarity include the BLASTP, BLASTN and FASTA (Atschul et al., J. Molec. Biol., 1990; 215:403-410), the BLASTX program available from NCBI, and the Gap program from Genetics Computer Group, Madison Wis. In some embodiments, the Gap program, with a Gap penalty of 12 and a Gap length penalty of 4 can be used for determining the amino acid sequence comparisons, and a Gap penalty of 50 and a Gap length penalty of 3 for the polynucleotide sequence comparisons. In some embodiments, the sequences can be aligned so that the highest order match is obtained. The match can be calculated using published techniques that include, for example, Computational Molecular Biology, Lesk, A. M., ed., Oxford University Press, New York, 1988; Biocomputing: Informatics and Genome Projects, Smith, D. W., ed., Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part I, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press, 1987; and Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991 , each of which is incorporated by reference herein.
[00122] As such, the term "similarity" is similar to "identity", but in contrast to identity, similarity can be used to refer to both identical matches and conservative substitution matches. For example, if two polypeptide sequences have 10/20 identical amino acids, and the remainder are all non-conservative substitutions, then the percent identity and similarity would both be 50%. On the other hand, if there are 5 five more positions where there are conservative substitutions, then the percent identity is 50%, whereas the percent similarity is 75%.
[00123] In some embodiments, the term "substantial sequence identity" can refer to an optimal alignment, such as by the programs GAP or BESTFIT using default gap penalties, having at least 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, or 99 percent sequence identity. The difference in what is "substantial" regarding identity can often vary according to a
corresponding percent similarity, since the factor of primary importance is often the function of the sequence in a system. The term "substantial percent identity" can be used to refer to a DNA sequence that is sufficiently similar to a reference sequence at the nucleotide level to code for the same protein, or a protein having substantially the same function, in which the comparison can allow for allelic differences in the coding region. Likewise, the term can be used to refer to a comparison of sequences of two polypeptides optimally aligned.
[00124] In some embodiments, sequence comparisons can be made to a reference
sequence over a "comparison window" of amino acids or bases that includes any number of amino acids or bases that is useful in the particular comparison. For example, the reference sequence may be a subset of a larger sequence. In some embodiments, the comparison window can include at least 10 residue or base positions, and sometimes at least 15-20 amino acids or bases. The reference or test sequence may represent, for example, a polypeptide or polynucleotide having one or more deletions, substitutions or additions.
[00125] The term "variant" refers to modifications to a peptide that allows the peptide to retain its binding properties, and such modifications include, but are not limited to, conservative substitutions in which one or more amino acids are substituted for other amino acids; deletion or addition of amino acids that have minimal influence on the binding properties or secondary structure; conjugation of a linker; post-translational modifications such as, for example, the addition of functional groups. Examples of such post-translational modifications can include, but are not limited to, the addition of modifying groups described below through processes such as, for example, glycosylation, acetylation, phosphorylation, modifications with fatty acids, formation of disulfide bonds between peptides, biotinylation, PEGylation, and combinations thereof. In fact, in most embodiments, the polypeptides can be modified with any of the various modifying groups known to one of skill.
[00126] The terms "conservatively modified variant," "conservatively modified
substitution," and "conservative substitution" can be used interchangeably in some embodiments. These terms can be used to refer to a conservative amino acid substitution, which is an amino acid substituted by an amino acid of similar charge density,
hydrophilicity/hydrophobicity, size, and/or configuration such as, for example, substituting valine for isoleucine. In comparison, a "non-conservatively modified variant" refers to a non- conservative amino acid substitution, which is an amino acid substituted by an amino acid of differing charge density, hydrophilicity/hydrophobicity, size, and/or configuration such as, for example, substituting valine for phenyalanine. One of skill will appreciate that there are a plurality of ways to define conservative substitutions, and any of these methods may be used with the teachings provided herein. In some embodiments, for example, a substitution can be considered conservative if an amino acid falling into one of the following groups is substituted by an amino acid falling in the same group: hydrophilic (Ala, Pro, Gly, Glu, Asp, Gin, Asn, Ser, Thr), aliphatic (Val, lie, Leu, Met), basic (Lys, Arg, His), aromatic (Phe, Tyr, Trp), and sulphydryl (Cys). See Dayhoff, MO. Et al. National Biomedical Research
Foundation, Georgetown University, Washington DC:89-99(1972), which is incorporated herein. In some embodiments, the substitution of amino acids can be considered conservative where the side chain of the substitution has similar biochemical properties to the side chain of the substituted amino acid.
Microbial systems - antimicrobial liqnin-derived compounds
[00127] The antimicrobial activity of lignin-derived compounds is a major problem
addressed by the systems taught herein. For example, typical industrial fermentation processes might utilize the microbes Escherichia coli K12 or Escherichia coli B, or the yeast Saccharomyces cerevisiae, and recombinant versions of these microbes, which are well characterized industrial strains. The problem is that the antimicrobial activities of aromatic compounds on such industrial microbes are toxic to the microbes, which negates an application to biotransformations of lignin-derived compounds.
[00128] The phenolic streams or soluble lignin streams derived from pretreated
lignocellulosic biomass, for example, might contain aromatic and nonaromatic compounds, such as gallic acid, hydroxymethylfurfural alcohol, hydroxymethylfurfural, furfural alcohol, 3,5-dihydroxybenzoate, furoic acid, 3,4-dihydroxybenzaldehyde, hydroxybenzoate, homovanillin, syringic acid, vanillin, and syringaldehyde. There are several lignin-derived compounds that are antimicrobials. For example, furfural, 4-hydroxybenzaldehyde, syringaldehyde, 5-hydroxymethylfurfural, and vanillin are each known to have antimicrobial activity against Escherichia coli, and might have an additive antimicrobial activity against Escherichia coli when present in combination. Moreover, veratraldehyde, cinnamic acid and the respective benzoic acid derivatives of vanillic acid, vanillylacetone, and the cinnamic acid derivatives o-coumaric acid, m-coumaric acid, and p-coumaric acid might be components of the phenolic streams from pretreated lignocellulosic biomass.
Veratraldehyde, cinnamic acid and the respective benzoic acid derivatives of vanillic acid, vanillylacetone, and cinnamic acid derivatives o-coumaric acid, m-coumaric acid, and p- coumaric acid, each have significant antifungal activities against the yeast Saccharomyces cerevisiae, and might have an additive antifungal activity against the yeast Saccharomyces cerevisiae when present in combination.
[00129] One or more of the following benzaldehyde derivatives might be present in the phenolic streams from pretreated lignocellulosic biomass: 2,4,6-trihydroxybenzaldehyde, 2,5-dihydroxybenzaldehyde, 2,3,4-trihydroxybenzaldehyde, 2-hydroxy-5- methoxybenzaldehyde, 2,3-dihydroxybenzaldehyde, 2-hydroxy-3-methoxybenzaldehyde, 4- hydroxy-2,6-dimethoxybenzaldehyde, 2,5-dihydroxybenzaldehyde, 2,4- dihydroxybenzaldehyde, and 2-hydroxybenzaldehyde. Likewise, 2,4,6- trihydroxybenzaldehyde, 2,5-dihydroxybenzaldehyde, 2,3,4-trihydroxybenzaldehyde, 2- hydroxy-5-methoxybenzaldehyde, 2,3-dihydroxybenzaldehyde, 2-hydroxy-3- methoxybenzaldehyde, 4-hydroxy-2,6-dimethoxybenzaldehyde, 2,5-dihydroxybenzaldehyde, 2,4-dihydroxybenzaldehyde, and 2-hydroxybenzaldehyde have each demonstrated antibacterial activity against Escherichia coli, and might have an additive antibacterial activity against Escherichia coli when present in combination.
Microbial systems - suitable microbes
[00130] The antimicrobial activity of lignin-derived compounds creates a need for a strain of microbe that is tolerant to such activity in the reaction environment. The teachings include the identification of recombinant or non-recombinant microbial species that are naturally capable of metabolizing aromatic compounds for the biotransformations of lignin- derived compounds to commercial products.
[00131 ] Some examples of microbial species particularly suited for biotransformations of phenolic streams from pretreated lignocellulosic biomass include, but are not limited to, Azotobacter chroococcum, Azotobacter vinelandii, Novosphingobium aromaticivorans, Pseudomonas aeruginosa, Pseudomonas putida, Pseudomonas fluorescens, Pseudomonas stutzerii, Pseudomonas diminuta, Pseudomonas pseudoalcaligenes, Rhodopseudomonas palustris, Spingomonas sp.A1 , Sphingomonas paucimobilis SYK-6, Sphingomonas japonicum, Sphingomonas alaskenesis, Sphingomonas wittichii, Streptomyces
viridosporus, Delftia acidivorans, and Rhodococcus equi. Both bio-informatic and
experimental data from the literature reveal the presence of extensive metabolic activity towards aromatic compounds in these strains, making them relevant species for the discovery of enzymes that hydrolyze lignin-derived oligomers, and for biotransformations of lignin core structures. Without intending to be bound by any theory or mechanism of action, these species exhibit, for example, metabolism of aromatic compounds such as benzoate; amino-, fluoro-, and chloro-benzoates; biphenyl; toluene and nitrotoluenes; xylenes;
alkylbenzenes; styrene; atrazine; caprolactam; and polycyclic aromatic hydrocarbons.
[00132] The microbes can be grown in a fermentor, for example, using methods known to one of skill. The enzymes used in the bioprocessing are obtained from the microbes, and they can be intracellular, extracellular, or a combination thereof. As such, the enzymes can be recovered from the host cells using methods known to one of skill in the art that include, for example, filtering or centrifuging, evaporation, and purification. In some embodiments, the method can include breaking open the host cells using ultrasound or a mechanical device, remove debris and extract the protein, after which the protein can be purified using, for example, electrophoresis. In some embodiments, however, the teachings include the use of a microbe, recombinant or non-recombinant, that has tolerance to lignin-derived compounds. A microbe that is tolerant to lignin-derived compounds can be used industrially, for example, to express any enzyme, recombinant or non-recombinant, having a desired enzyme activity while directly in association with the lignin-derived compounds. Such activities include, for example, beta etherase activity, C-alpha-dehydrogenase activity, glutathione lyase activity, or any other enzyme activity that would be useful in the
biotransformation of lignin-derived compounds. The activities can be wild-type or produce through methods known to one of skill, such as transfection or transformation, for example.
Microbial systems - Azotobacter strains
[00133] The teachings herein are also directed to the discovery and use of recombinant Azotobacter strains heterologously expressing novel beta-etherase enzymes for the hydrolysis of lignin oligomers.
[00134] Research directed to the discovery of a suitable microbe has shown that
Azotobacter vinelandii may possess the industrially relevant strain criteria desired for the teachings provided herein. In some embodiments, the criteria includes (i) growth on inexpensive and defined medium, (ii) resistance to inhibitors in hydrolysates of
Iignocellulose, (iii) tolerance to acidic pH and higher temperatures, (iv) the co-fermentation of pentose and hexose sugars, (v) genetic tractability and availability of gene expression tools, (vi) rapid generation times, and (vii) successful growth performance in pilot scale
fermentations. Additionally, key physiological traits that contribute to the potential suitability of A. vinelandii to the conversion of lignin-streams include an ability to metabolize aromatic compounds and xenobiotics. Moreover, it has been shown to have a tolerance to phenolic compounds in industrial waste streams. The annotated genome sequence of A. vinelandii, and the availability of genetic tools for its transformation and for the heterologous expression of enzymes, contribute to the potential of this microbe to function, in it's native form or as a transformant, for example, in a high-yield production of industrial chemicals from lignin streams. [00135] The teachings are also directed to a method of cleaving a beta-aryl ether bond, the comprising contacting a polypeptide taught herein with a lignin-derived compound having (i) a beta-aryl ether bond and (ii) a molecular weight ranging from about 180 Daltons to about 3000 Daltons; wherein, the contacting occurs in a solvent environment in which the lignin-derived compound is soluble. The term "contacting" refers to placing an agent, such as a compound taught herein, with a target compound, and this placing can occur in situ or in vitro, for example.
[00136] The teachings are also directed to a method of cleaving a beta-aryl ether bond, the comprising contacting a polypeptide taught herein with a lignin-derived compound having (i) a beta-aryl ether bond and (ii) a molecular weight ranging from about 180 Daltons to about 3000 Daltons; wherein, the contacting occurs in a solvent environment in which the lignin-derived compound is soluble. In some embodiments, the lignin-derived compound has a molecular weight of about 180 Daltons to about 1000 Daltons. In some embodiments, the solvent environment comprises water. And, in some embodiments, the solvent environment comprises a polar organic solvent.
[00137] The teachings are also directed to a system for bioprocessing lignin-derived
compounds, the system comprising a polypeptide taught herein, a lignin-derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; and, a solvent in which the lignin-derived compound is soluble;
wherein, the system functions to cleave the beta-aryl ether bond by contacting the polypeptide with the lignin-derived compound in the solvent.
[00138] The teachings are also directed to a recombinant polynucleotide comprising a nucleotide sequence that encodes a polypeptide taught herein. Likewise, the teachings are also directed to a vector or plasmid comprising the polynucleotide, as well as a host cell transformed by the vector or plasmid to express the polypeptide.
[00139] The teachings are also directed to a method of cleaving a beta-aryl ether bond, the method comprising (i) culturing a host cell taught herein under conditions suitable to produce a polypeptide taught herein; (ii) recovering the polypeptide from the host cell culture; and, (iii) contacting the polypeptide of claim 1 with a lignin-derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; wherein, the contacting occurs in a solvent environment in which the lignin- derived compound is soluble. [00140] In some embodiments, the host cell can be E. Coli or an Azotobacter strain, such as Azotobacter vinelandii. And, in some embodiments, the lignin-derived compound can have a molecular weight of about 180 Daltons to about 1000 Daltons.
[00141 ] The teachings are also directed to a system for bioprocessing lignin-derived
compounds, the system comprising (i) a transformed host cell taught herein; (ii) a lignin- derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; and, (iii) a solvent in which the lignin-derived compound is soluble; wherein, the system functions to cleave the beta-aryl ether bond by contacting a polypeptide taught herein with the lignin-derived compound in the solvent.
EXAMPLES
[00142] The following examples illustrate, but do not limit, the present invention.
EXAMPLE 1
[00143] Microbial growth and metabolism studies on soluble lignin samples are
performed to test the tolerance of microbes on lignin-derived compounds. A set of aromatic and nonaromatic compounds known to inhibit growth of E. coli and S. cerevisiae strains might be used to characterize the growth, tolerance and metabolic capability of Azotobacter vinelandii strain BAA1303, and A. chroococcum strain 4412 (EB Fred) X-50. Metabolism of various aromatic and nonaromatic compounds by microbial strains might be determined as a function of cellular respiration by the reduction of soluble tetrazolium salts by actively metabolizing cells. XTT (2,3-Bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5- carboxanilide inner salt, Sigma) is reduced to a soluble purple formazan compound by respiring cells. E. coli might be used as the negative control strain in this study. Strains might be grown in rich medium to saturation, washed, and OD600nm of the cultures determined. Equal numbers of bacteria will be inoculated into wells of the 48-well growth asing concentrations of aromatic and non-aromatic compounds in the range of 0-500mM, will be added to the wells to a final volume of 0.8ml. Following incubation for 24-48 hours with shaking at 25-37°C, the cultures will be tested for growth upon exposure to the test compounds using the XTT assay kit (Sigma). Culture samples will removed from the 48 well growth plate, and diluted appropriately in 96 well assay plates to which the XTT reagent will be added. Soluble formazan formed will be quantified by absorbance at 450nm. Increased absorbance at 450nm will be indicative of growth or survival, or metabolism of a particular test compound by the strains. Table 3 lists some example compounds that can be used to test the tolerance of microbes on lignin-derived compounds.
[00144] Table 3.
Figure imgf000045_0001
[00145] The set of lignin compounds to be tested might be expanded to any of the
teachings provided herein. And, the microbial growth and metabolism studies on soluble lignin samples can also be performed actual industrial samples such as, for example, kraft lignins and biorefinery lignins.
EXAMPLE 2
[00146] This example illustrates how prospective enzymes were identified for use with the teachings provided herein. Although never successfully expressed heterologously as an industrial microbe in a commercial scale process, Sphingomonas paucimobilis has been shown to produce enzymes that have some activity in cleaving the beta aryl ether bond in lignin. See Masai, E., et al. Accordingly, the enzyme discovery effort started with running BLAST searches against the two enzymes identified by Masai as having beta etherase activity, "HgE" and "HgF". See Id. at Abstract. Table 4 lists genes identified in the BLAST searches for initial screening. [00147] Table 4.
Gene Species Activity Genbank Identity/Similarity
Accession # (%)
1 HgE Sphingomonas Beta-etherase BAA02032.1
paucimobilis
2 HgE- 1 Novosphingobium Putative ABD26841 .1 (62%) (75%)
aromaticivorans Beta-etherase
3 HgF Sphingomonas Beta-etherase BAA02031 .1
paucimobilis
4 ligF-1 Novosphingobium Putative ABD26530.1 (60%) (77%)
aromaticivorans Beta-etherase
5 HgF -2 Novosphingobium Putative ABD27301 .1 (47%) (59%)
aromaticivorans Beta-etherase
6 HgF -3 Novosphingobium Putative ABD27309.1 (37%) (57%)
aromaticivorans Beta-etherase
[00148] The nucleotide and amino acid sequences in Table 4 are incorporated herein by reference in their entirety through the GenBank Accession Numbers.
EXAMPLE 3
[00149] This example describes a method for preparing recombinant host cells for the heterologous expression of known and putative beta-etherase encoding gene sequences in Escherichia coli (£. coli). E. coli is used in this example as a surrogate enzyme production host organism for the enzyme discovery. The construction of a novel industrial host microbe, A. vinelandii is described below.
[00150] The gene sequences with accession numbers in Table 3 were synthesized
directly as open reading frames (ORFs) from oligonucleotides by using standard PCR-based assembly methods, and using the E. coli codon bias with 10% threshold. The end sequences contained adaptors (Ndel and Xhol) for restriction digestion and cloning into the E. coli expression vector pET24b (Novagen). Internal Ndel and Xhol sites were excluded from the ORF sequences during design of the oligonucleotides. Assembled genes were cloned into a cloning vector (pGOV4), transformed into E. coli CH3 chemically competent cells, and DNA sequences determined from purified plasmid DNA. After sequence verification, restriction digestion was used to excise each ORF fragment from the cloning vector, and the sequence sub-cloned into pET24b. The entire set of HgE and HgF bearing plasmids were then transformed into E. coli BL21 (DE3) which served as the host strain for beta-etherase expression and biochemical activity testing. [00151 ] LigE, from Accession No BAA2032.1 , is listed herein as SEQ ID NO:1 for the protein and SEQ ID NO:2 for the gene. An "optimized" nucleic acid sequence was created to facilitate the transformation in E co//' and is listed herein as SEQ ID NO:977.
[00152] LigE-1 , from Accession No ABD26841 .1 , is listed herein as SEQ ID NO:101 for the protein and SEQ ID NO:102 for the gene. An "optimized" nucleic acid sequence was created to facilitate the transformation in E. co//' and is listed herein as SEQ ID NO:978.
[00153] LigF, from Accession No BAA2031 .1 (P30347.1 ), is listed herein as SEQ ID NO:513 for the protein and SEQ ID NO:514 for the gene. An "optimized" nucleic acid sequence was created to facilitate the transformation in E co//' and is listed herein as SEQ ID NO:979.
[00154] LigF-1 , from Accession No ABD26530.1 , is listed herein as SEQ ID NO:539 for the protein and SEQ ID NO:540 for the gene. An "optimized" nucleic acid sequence was created to facilitate the transformation in E. co//' and is listed herein as SEQ ID NO:980.
[00155] LigF-2, from Accession No ABD27301 .1 , is listed herein as SEQ ID NO:541 for the protein and SEQ ID NO:542 for the gene. An "optimized" nucleic acid sequence was created to facilitate the transformation in E. co//' and is listed herein as SEQ ID NO:981 .
[00156] LigF-3, from Accession No ABD27309.1 , is listed herein as SEQ ID NO:545 for the protein and SEQ ID NO:546 for the gene. An "optimized" nucleic acid sequence was created to facilitate the transformation in E. co//' and is listed herein as SEQ ID NO:982.
EXAMPLE 3
[00157] This example describes a method for gene expression in E coli, as well as beta- etherase biochemical assays. Expression of known and putative beta-etherase genes was performed using 5ml cultures of the recombinant E. coli strains described herein in Luria Broth medium by induction of gene expression using isopropylthiogalactoside (IPTG) to a final concentration of 0.1 mM. Following induction, and cell harvest, the cells were disrupted using either sonication or the BPER (Invitrogen) cell lysis system.
[00158] Clarified cell extracts were tested in the in vitro biochemical assay for beta- etherase activity on a fluorescent substrate, a model lignin dimer compound α-0-(β- methylumbelliferyl) acetovanillone (MUAV). In vitro reactions were performed in a total volume of 200ul and contained: 25mM TrisHCI pH 7.5; 0.5mM dithiothreitol; 1 mM
glutathione;0.05mM or 0.1 mM MUAV; 10ul of clarified cell extract used to initiate the reactions. Following incubation for 2.5 hours at room temperature, a 50ul sample of the reactions was terminated using 150uL of 300mM glycine/NaOH buffer pH 9. The formation of 4 methylumbelliferone (4MU) upon hydrolysis of the aryl ether bond was monitored by the increase in fluorescence at λβχ=360ηηι and λβΓΤ1=450ηΓη using a Spectramax
UV/visible/fluorescent spectrophotometer.
[00159] The total protein concentrations of the cell lysates were determined using the BCA reagent system for protein quantification (Pierce).
[00160] Induction might be also performed using IPTG concentrations in the range of 0.01 -1 mM. Cell disruption might be also performed using toluene permeabilization, French pressure techniques, or using multiple freeze/thaw cycles in conjunction with lysozyme. Assay conditions might be varied to include TrisHCI at 10-150mM concentrations and in the pH range of 6.5-8.5; 0-2mM dithiothreitol; 0.05-2mM glutathione; 0.01 -5mM MUAV substrate; 22-42°C reaction temperatures. The biochemical assay might be performed as a fixed time point assay with reaction times ranging from 5 minutes-12 hours, or performed continuously without quenching with glycine/NaOH buffer to extract enzyme kinetic parameters.
EXAMPLE 4
[00161 ] This example describes the tested biochemical activities of the newly-discovered beta-etherase enzymes.
[00162] FIG. 4 illustrates unexpected results from biochemical activity assays for beta- etherase function for the S. paucimobilis positive control polypeptides, and the N. aromaticivorans putative beta-etherase polypeptide, according to some embodiments. The much elevated beta-etherase activity exhibited by the putative ligEI gene product from N. aromaticivorans as compared to the S. paucimobilis ligE gene product was a completely unexpected result of the enzyme discovery program.
[00163] In reactions containing 0.1 mM MUAV substrate, E. coli cell extracts expressing the N. aromaticovorans ligEI protein yielded a total activity of 529rfu/ug compared to 7rfu/ug for the S. paucimobilis ligE protein. The newly discovered beta-etherase from N. aromaticovorans is approximately 75-fold more efficient than the previously described S. paucimobilis ligE beta-etherase enzyme. The highly efficient novel beta-etherase is ideally suited to be a biocatalyst for conversion of lignin aryl ethers to monomers in biotechnological processes.
[00164] It was also surprising to find that 3 novel N. aromaticivorans polypeptides having identities to the S. paucimobilis LigF sequence showed beta-etherase activity on the MUAV substrate. While all 3 putative HgFgene products from N. aromaticivorans exhibited beta- etherase activity, the LigF2 polypeptide is approximately 2-fold more efficient than the S. paucimobilis LigF protein. The N. aromaticovorans LigF2 protein yielded a total activity of 1206rfu/ug compared to 558rfu/ug for the S. paucimobilis LigF protein.
[00165] As such, the enzyme discovery program unexpectedly and surprisingly
generated four (4) novel polypeptides from N. aromaticivorans with beta-etherase activity. This set of enzymes show great potential for the catalysis of a complete depolymerization of lignin-derived compounds. The results were unexpected and surprising for at least the following reasons:
[00166] Four (4) novel gene sequences encoding polypeptides with beta-etherase activity were discovered from N. aromaticivorans. These sequences have Gen Bank Nos.
ABD26841 .1 (SEQ ID NO:101 ); ABD26530.1 (SEQ ID NO:539); ABD27301 .1 (SEQ ID NO:541 ); and ABD27309.1 (SEQ ID NO:545).
[00167] One of skill will appreciate that the bioinformatic screen that was used to help identify putative enzymes is not a definitive predictor in itself of biochemical activities, particularly in view of (i) having only one known active enzyme for LigE in a different species, (ii) one known active enzyme for LigF, and (iii) the unexpected extent of such activities discovered. The tests for function therefore had to be performed empirically on the N. aromaticivorans putative beta-etherase gene set.
[00168] One of skill will also appreciate that the discovery of beta-etherase activities for all 4 N. aromaticivorans polypeptides was a complete surprise given the relatively low levels of identities (37%-62%) the sequences had with respect to the S. paucimobilis LigE and LigF proteins.
[00169] One of skill will also appreciate that the discovery of 2 novel beta-etherases from the N. aromaticivorans with improved activities over the corresponding LigE and LigF proteins from S. paucimobilis were completely unexpected, and this exciting discovery provides a foundation for further enzyme development for industrial applications.
EXAMPLE 5
[00170] This example describes the extended use of bioinformatics to identify a pool of putative enzymes in the discovery program. As noted above, the bioinformatic screen that was used to help identify putative enzymes initially was not a definitive predictor in itself of biochemical activities, particularly in view of (i) having only one known active enzyme for LigE in a different species, (ii) one known active enzyme for LigF, and (iii) the unexpected extent of such activities discovered. Having the additional known active enzymes provided more information that could be used to enhance the effectiveness of the bioinformatics in identifying the pool of putative enzymes for both LigE-type and LigF-type enzymes.
[00171 ] Sequence to function correlations for the newly discovered beta-etherases were analyzed and identified. A bioinformatic survey of functional domains, essential catalytic residues, and sequence alignments was performed for the N. aromaticivorans LigE and LigF polypeptides. While not intending to be bound by any theory or mechanism of action, the rationale and key results of the survey include at least the following:
[00172] Identifying functional domains
[00173] As shown in FIG. 4, high levels of beta-etherase activities were discovered for the N. aromaticivorans LigE1 and LigF2 polypeptide sequences compared to the S.
paucimobilis LigE and LigF proteins. The N. aromaticivorans LigE1 and LigF2 polypeptide sequences were used as query sequences for the identification of functional domains using the Conserved Domain Database (CDD) in GenBank.
[00174] The N. aromaticivorans LigE1 polypeptide is annotated as a glutathione S- transferase (GST)-like protein with similarity to the GST C family, and the beta-etherase LigE subfamily. The LigE sub-family is composed of proteins similar to S. paucimobilis beta etherase, LigE, a GST-like protein that catalyzes the cleavage of the beta-aryl ether linkages present in low-moleculer weight lignins using reduced glutathione (GSH) as the hydrogen donor in the reaction. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. [00175] Table 5 describes conserved domains and essential amino acid residues in the N. aromaticivorans LigE1 polypeptide (ABD26841 .1 ), according to some embodiments. The three (3) conserved functional domains annotated in the N. aromaticivorans LigE1 polypeptide are: i) the dimer interface; ii) the N terminal domain; iii) the lignin substrate binding pocket or the H site. Amino acid residues defining the functional domains in such embodiments are residues 98-221 in the N. aromaticivorans LigE1 polypeptide.
[00176] Table 5 also lists fifteen (15) amino acid residues as conserved and essential for catalytic activity (column 3 of Table 5), , according to some embodiments. These include: K100; A101 ; N104; P166; W107; Y184; Y187; R188; G191 ; G192; F195; V1 1 1 ; G1 12; M1 15; F1 16. While not intending to be bound by any theory or mechanism of action, these residues appear responsible for the high beta-etherase catalytic activity discovered for the N. aromaticivorans LigE1 polypeptide compared to the S. paucimobilis ligE polypeptide.
[00177] In such embodiments, the essential amino acid residues of the N.
aromaticivorans LigE1 polypeptide might be altered conservatively, and singly or in combination with similar amino acid residues that would retain or improve the catalytic function of the N. aromaticivorans LigE1 polypeptide. Examples of such alternate residues that might be incorporated at the essential positions are also shown in column 4 of Table 5.
[001781 Table 5.
Figure imgf000052_0001
[00179] The N. aromaticivorans LigF2 polypeptide is annotated as a glutathione S- transferase (GST)-like protein with similarity to the GST C family, catalyzing the conjugation of glutathione with a wide range of xenobiotic agents.
[00180] Table 6 describes conserved domains and essential amino acid residues in the N. aromaticivorans LigF2 polypeptide (ABD27301 .1 ), according to some embodiments. The three (3) conserved functional domains annotated for the N. aromaticivorans LigF2 polypeptide are similar to those described for the N. aromaticivorans LigE polypeptide and comprise: i) the dimer interface; ii) the N terminal domain; iii) the substrate binding pocket or the H site. In such embodiments, amino acid residues defining the functional domains are residues 99-230 in the N. aromaticivorans LigF2 polypeptide.
[00181 ] Table 6 also lists sixteen (16) amino acid residues as conserved and essential for catalytic activity (column 3 of Table 6) of the N. aromaticivorans LigF2 polypeptide, according to some embodiments. These include: R100; Y101 ; K104; K176; D107; L194; 1197; N198; S201 ; M206; M1 1 1 ; N1 12; S1 15; M1 16; M206; H202. While not intending to be bound by any theory or mechanism of action, these 16 residues appear to be responsible for the high beta-etherase catalytic activity discovered for the N. aromaticivorans LigF2 polypeptide compared to the S. paucimobilis LigF polypeptide. [00182] In such embodiments, the essential amino acid residues of the N.
aromaticivorans LigF2 polypeptide might be altered conservatively, and singly or in combination with similar amino acid residues that would retain or improve the catalytic function of the N. aromaticivorans LigF2 polypeptide. Examples of such alternate residues that might be incorporated at the essential positions are shown in column 4 of Table 6.
[00183] Table 6.
Figure imgf000053_0001
[00184] Identifying additional functional domains
[00185] Bioinformatic methods were used to further understand the protein structure that may result in the desired activities. First, the LigE1 and LigF2 were analyzed together. Amino acid sequence alignments were performed using the N. aromaticivorans ligE1 (ABD26841 .1 ) and ligF2 (ABD27301 .1 ) sequences using the BLAST-P program in
GenBank, and the ProDom and PraLine programs. Full length sequence alignments yielded hits with relatively low identities, for example, identities of <70%.
[00186] Next, regions in LigE1 and LigF2 were analyzed independently in GENBANK.
For LigE1 , an alignment was performed against the database in GENBANK using the following query sequence: "tispfvwatkyalkhkgfdldvvpggftgilertgg" (residues 19-54 of SEQ ID NO:101 ), from N. aromaticivorans ligE1 . The BLAST yielded at least 3 subject sequences with high identities in the thioredoxin (TRX)-like superfamily of proteins containing a TRX fold. Many members contain a classic TRX domain with a redox active CXXC motif.
[00187] Without intending to be bound by any theory or mechanism of action, they are thought to function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include the families of TRX, protein disulfide isomerase (PDI), tlpA, glutaredoxin, NrdH redoxin, and bacterial Dsb proteins (DsbA, DsbC, DsbG, DsbE, DsbDgamma). Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins, glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others.
[00188] Table 7 lists 3 subject sequences having high identities (>80%) to residues 19-54 of LigE-1 (SEQ ID NO:101 ). In some embodiments, these sequences are likely to be essential to catalytic functions similar to those discovered for the N. aromaticivorans ligEI polypeptide.
[00189] Table 7.
Figure imgf000054_0001
[00190] The nucleotide and amino acid sequences in Table 7 are incorporated herein by reference in their entirety through the GenBank Accession Numbers.
[00191 ] Likewise, for LigF2, separate alignments were performed against the database in GENBANK using the following 2 query sequences: "ainpegqvpvl" (residues 47-57 of SEQ ID NO:541 ); and "iithttvineyled" (residues 63-76 of SEQ ID NO:541 ), from N. aromaticivorans ligF2 (ABD27301 .1 ) yielded multiple subject sequences with high identities in the GST-N superfamily of proteins. Without intending to be bound by any theory or mechanism of action, the N terminal region (residues 43-75 of SEQ ID NO:541 ) of the N. aromaticivorans ligF2 polypeptide is annotated in the CDD to encompass:
[00192] i. N terminal residues thought to make contact with the C terminal interface in forming the tertiary protein structure for the GST-N family of proteins;
[00193] ii. N terminal residues thought to be involved in dimerization of the
polypeptides; and,
[00194] iii. Residues thought to be involved in the binding of glutathione substrate.
[00195] Table 8 provides the percent identities and similarities to N. aromaticovorans LigF2 query sequence residues 47-57.
[001961 Table 8.
Figure imgf000056_0001
[00197] The nucleotide and amino acid sequences in Table 8 are incorporated herein by reference in their entirety through the GenBank Accession Numbers.
[00198] Table 9 provides the percent identities and similarities to N. aromaticovorans LigF2 query sequence residues 63-76. [001991 Table 9.
Figure imgf000057_0001
[00200] The nucleotide and amino acid sequences in Table 9 are incorporated herein by reference in their entirety through the GenBank Accession Numbers.
[00201 ] The bioinformatics provides valuable information about protein structure that can assist in identifying test candidates. For example, the LigE1 has the 98-221 region, which is annotated in the databases as potentially responsible as component of binding and activity, dimerization, and for binding and catalysis in general. While not intending to be bound by any theory or mechanism of action, the variability in active site structures is reflected by the variability in substrate structures. Likewise, upon further research using bioinformatics, it was further discovered that the 19-54 region, which is annotated in the databases as a second region that is potentially responsible as component of the reductase function, and thus potentially responsible for catalysis in addition to the 98-221 region, while having more conservation between members.
[00202] Obtaining additional structural information that will assist in finding high
performing proteins within each family of strains is within the scope of the teachings to the extent that the methodology is known to one of skill. A variety of research techniques are known to one of skill. Bioinformatic methods, such as motif finding, are an example of one way to obtain the additional structural information. Motif finding, also known as profile analysis, constructs global multiple sequence alignments that attempt to align short conserved sequence motifs among the sequences in the query set. This can be done, for example, by first constructing a general global multiple sequence alignment, after which highly conserved regions are isolated, in a manner similar to what is taught herein, and used to construct a set of profile matrices. The profile matrix for each conserved region is arranged like a scoring matrix but its frequency counts for each amino acid or nucleotide at each position are derived from the conserved region's character distribution rather than from a more general empirical distribution. The profile matrices are then used to search other sequences for occurrences of the motif they characterize.
03] LigE-1 and LigF-2 were further examined by comparing their structures to other polypeptides of the LigE-type and LigF-type, respectively. Table 10A shows conserved residues between the polypeptide sequences of LigE and LigE-1 , and Table 10B shows shows conserved residues between the polypeptide sequences of LigF and LigF-2.
[00204] Table 10A.
Res Pos Res Pos Res Pos Res Pos Res Pos Res Pos
M 1 P 42 Y 78 Q 129 P 184 P 235
A 2 G 43 L 79 D 130 N 185 L 236
N 4 G 44 D 80 Y 133 A 187 F 237
N 5 F 45 K 82 V 134 D 188 G 238
T 6 T 46 Y 83 S 137 Y 189 L 239
I 7 G 47 P 84 R 138 T 198 R 242
T 8 I 48 D 85 E 139 A 199 E 243
Y 10 L 49 R 86 L 148 S 200 G 244
D 1 1 E 50 P 87 E 149 V 201 D 245
L 12 R 51 L 89 V 151 T 204 P 246
L 14 T 52 K 100 Q 152 P 205 F 249
G 17 G 53 L 102 A 153 L 207 R 251
T 19 G 54 D 103 G 154 D 210 G 254
I 20 E 57 N 104 R 155 D 21 1 G 257 s 21
P 22
V 24 R 58 W 105 E 156 P 212 N 264 w 25 P 60 W 107 L 213 G 266
T 27 I 62 A 1 10 R 158 R 214 P 267
K 28 V 63 V 1 1 1 L 159 D 215
Y 29 D 64 G 1 12 P 160 W 216 T 270
A 30 D 65 P 1 13 L 166 R 219 R 275
L 31 G 66 W 1 14 E 167 D 222 E 278
K 32 E 67 C 1 17 P 168 L 223
H 33 V 69 D 121 R 170 G 226
K 34 L 70 Y 122 L 173 L 227
G 35 D 71 D 124 A 174 G 228
F 36 S 72 L 125 W 178 R 229
D 37 W 73 S 126 L 179 H 230
D 39 I 75 L 127 G 180 P 231
V 41 E 77 P 128 G 181 G 232
[00205] As can be seen, there is a high degree of between-species similarity between LigE and LigE-1 in the LigE-type family. The LigE residues are from S. paucimobilis (BAA02032.1 ) and the LigE-1 residues are from N. aromaticivorans LigE1 (ABD26841 .1 ). The numbering is done according to the S. paucimobilis sequence (BAA02032.1 ) in the PRALINE alignment file (gaps not included). [00206] Table 10B.
Res Pos Res Pos
M 1 D 89
Y 6 R 97
P 10 W 99
A 12 K 101
N 13 L 161
S 14 K 167
K 16
L 21
E 23 E 176
K 24 L 179
G 25 L 185
L 26 Y 190
E 29 L 192
D 34 A 193
F 38 D 194
E 39 I 195
H 41 P 221
F 45 L 223
I 48 W 226
N 49 R 229
P 50 R 233
G 52 P 234
V 54 A 235
P 55
T 65
T 68
I 70
E 72
Y 73
L 74
E 75
D 76
L 85
P 87
[00207] As can be seen, there is less between-species similarity between LigF and LigF- 2 in the LigF-type family. The LigF residues are from S. paucimobilis (BAA02031 .1 ) and the LigF-2 residues are from N. aromaticivorans (ABD27301 .1 ). Numbering is according to the S. paucimobilis sequence (BAA02031 .1 ) in the PRALINE alignment file (gaps not included.
EXAMPLE 6
[00208] This example provides additional sequences for a second round of assays, the sequences containing the 3 conserved functional domains described herein for the GST C family of proteins, and belong to the beta-etherase LigE subfamily. Table 1 1 lists nine (9) additional sequences having identities of 51 % -73% at the amino acid level that were identified in the SwissProt database using the S. paucimobilis LigE sequence (P27457.3) as the query. The bioinformatics information suggests that these 9 sequences are excellent candidates for the next round of synthesis, cloning, expression and testing for the desired biochemical functions using the methods described herein.
[00209] Table 1 1 .
Figure imgf000061_0001
[00210] The nucleotide and amino acid sequences in Table 1 1 are incorporated herein by reference in their entirety through the GenBank Accession Numbers.
EXAMPLE 7
[0021 1 ] This example describes how native lignin core structures can be hydrolyzed by the action of C alpha-dehydrogenases, beta-etherases, and glutathione-eliminating enzymes.
[00212] FIG. 5 illustrates beta-aryl-ether compounds to be tested as substrates
representing native lignin structures, according to some embodiments. While MUAV was used as a model substrate in the identification of novel beta-etherase enzymes, additional aryl-ether compounds such as those shown in FIG. 5 might be used to assess substrate specificities of the beta-etherases towards dimers and trimers of aromatic compounds containing the beta-aryl ether linkage and representative of native lignin structures. Higher order oligomers of molecular weights <2000 might be synthesized and tested as well. The compounds might be obtained by custom organic synthesis, as for the fluorescent substrate MUAV.
[00213] FIG. 6 illustrates pathways of guaiacylglycerol^-guaiacyl ether (GGE)
metabolism by S. paucimobilis, according to some embodiments. Enzymes in addition to LigE/F-like beta etherases might be required to hydrolyze native lignin core structures. The model β-aryl ether compound guaiacylglycerol- β -guaiacyl ether (GGE) is believed to contain the main chemical linkages present in native lignin, including the hydroxyl, aryl-ether and methoxy functionalities. The biotransformation of GGE to the lignin monomer beta- hydroxypropiovanillone (beta-HPV) is partially understood for S. paucimobilis, and proposed to occur via the action of 3 separate enzymes in a step-wise manner. The ligD gene product encodes a C alpha-dehydrogenase which oxidizes GGE to a-(2-methoxyphenoxy)-p- hydroxypropiovanillone (MPHPV); the ether bond of MPHPV is cleaved by the beta-etherase activities of the ligE and HgFgene products to yield the lignin monomer guaiacol, and oc- glutathionylhydroxypropiovanillone (GS-HPV), respectively. The HgG gene product encodes a glutathione (GSH)-eliminating glutathione S transferase (GST) which catalyzes the elimination of glutathione (GSH) from GS-HPV to yield the lignin hydroxypropiovanillone (HPV).
[00214] While the LigE and LigF polypeptides, or similar ones described herein, might be sufficient to hydrolyze native lignin structures, it would be useful to discover novel C alpha dehydrogenases (S. paucimobilis LigD homologs) and glutathione (GSH)-eliminating glutathione S transferases (S. paucimobilis LigG homologs) for industrial applications. The enzyme discovery programs might be conducted by methods similar to those described herein. The detection of lignin substrates, intermediates, and products of biochemical reactions might be measured following filtration, and the extraction of substrates and products into ethyl acetate. Substrates and products might be separated using reverse phase HPLC conditions with a C18 column developed with a gradient solvent system of methanol and water, and detected at 230nm or 254nm.
[00215] Table 12 lists potential C alpha-dehydrogenase polypeptide sequences, the
LigD-type, for use in conjunction with beta etherases including, but not limited to, LigE/F. The sequences were identified using bioinformatic methods, such as those taught herein. These C alpha-dehydrogenases are classified in the CDD as short-chain
dehydrogenase/reductases (SDRs) and are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns.
[00216] Without intending to be bound by any theory or mechanism of action, these
enzymes are thought to catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151 , human prostaglandin dehydrogenase (PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107, PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity.
[00217] Without intending to be bound by any theory or mechanism of action, the
standard reaction mechanism is thought to be a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase can have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases can have a TGXXXGX(1 -2)G NAD(P)-binding motif. Some atypical SDRs are thought to have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues.
Reactions catalyzed within the SDR family can include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. [002181 Table 12.
Figure imgf000064_0001
[00219] The nucleotide and amino acid sequences in Table 12 are incorporated herein by reference in their entirety through the GenBank Accession Numbers.
[00220] Table 13 lists potential LigG (glutathione-eliminating)-like enzyme sequences for use in conjunction with beta etherases including, but not limited to, LigE/F. The sequences were identified using bioinformatic methods, such as those taught herein. These might be utilized in conjunction with C-alpha dehydrogenases, and/or with LigE/F-like beta-etherases. The LigG-like proteins are annotated in the CDD as glutathione S-transferase (GST)-like proteins with similarity to the GST C family, the GST-N family, and the thioredoxin (TRX)- like superfamily of proteins containing a TRX fold.
[00221 ] Table 13.
Figure imgf000064_0002
[00222] The nucleotide and amino acid sequences in Table 13 are incorporated herein by reference in their entirety through the GenBank Accession Numbers.
EXAMPLE 8
[00223] This example describes the creation of a novel recombinant microbial system for the conversion of lignin oligomers to monomers. Azotobacter vinelandii strain BAA-1303 DJ, for example, might be transformed with beta-etherase encoding genes from N. aromaticovorans with the objective of creating a lignin phenolics-tolerant A. vinelandii strain capable of converting lignin oligomers to monomers at high yields in industrial processes. Table 14 lists additional A. vinelandii strains that might be used as host strains for beta- etherase gene expression, for example, by their strain designation and American Type
Culture Collection (ATCC) number.
[00224] Table 14.
Figure imgf000065_0001
[00225] The heterologous production of beta etherases, Coc dehydrogenases, and other enzymes for the production of lignin monomers and aromatic products in A. vinelandii might be achieved using the expression plasmid system described herein. The broad host range multicopy plasmid pKT230 (ATCC) encoding streptomycin resistance might be used for gene cloning. Genes can be synthesized by methods describe above, and cloned into the Smal site of pKT230. The nifH promoter from A. vinelandii strain BAA 1 303 DJ can be used to control gene expression.
[00226] A. vinelandii strain BAA 1303 DJ might be transformed with pKT230 derivatives using electroporation of electrocompetent cell (Eppendorf method), or by incubation of plasmid DNA with chemically competent cells prepared in TF medium (1 .9718g of MgS04, 0.0136 g of CaS04, 1 .1 g of CH3COONH4, 1 0 g of glucose, 0.25 g of KH2P04, and 0.55 g of K2HP04 per liter). Transformants might be selected by screening for resistance to streptomycin. Gene expression might be induced by cell growth under nitrogen-free Burk's medium (0.2 g of MgS04, 0.1 g of CaS04, 0.5 g of yeast extract, 20 g of sucrose, 0.8 g of K2HP04, and 0.2 g of KH2P04, with trace amounts of FeCI3 and Na2Mo04, per liter).
[00227] The biochemical activity of a newly-discovered beta-etherase enzyme
functionally expressed in A. vinelandii strain BAA 1303 DJ can be tested using methods known to one of skill, such as the methods provided herein. Biochemical activity assays for beta-etherase function, and for total protein might be performed as described herein. EXAMPLE 9 28] This example describes the design and use of recombinant Azotobacter strains heterologously expressing enzymes for the production of high value aromatic compounds from lignin core structures. Table 15 lists a few examples of aromatic compounds that might be produced by the microbial platforms described herein.
[002291 Table 15.
Figure imgf000067_0001
[00230] One example of a microbial process to a commercial aromatic compound might be the production of catechol from lignin-derived phenolic compounds. Catechol might be produced from guaiacol using an A. vinelandii or A. chroococcum strain engineered with enzymes including beta-etherases and demethylases, or demethylase enzymes alone. Azotobacter strains might be engineered to express the heterologous enzymes by the methods described herein.
[00231 ] FIG. 7 illustrates an example of a biochemical process for the production of catechol from lignin oligomers, according to some embodiments. The biochemical processes leading to aromatic products such as catechol might be designed as 3 unit operations described below:
[00232] i) Fractionation of soluble lignin - Concentration or partial purification of soluble biorefinery lignin fractions or phenolic streams using methods known to one of skill.
[00233] ii) Biotransformation - The biotransformation of the phenolic substrate stream might be carried out in a fed-batch bioprocess using Azotobacter strains engineered to specifically and optimally convert specific lignin-derived phenolic substrates to the final product, such as catechol. Corn steep liquor might be used the base medium used in the biotransformations. The phenolic stream might be introduced in fed-batch mode, at concentrations that will be tolerated by the strains.
[00234] iii) Product separation - The product, such as catechol, might be purified from the aqueous culture broths using standard chemical separation methods such as liquid-liquid extractions (LLE) with solvents of varying polarities applied in a sequential manner.
[00235] Additional examples of designed biochemical routes to aromatic products are described below:
[00236] i) lignin-derived syringic acid might be converted to gallic acid via a 2-step biochemical conversion using aryl aldehyde oxidases and demethylases.
[00237] ii) Lignin-derived vanillin might be converted to protocatechuic acid via a 2- step biochemical conversion using aryl aldehyde oxidases and demethylases.
[00238] iii) Lignin-derived vanillin might be converted to catechol via a 3-step
biochemical conversion using aryl aldehyde oxidases, aromatic decarboxylases, and demethylases.
[00239] iv) Lignin-derived 2-methoxytoluene might be converted to the urethane
precursor 2,4-diaminotoluene via a 4-step biochemical conversion using demethylases, ferulate-5-hydroxylases, 2,4-nitrophenol oxidoreductases, and 2,4-nitrobenzene reductases. [00240] In each case, the specific enzymes might be engineered into A. vinelandii or A. chroococcum strains, for example, and the process might be performed using unit operations similar to those described herein for the biochemical production of catechol.
[00241 ] FIG. 8 illustrates an example of a biochemical process for the production of vanillin from lignin oligomers, according to some embodiments. Vanillin can be used as a flavoring agent, and as a precursor for pharmaceuticals such as methyldopa. Synthetic vanillin, for example, can be produced from petroleum-derived guaiacol by reaction with glyoxylic acid. Vanillin, however, can also be produced from lignin-derived β- hydroxypropiovanillone (β-HPV) according to the process scheme indicated in FIG. 8. A 2- step biochemical route to vanillin from β-HPV can be achieved using the enzymes 2,4- dihydroxyacetophenone oxidoreductase, and vanillin dehydrogenase or carboxylic acid reductases, engineered into A. vinelandii.
[00242] FIG. 9 illustrates an example of a biochemical process for the production of 2,4- diaminotoluene from lignin oligomers, according to some embodiments. Toluene diisocyanate (TDI) can be used in the manufacture of polyurethanes. For example, 2,4- diaminotoluene (2,4-DAT) is the key precursor to TDI. Diaminotoluenes can be produced industrially by the sequential nitration of toluene with nitric acid, followed by the reduction of the dinitrotoluenes to the corresponding diaminotoluenes. Both nitration and reduction reactions yield mixtures of toluene isomers from which the 2,4-DAT isomer is purified by distillation. The conversion of lignin-derived 2-methoxytoluene to 2,4-DAT can be achieved according to the process scheme outlined in FIG. 9. 2-methoxytoluene can be be converted to 2,4-DAT by A. vinelandii engineered with 4 enzymes to specifically demethylate, hydroxylate, nitrate and aminate methoxytoluene.
[00243] FIG. 10 illustrates process schemes for additional product targets that include ortho-cresol, salicylic acid, and aminosalicylic acid, for the production of valuable chemicals from lignin oligomers, according to some embodiments. These chemicals, as with the others, have traditionally been obtained from the problematic petrochemical processes. A few of the process schemes for producing these chemicals using the teachings herein, based on guaiacol or 2-methoxytoluene, are shown schematically in FIG. 10. Designed biochemical routes, combined with the remarkable phenolics-tolerance traits of Azotobacter strains are proposed for conversions of lignin structures to industrial and fine chemicals. EXAMPLE 10
[00244] This example describes potential LigE-, LigF-, LigG-, and LigD-type polypeptides, and the genes encoding them. The potential polypeptides were identified using
bioinformatic methods, such as those taught herein.
[00245] As described above, the query sequences in the initial pass for the LigE-type and LigF-type were Sphingomonas paucimobilis sequences, such as those discussed in Masai, E., et al. Likewise, the query sequences for the LigG-type and LigD-type were also
Sphingomonas paucimobilis sequences, such as those discussed in Masai. The following sequences were used in the initial pass for all queries:
[00246] LigE, from Accession No BAA2032.1 , is listed herein as SEQ ID NO:1 for the protein and SEQ ID NO:2 for the gene.
[00247] LigF, from Accession No BAA2031 .1 (P30347.1 ), is listed herein as SEQ ID
NO:513 for the protein and SEQ ID NO:514 for the gene.
[00248] LigG, from Accession No Q9Z339.2, is listed herein as SEQ ID NO:733 for the protein and SEQ ID NO:734 for the gene.
[00249] LigD, from Accession No Q01 198.1 , is listed herein as SEQ ID NO:777 for the protein and SEQ ID NO:778 for the gene.
[00250] The following sequences were used in a modified query to further refine the LigE- type and LigF-type, and the query sequences were the LigE-1 and LigF-2 that showed the surprising and unexpected results shown in FIG. 4:
[00251 ] LigE-1 , from Accession No ABD26841 .1 , is listed herein as SEQ ID NO:101 for the protein and SEQ ID NO:102 for the gene.
[00252] LigF-2, from Accession No ABD27301 .1 , is listed herein as SEQ ID NO:541 for the protein and SEQ ID NO:542 for the gene.
[00253] Table 16 lists SEQ ID NOs:1 -246, which are potential protein sequences of the LigE-type, as well as a respective gene sequence encoding the protein. Table 17 lists SEQ ID NOs:247-576, which are potential protein sequences of the LigF-type, as well as a respective gene sequence encoding the protein. Table 18 lists SEQ ID NOs:577-776, which are potential protein sequences of the LigG-type, as well as a respective gene sequence encoding the protein. Table 19 lists SEQ ID NOs: 777-976, which are potential protein sequences of the LigD-type, as well as a respective gene sequence encoding the protein. 54] Bioinformatic methods, such as those described herein, can be used to suggest an efficient order of experimentation to identify additional potential enzymes for use with the teachings provided herein. Moreover, mutations and amino acid substitutions can be used to test affects on enzyme activity to further understand the structure of the most active proteins with respect to the enzyme functions sought by teachings provided herein.
[00255] Table 16.
PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO: NO: NO:
1 2 BAA02032.1 Sphingomonas paucimobilis LIGE
3 4 BAJ 1 1989.1 beta-etherase [Sphingobium sp. SYK-6] LIGE glutathione S-transferase domain-containing LIGE
5 6 EFV85608.1 protein [Achromobacter xylosoxidans C54l
7 8 EFW42705.1 predicted protein [Capsaspora owczarzaki ATCC LIGE
Glutathione S-transferase domain-containing LIGE
9 10 EGE55257.1 protein [Rhizobium etli CNPAF5121
glutathione S-transferase domain-containing LIGE
1 1 12 EGP48556.1 protein [Achromobacter xylosoxidans AXX-Al
13 14 EGP57475.1 lignin degradation protein [Agrobacterium LIGE
Glutathione S-transferase [Rhodotorula glutinis LIGE
15 16 EGU12703.1 ATCC 2040911
glutathione S-transferase domain-containing LIGE
17 18 EGU56510.1 protein [Vibrio tubiashii ATCC 191091
hypothetical protein pTi-SAKURA_p086 LIGE [Agrobacterium tumefaciens] >dbj|BAA87709.11
19 20 NP 053324.1 tiorf84 [Agrobacterium tumefaciensl
lignin beta-ether hydrolase [Mesorhizobium loti LIGE MAFF303099] >dbj|BAB54276.11 lignin beta-
21 22 NP 108131.1 ether hydrolase [Mesorhizobium loti
lignin degradation protein [Agrobacterium LIGE tumefaciens str. C58] >gb|AAK86925.2| lignin
23 24 NP 354140.2 degradation protein [Agrobacterium tumefaciens
putative BETA-etherase (BETA-aryl ether LIGE cleaving enzyme) protein [Sinorhizobium meliloti 1021] >emb|CAC45742.1 | Putative beta- etherase (beta-aryl ether cleaving enzyme)
protein [Sinorhizobium meliloti 1021]
>gb|AEG03720.1 | Glutathione S-transferase domain protein [Sinorhizobium meliloti BL225C]
25 26 NP 385269.1 >gb|AEH79753.1 | putative BETA-etherase
ligninase [Bradyrhizobium japonicum USDA 1 10] LIGE >dbj|BAC52692.1 | NgE [Bradyrhizobium
27 28 NP 774067.1 japonicum USDA 1 101
putative lignin beta-ether hydrolase LIGE [Rhodopseudomonas palustris CGA009]
29 30 NP 949676.1 >emb|CAE29781.1 | putative lignin beta-ether PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO: NO: NO:
RecName: Full=Beta-etherase; AltName: LIGE Full=Beta-aryl ether cleaving enzyme
>gb|AAA25878.1 | beta-etherase [Sphingomonas
31 32 P27457.3 paucimobilis] >dbj|BAA02032.1 | beta-etherase
hypothetical protein SCHCODRAFT_85860 LIGE [Schizophyllum commune H4-8]
33 34 :P 003028922. >gb|EFI94019.1 | hypothetical protein
hypothetical protein SCHCODRAFT_57691 LIGE [Schizophyllum commune H4-8]
35 36 :P 003030384. >gb|EFI95481.1 | hypothetical protein
hypothetical protein SCHCODRAFT_81614 LIGE [Schizophyllum commune H4-8]
37 38 :P 003033715. >gb|EFI98812.1 | hypothetical protein
hypothetical protein NECHADRAFT_55532 LIGE [Nectria haematococca mpVI 77-13-4]
>gb|EEU35500.1 | hypothetical protein
39 40 :P 003041213. NECHADRAFT_55532 [Nectria haematococca
41 42 XP 382462.1 hypothetical protein FG02286.1 [Gibberella zeae LIGE putative glutathione S-transferase (GST) LIGE [Bradyrhizobium sp. ORS278]
43 44 'P 001207860. >emb|CAL79645.1 | putative glutathione S- glutathione S-transferase domain-containing LIGE protein [Acidiphilium cryptum JF-5]
>gb|ABQ32287.1 | Glutathione S-transferase, N-
45 46 'P 001236206. terminal domain protein [Acidiphilium cryptum JF
putative glutathione S-transferase LIGE [Bradyrhizobium sp. BTAi 1 ] >gb|ABQ33995.11
47 48 'P 001237901. putative glutathione S-transferase (GST)
hypothetical protein Swit_1652 [Sphingomonas LIGE wittichii RW1] >gb|ABQ68015.1 | hypothetical
49 50 'P 001262153. protein Swit 1652 [Sphingomonas wittichii RW1]
glutathione S-transferase domain-containing LIGE protein [Sinorhizobium medicae WSM419]
>gb|ABR59630.1 | Glutathione S-transferase
51 52 'P 001326465. domain [Sinorhizobium medicae WSM4191
glutathione S-transferase domain-containing LIGE protein [Parvibaculum lavamentivorans DS-1]
>gb|ABS63563.1 | Glutathione S-transferase
53 54 'P 001413220. domain [Parvibaculum lavamentivorans DS-1] PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO: NO: NO:
glutathione S-transferase [Azorhizobium LIGE caulinodans ORS 571] >dbj|BAF89264.1 |
55 56 'P 001526182. glutathione S-transferase [Azorhizobium
lignin degradation protein [Sorangium ceiiuiosum LIGE 'So ce 56'] >emb|CAN96036.1 | lignin
57 58 'P 001616516. degradation protein [Sorangium ceiiuiosum 'So
glutathione S-transferase domain-containing LIGE protein [Methylobacterium sp. 4-46]
59 60 'P 001772944. >gb|ACA20510.1 | Glutathione S-transferase
glutathione S-transferase domain-containing LIGE protein [Beijerinckia indica subsp. indica ATCC
9039] >gb|ACB95969.1 | Glutathione S-
61 62 'P 001833458. transferase domain [Beijerinckia indica subsp.
beta-aryl ether cleaving enzyme, lignin LIGE degradation protein [Rhizobium etli CIAT 652]
>gb|ACE90517.1 | beta-aryl ether cleaving
63 64 'P 001977695. enzyme, lignin degradation protein [Rhizobium
glutathione S-transferase domain-containing LIGE protein [Rhodopseudomonas palustris TIE-1]
>gb|ACF03309.1 | Glutathione S-transferase
65 66 'P 001993784. domain [Rhodopseudomonas palustris TIE-11
glutathione S-transferase domain [Rhizobium LIGE leguminosarum bv. trifolii WSM2304]
>gb|ACI54372.1 | Glutathione S-transferase
67 68 'P 002280598. domain [Rhizobium leguminosarum bv. trifolii
glutathione S-transferase [Oligotropha LIGE carboxidovorans OM5] >ref|YP_004631892.11
beta etherase [Oligotropha carboxidovorans
OM5] >gb|ACI94284.11 glutathione S- transferase [Oligotropha carboxidovorans OM5] >gb|AEI02075.1 | putative beta etherase
69 70 'P 002290149. [Oligotropha carboxidovorans OM4]
glutathione S-transferase domain-containing LIGE protein [Methylocella silvestris BL2]
71 72 'P 002362903. >gb|ACK51541.1 | glutathione S-transferase
glutathione S-transferase domain-containing LIGE protein [Methylobacterium nodulans ORS 2060] >gb|ACL61802.1 | Glutathione S-transferase
73 74 'P 002502105. domain protein [Methylobacterium nodulans PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO: NO: NO:
lignin degradation protein [Agrobacterium vitis LIGE S4] >gb|ACM36110.1 | lignin degradation protein
75 76 'P 0025491 16. [Agrobacterium vitis S4]
glutathione S-transferase-like protein LIGE [Azotobacter vinelandii DJ] >gb|ACO76830.1 |
77 78 'P 002797805. Glutathione S-transferase-like protein
putative lignin beta-ether hydrolase LIGE [Sinorhizobium fredii NGR234]
79 80 'P 002825455. >gb|ACP24702.1 | putative lignin beta-ether
glutathione S-transferase domain protein LIGE [Rhizobium leguminosarum bv. trifolii WSM1325] >gb|ACS55517.1 | Glutathione S-transferase
81 82 'P 002975056. domain protein [Rhizobium leguminosarum bv.
lignin degradation protein [Agrobacterium sp. LIGE H13-3] >gb|ADY64039.1 | lignin degradation
83 84 'P 004278359. protein [Agrobacterium sp. H13-31
putative beta-etherase [Acidiphilium multivorum LIGE AIU301] >dbj|BAJ82791.1 | putative beta-
85 86 'P 004285673. etherase [Acidiphilium multivorum AIU3011
glutathione S-transferase-like protein LIGE [Pseudomonas mendocina NK-01]
87 88 'P 004378290. >gb|AEB56538.1 | glutathione S-transferase-like
glutathione S-transferase-like protein LIGE [Novosphingobium sp. PP1Y]
89 90 'P 004533906. >emb|CCA92088.1 | glutathione S-transferase- glutathione S-transferase domain-containing LIGE protein [Sinorhizobium meliloti AK83]
91 92 'P 004548326. >gb|AEG52712.1 | Glutathione S-transferase
glutathione S-transferase domain-containing LIGE protein [Mesorhizobium opportunistum
WSM2075] >gb|AEH89616.1 | Glutathione S-
93 94 'P 004613710. transferase domain protein [Mesorhizobium
putative lignin beta-etherase [Colwellia LIGE psychrerythraea 34H] >gb|AAZ24120.1 | putative
95 96 YP 269568.1 lignin beta-etherase [Colwellia psychrerythraea
beta-aryl ether cleaving enzyme, lignin LIGE degradation protein [Rhizobium etli CFN 42]
>gb|ABC90274.1 | beta-aryl ether cleaving
97 98 YP 469001.1 enzyme, lignin degradation protein [Rhizobium PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO: NO: NO:
glutathione S-transferase-like protein LIGE [Rhodopseudomonas palustris HaA2]
99 100 YP 487746.1 >gb|ABD08835.1 | Glutathione S-transferase-like
glutathione S-transferase-like protein LIGE [Novosphingobium aromaticivorans DSM 12444]
>gb|ABD26841.1 | glutathione S-transferase-like
101 102 YP_497675.1 protein [Novosphingobium aromaticivorans DSM
glutathione S-transferase-like protein LIGE [Rhodopseudomonas palustris BisB18]
103 104 YP 533979.1 >gb|ABD89660.1 | glutathione S-transferase-like
glutathione S-transferase-like protein LIGE [Chromohalobacter salexigens DSM 3043]
>gb|ABE60032.1 | glutathione S-transferase-like
105 106 YP 574731.1 protein [Chromohalobacter salexigens DSM
glutathione S-transferase-like protein LIGE [Trichodesmium erythraeum IMS101]
107 108 YP 723508.1 >gb|ABG53035.1 | glutathione S-transferase-like
etherase [Rhizobium leguminosarum bv. viciae LIGE 3841] >emb|CAK07074.1 | putative etherase
109 1 10 YP 767183.1 [Rhizobium leguminosarum bv. viciae 38411
glutathione S-transferase [Rhodopseudomonas LIGE palustris BisA53] >gb|ABJ0811 1.11 Glutathione
1 11 1 12 YP 783091.1 S-transferase [Rhodopseudomonas palustris
glutathione S-transferase domain-containing LIGE protein [Paracoccus denitrificans PD1222]
>gb|ABL69699.1 | Glutathione S-transferase, N-
1 13 1 14 YP 915395.1 terminal domain [Paracoccus denitrificans
putative beta-etherase (beta-aryl ether cleaving LIGE enzyme) protein [Phaeobacter gallaeciensis
BS107] >gb|EDQ1 1875.11 putative beta-
1 15 1 16 IP 02146530." etherase (beta-aryl ether cleaving enzyme)
putative beta-etherase (beta-aryl ether cleaving LIGE enzyme) protein [Phaeobacter gallaeciensis
2.10] >gb|EDQ08644.1 | putative beta-etherase
1 17 1 18 ZP 02149699." (beta-aryl ether cleaving enzyme) protein
putative beta-etherase (beta-aryl ether cleaving LIGE enzyme) protein [Hoeflea phototrophica DFL-43] >gb|EDQ33834.1 | putative beta-etherase (beta-
1 19 120 ZP 02166231.- aryl ether cleaving enzyme) protein [Hoeflea PROTEI N GENE GENBANK DESCRI PTION: TYPE SEQ ID SEQ I D ACCESSION NO: NO: NO:
glutathione S-transferase-like protein [alpha LIGE proteobacterium BAL199] >gb| EDP62276.11
121 122 IP 02190934. " glutathione S-transferase-like protein [alpha
123 124 ZP 03503368. " Glutathione S-transferase domain [Rhizobium LIGE
125 126 ZP 03507162. - Glutathione S-transferase domain [Rhizobium LIGE
127 128 ZP 03513891 . - Glutathione S-transferase domain [Rhizobium LIGE
129 130 ZP 03519388. - Glutathione S-transferase domain [Rhizobium LIGE
131 132 ZP 03520502. - putative etherase [Rhizobium etli GR56] LIGE glutathione S-transferase, N-terminal domain LIGE [Pseudovibrio sp. JE062] >gb| EEA94709.1 |
133 134 ZP 05084767. - glutathione S-transferase, N-terminal domain
lignin degradation protein [Achromobacter LIGE piechaudii ATCC 43553] >gb| EFF74366.11 lignin
135 136 ZP 06688745. - degradation protein [Achromobacter piechaudii
glutathione S-transferase family protein LIGE [Roseomonas cervicalis ATCC 49957]
>gb|EFH10151 .1 | glutathione S-transferase
137 138 ZP 06898146. - family protein [Roseomonas cervicalis ATCC
Glutathione S-transferase domain protein [Afipia LIGE sp. 1 NLS2] >gb|EFI51229.1 | Glutathione S-
139 140 ZP 07027473. - transferase domain protein [Afipia sp. 1 NLS21
beta-etherase [Ahrensia sp. R2A130] LIGE
141 142 ZP 07373940. - >gb|EFL90585.1 | beta-etherase [Ahrensia sp.
Glutathione S-transferase [gamma LIGE proteobacterium IMCC1989] >gb| EGG95341 .11
143 144 ZP 08328512. - Glutathione S-transferase [gamma
lignin degradation protein [Agrobacterium sp. LIGE ATCC 31749] >gb|EGL63395.11 lignin
145 146 ZP 08529965. - degradation protein [Agrobacterium sp. ATCC
lignin beta-ether hydrolase [Bradyrhizobiaceae LIGE bacterium SG-6C] >gb| EGP10168.1 | lignin beta-
147 148 ZP 08627134. - ether hydrolase [Bradyrhizobiaceae bacterium
Glutathione S-transferase domain-containing LIGE protein [Acidiphilium sp. PM] >gb|EG096849.1 |
149 150 ZP 08631370. - Glutathione S-transferase domain-containing
Glutathione S-transferase domain-containing LIGE protein [Acidiphilium sp. PM] >gb|EGO93307.1 |
151 152 ZP 08634908. - Glutathione S-transferase domain-containing PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO: NO: NO:
glutathione S-transferase domain-containing LIGE protein [Halomonas sp. TD01] >gb|EGP21558.11
153 154 IP 08635074/ glutathione S-transferase domain-containing
hypothetical protein SERLA73DRAFT_1 15219 LIGE [Serpula lacrymans var. lacrymans S7.3]
>gb|EG019163.1 | hypothetical protein
155 156 EGN93792.1 SERLADRAFT_453680 [Serpula lacrymans var.
hypothetical protein SERLA73DRAFT_188253 LIGE [Serpula lacrymans var. lacrymans S7.3]
>gb|EG019875.11 hypothetical protein
157 158 EGN94392.1 SERLADRAFT_478300 [Serpula lacrymans var.
hypothetical protein SERLA73DRAFT_186005 LIGE [Serpula lacrymans var. lacrymans S7.3]
>gb|EG021854.1 | hypothetical protein
159 160 EGN96317.1 SERLADRAFT_474829 [Serpula lacrymans var.
hypothetical protein SERLA73DRAFT_185168 LIGE [Serpula lacrymans var. lacrymans S7.3]
>gb|EG022516.1 | hypothetical protein
161 162 EGN96924.1 SERLADRAFT_473468 [Serpula lacrymans var.
hypothetical protein SERLA73DRAFT_107446 LIGE [Serpula lacrymans var. lacrymans S7.3]
>gb|EG025928.1 | hypothetical protein
163 164 EGO00367.1 SERLADRAFT_415302 [Serpula lacrymans var.
conserved hypothetical protein [Aspergillus LIGE terreus NIH2624] >gb|EAU33805.1 | conserved
165 166 :P 001215222. hypothetical protein [Aspergillus terreus
hypothetical protein AOR_1_322094 [Aspergillus LIGE oryzae RIB40] >dbj|BAE62801.11 unnamed
167 168 :P 001823934. protein product [Aspergillus oryzae RIB401
hypothetical protein CC1 G_07903 [Coprinopsis LIGE cinerea okayama7#130] >gb|EAU82621.1 |
169 170 :P 001839188. hypothetical protein CC1 G_07903 [Coprinopsis
predicted protein [Laccaria bicolor S238N-H82] LIGE >gb|EDR03530.1 | predicted protein [Laccaria
171 172 :P 001885678. bicolor S238N-H821
conserved hypothetical protein [Penicillium LIGE marneffei ATCC 18224] >gb|EEA19427.1 |
173 174 :P 002152364. conserved hypothetical protein [Penicillium PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO: NO: NO:
conserved hypothetical protein [Aspergillus LIGE flavus NRRL3357] >gb|EED49097.1 | conserved
175 176 :P 002380998. hypothetical protein [Aspergillus flavus
hypothetical protein MPER_07394 LIGE [Moniliophthora perniciosa FA553]
177 178 :P 002392962. >gb|EEB93892.1 | hypothetical protein
predicted protein [Postia placenta Mad-698-R] LIGE >gb|EED86077.1 | predicted protein [Postia
179 180 :P 002468854. placenta Mad-698-Rl
predicted protein [Postia placenta Mad-698-R] LIGE >gb|EED82308.1 | predicted protein [Postia
181 182 :P 002472522. placenta Mad-698-Rl
Pc12g05530 [Penicillium chrysogenum LIGE Wisconsin 54-1255] >emb|CAP80180.1 |
183 184 :P 002557398. Pc12g05530 [Penicillium chrysogenum
hypothetical protein SCHCODRAFT_12387 LIGE [Schizophyllum commune H4-8]
185 186 :P 003026159. >gb|EFI91256.1 | hypothetical protein
hypothetical protein SCHCODRAFT_1 11982 LIGE [Schizophyllum commune H4-8]
187 188 :P 003028923. >gb|EFI94020.1 | hypothetical protein
Glutathione S-transferase domain-containing LIGE protein [Cyanothece sp. PCC 7822]
189 190 'P 003890246. >gb|ADN 16971.11 Glutathione S-transferase
glutathione S-transferase-like [Halomonas LIGE elongata DSM 2581] >emb|CBV41472.1 |
191 192 'P 003896657. glutathione S-transferase-like [Halomonas
glutathione S-transferase [Achromobacter LIGE xylosoxidans A8] >gb|ADP17667.11 glutathione
193 194 'P 003980382. S-transferase, N-terminal domain protein 4
glutathione S-transferase domain-containing LIGE protein [Rhodopseudomonas palustris DX-1]
>gb|ADU46105.1 | Glutathione S-transferase
195 196 'P 004110838. domain [Rhodopseudomonas palustris DX-11
glutathione S-transferase [Mesorhizobium ciceri LIGE biovar biserrulae WSM1271] >gb|ADV13817.1 | Glutathione S-transferase domain
197 198 'P 004143867. [Mesorhizobium ciceri biovar biserrulae PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO: NO: NO:
conserved hypothetical protein [Congregibacter LIGE litoralis KT71] >gb|EAQ98305.1 | conserved
199 200 IP 01102591.' hypothetical protein [Congregibacter litoralis
201 202 AAA87183.1 auxin-induced protein [Vigna radiata] LIGE
203 204 AAG34797.1 glutathione S-transferase GST 7 [Glycine max] LIGE
205 206 AA069664.1 glutathione S-transferase [Phaseolus acutifolius] LIGE
207 208 ACU24385.1 unknown [Glycine max] LIGE
209 210 ADP99065.1 glutathione S-transferase [Marinobacter LIGE putative glutathione S-transferase [Acinetobacter LIGE
211 212 ADY82158.1 calcoaceticus PHEA-21
213 214 BAA77215.1 beta-etherase [Sphingomonas paucimobilis] LIGE hypothetical protein CC1 G_12612 [Coprinopsis LIGE cinerea okayama7#130] >gb|EAU82225.1 |
215 216 :P 001839584. hypothetical protein CC1 G_12612 [Coprinopsis
predicted protein [Populus trichocarpa] LIGE
217 218 :P 002336443. >gb|EEE73479.1 | predicted protein [Populus
hypothetical protein SCHCODRAFT_59314 LIGE [Schizophyllum commune H4-8]
219 220 :P 003028624. >gb|EFI93721.1 | hypothetical protein
DEHA2A00660p [Debaryomyces hansenii LIGE CBS767] >emb|CAG84310.1 | DEHA2A00660p
221 222 XP 456365.1 [Debaryomyces hanseniil
hypothetical protein [Cryptococcus neoformans LIGE var. neoformans JEC21] >ref|XP_773999.11
hypothetical protein CNBH0460 [Cryptococcus neoformans var. neoformans B-3501A]
>gb|EAL19352.11 hypothetical protein
CNBH0460 [Cryptococcus neoformans var.
223 224 XP 572781.1 neoformans B-3501A] >gb|AAW45474.1 |
glutathione S-transferase domain-containing LIGE protein [Acidiphilium cryptum JF-5]
>gb|ABQ32287.1 | Glutathione S-transferase, N-
225 226 'P 001236206. terminal domain protein [Acidiphilium cryptum JF
putative glutathione S-transferase LIGE [Bradyrhizobium sp. BTAi 1 ] >gb|ABQ33995.11
227 228 'P 001237901. putative glutathione S-transferase (GST)
hypothetical protein Swit_1652 [Sphingomonas LIGE wittichii RW1] >gb|ABQ68015.1 | hypothetical
229 230 'P 001262153. protein Swit 1652 [Sphingomonas wittichii RW1] PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO: NO: NO:
glutathione S-transferase domain-containing LIGE protein [Sinorhizobium medicae WSM419]
>gb|ABR59630.1 | Glutathione S-transferase
231 232 'P 001326465. domain [Sinorhizobium medicae WSM4191
glutathione S-transferase domain-containing LIGE protein [Parvibaculum lavamentivorans DS-1]
>gb|ABS63563.1 | Glutathione S-transferase
233 234 'P 001413220. domain [Parvibaculum lavamentivorans DS-11
glutathione S-transferase [Azorhizobium LIGE caulinodans ORS 571] >dbj|BAF89264.1 |
235 236 'P 001526182. glutathione S-transferase [Azorhizobium
glutathione S-transferase [Synechococcus LIGE elongatus PCC 6301] >ref|YP_399807.1 |
glutathione S-transferase [Synechococcus
elongatus PCC 7942] >dbj|BAD78939.11
glutathione S-transferase [Synechococcus
237 238 YP 171459.1 elongatus PCC 6301] >gb|ABB56820.1 |
glutathione S-transferase-like protein [Anabaena LIGE variabilis ATCC 29413] >gb|ABA21529.11
239 240 YP 322424.1 Glutathione S-transferase-like protein
glutathione S-transferase, putative [marine LIGE gamma proteobacterium HTCC2080]
>gb|EAW41324.1 | glutathione S-transferase,
241 242 IP 01625805." putative [marine gamma proteobacterium
Glutathione S-transferase-like protein [Nodularia LIGE spumigena CCY9414] >gb|EAW44220.11
243 244 ZP 01631145." Glutathione S-transferase-like protein [Nodularia
glutathione S-transferase [Acinetobacter LIGE calcoaceticus RUH2202] >gb|EEY78560.11
245 246 ZP 06057261.- glutathione S-transferase [Acinetobacter
[00256] Table 17.
Figure imgf000084_0001
Figure imgf000085_0001
Figure imgf000086_0001
Figure imgf000087_0001
Figure imgf000088_0001
Figure imgf000089_0001
Figure imgf000090_0001
341 342 YP 002828116.1 fredii NGR2341
Figure imgf000091_0001
Figure imgf000092_0001
369 370 ZP 05125190.1 bacterium KLH1 11
Figure imgf000093_0001
Figure imgf000094_0001
Figure imgf000095_0001
4 7 4 XP 7 . marinus ATCC 509831
Figure imgf000096_0001
Figure imgf000097_0001
Figure imgf000098_0001
Figure imgf000099_0001
473 474 YP 957873.1 domain [Marinobacter aquaeolei VT81
Figure imgf000100_0001
Figure imgf000101_0001
Figure imgf000102_0001
5 5 5 XP 4 7 . moellendorffiil
Figure imgf000103_0001
529 530 YP 004229981.1 protein [Burkholderia sp. CCGE10011
Figure imgf000104_0001
Figure imgf000105_0001
Figure imgf000106_0001
Figure imgf000107_0001
[00257] Table 18.
PROTEIN GENE GENBANK DESCRIPTION : TYPE SEQ ID SEQ ID ACCESSION NO: NO: NO:
glutathione S-transferase homolog LigG
577 578 BAA77216.1 [Sphingomonas paucimobilisl
glutathione S-transferase family protein LigG [Novosphingobium sp. PP1 Y]
>emb|CCA92089.1 | glutathione S-
579 580 YP 004533907.- transferase family protein
glutathione S-transferase family protein LigG [Thiobacillus denitrificans ATCC 25259]
>gb|AAZ97003.11 glutathione S-
581 582 YP 314808.1 transferase family protein [Thiobacillus
glutathione S-transferase family protein LigG [Ruegeria pomeroyi DSS-3]
>gb|AAV95330.11 glutathione S-
583 584 YP 167289.1 transferase family protein [Ruegeria
glutathione S-transferase family protein LigG [Maritimibacter alkaliphilus HTCC2654]
>gb|EAQ14262.11 glutathione S-
585 586 ZP 0101 1943.1 transferase family protein
glutathione S-transferase protein LigG [Agrobacterium radiobacter K84]
587 588 YP 002540613.- >gb|ACM29018.11 glutathione S-
Novel glutathione S-transferase omega LigG
589 590 CAJ81793.1 protein [Xenopus (Silurana) tropicalisl
glutathione S-transferase omega 2 LigG [Xenopus (Silurana) tropicalis]
591 592 SIP 001005086.- >gb|AAH77010.1 | MGC89704 protein
PREDICTED: glutathione S-transferase LigG
593 594 XP 624501 .1 omega-1 [Apis melliferal
GM24932 [Drosophila sechellia] LigG
595 596 XP 002029736.- >gb|EDW40722.1 | GM24932 [Drosophila
hypothetical protein LOC436894 [Danio LigG
597 598 SIP 001002621 .' rerio] >gb|AAH75965.11 Zgc:92254 [Danio
predicted protein [Pediculus humanus LigG corporis] >gb|EEB18748.11 predicted
599 600 XP 002431486.- protein [Pediculus humanus corporisl
glutathione S-transferase [Glossina LigG
601 602 ADD18952.1 morsitans morsitans]
Figure imgf000110_0001
PROTEIN GENE GEN BANK DESCRIPTION : TYPE SEQ ID SEQ ID ACCESSION NO: NO: NO:
GL15567 [Drosophila persimilis] LigG
627 628 XP 002026470.- >gb|EDW33419.1 | GL15567 [Drosophila
glutathione S-transferase omega 4 LigG [Bombyx mori] >gb|ABY66601 .11
629 630 SIP 001 108461 .' glutathione S-transferase 13 [Bombyx
glutathione S-transferase omega-1 [Sus LigG scrofa] >ref|XP_001929519.1 |
PREDICTED: glutathione S-transferase omega-1 -like [Sus scrofa]
>sp|Q9N1 F5.2|GSTO1_PIG RecName:
Full=Glutathione S-transferase omega-1 ;
Short=GSTO-1 ; AltName:
Full=Glutathione-dependent
631 632 NP 999215.1 dehydroascorbate reductase
hypothetical protein LOC492500 [Danio LigG rerio] >gb|AAH85467.11 Zgc:101897
633 634 SIP 001007373.- [Danio rerio] >gb|AAI65433.11 Zgc:101897
glutathione S-transferase domain- LigG containing protein [Delftia acidovorans
SPH-1 ] >gb|ABX38269.11 Glutathione S-
635 636 YP 001566654.- transferase domain [Delftia acidovorans
omega class glutathione S-transferase LigG
637 638 ADY80021 .1 [Oplegnathus fasciatusl
glutathione S-transferase domain- LigG containing protein [Sinorhizobium
medicae WSM419] >gb|ABR62323.11
639 640 YP 001329158.- Glutathione S-transferase domain
hypothetical protein LOC431979 LigG [Xenopus laevis] >g b|AAH 70673.1 |
641 642 SIP 001084924.- MGC82327 protein [Xenopus laevisl
PREDICTED: glutathione S-transferase LigG
643 644 XP 003396907.- omega-1 -like [Bombus terrestrisl
PREDICTED: glutathione S-transferase LigG
645 646 XP 001368758.- omega-1 -like isoform 1 [Monodelphis
GH16193 [Drosophila grimshawi] LigG
647 648 XP 001983981 .- >gb|EDV96329.1 | GH16193 [Drosophila
649 650 ADK66966.1 glutathione s-transferase [Chironomus LigG PROTEIN GENE GEN BANK DESCRIPTION : TYPE SEQ ID SEQ ID ACCESSION NO: NO: NO:
PREDICTED: similar to glutathione-S- LigG
651 652 XP 001232808.- transferase homolog isoform 1 [Gallus
GK20354 [Drosophila willistoni] LigG
653 654 XP 002068565.- >gb|EDW79551 .1 | GK20354 [Drosophila
hypothetical protein sce0602 [Sorangium LigG cellulosum 'So ce 56'] >emb|CAN90759.11
655 656 YP 00161 1239.- gst2 [Sorangium cellulosum 'So ce 56'l
PREDICTED: glutathione S-transferase LigG
657 658 XP 001499427.. omega-1 -like isoform 1 [Equus caballusl
putative glutathione S-transferase protein LigG [Sinorhizobium meliloti 1021 ]
>ref|YP_004550950.11 glutathione S- transferase domain-containing protein
[Sinorhizobium meliloti AK83]
>emb|CAC41740.1 | Putative glutathione
S-transferase [Sinorhizobium meliloti
1021 ] >gb|AEG06303.11 Glutathione S- transferase domain protein
[Sinorhizobium meliloti BL225C]
659 660 NP 384409.1 >gb|AEG55336.1 | Glutathione S-
661 662 CAG05035.1 unnamed protein product [Tetraodon LigG hypothetical protein PaerPA_01002475 LigG [Pseudomonas aeruginosa PACS2]
>ref|YP_002440902.1 |
maleylacetoacetate isomerase
[Pseudomonas aeruginosa LESB58]
>ref|ZP_04928412.11 maleylacetoacetate isomerase [Pseudomonas aeruginosa
C3719] >gb|EAZ52531 .1 |
maleylacetoacetate isomerase
[Pseudomonas aeruginosa C3719]
>emb|CAW28043.11 maleylacetoacetate
663 664 ZP 01365353.1 isomerase [Pseudomonas aeruginosa
maleylacetoacetate isomerase LigG [Pseudomonas aeruginosa PA7]
>gb|ABR84080.11 maleylacetoacetate
665 666 YP 001348642.- isomerase [Pseudomonas aeruginosa PROTEIN GENE GEN BANK DESCRIPTION : TYPE SEQ ID SEQ ID ACCESSION NO: NO: NO:
maleylacetoacetate isomerase LigG [Pseudomonas aeruginosa 2192]
>gb|EAZ57884.11 maleylacetoacetate
667 668 ZP 04933765.1 isomerase [Pseudomonas aeruginosa
maleylacetoacetate isomerase LigG [Pseudomonas aeruginosa PAO1 ]
>sp|P57109.1 |MAAI_PSEAE RecName:
Full=Maleylacetoacetate isomerase;
Short=MAAI
669 670 NP 250697.1 >gb|AAG05395.1 |AE004627_3
hypothetical protein LigG
671 672 EFN59352.1 CHLNCDRAFT_137800 [Chlorella
glutathione S-transferase domain- LigG containing protein [Variovorax paradoxus S1 10] >gb|ACS20318.11 Glutathione S-
673 674 YP 002945584.- transferase domain protein [Variovorax
PREDICTED: glutathione S-transferase LigG
675 676 XP 002197460.- omega 1 [Taeniopygia guttatal
GG15075 [Drosophila erecta] LigG
677 678 XP 001971643.- >gb|EDV50669.1 | GG15075 [Drosophila
glutathione S-transferase omega-1 -like LigG [Acyrthosiphon pisum] >dbj|BAH71013.11
679 680 SIP 001 155757.- ACYPI008340 [Acyrthosiphon pisuml
GL15565 [Drosophila persimilis] LigG
681 682 XP 002026468.- >gb|EDW33417.1 | GL15565 [Drosophila
GA19760 [Drosophila pseudoobscura LigG pseudoobscura] >gb|EAL29555.1 |
683 684 XP 001353820.- GA19760 [Drosophila pseudoobscura
maleylacetoacetate isomerase LigG [Pseudomonas aeruginosa UCBPP-PA14] >gb|ABJ1 1 194.11 maleylacetoacetate
685 686 YP 791232.1 isomerase [Pseudomonas aeruginosa
Figure imgf000114_0001
Figure imgf000115_0001
Figure imgf000116_0001
Figure imgf000117_0001
[00258] Table 19.
PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO:
NO: NO:
RecName: Full=C alpha-dehydrogenase LigD >dbj|BAA02030.1 | C alpha-dehydrogenase
[Sphingomonas paucimobilis]
>dbj|BAA01953.1 | C alpha-dehydrogenase
[Sphingomonas paucimobilis]
>gb|AAC60455.1 | C alpha-dehydrogenase
777 778 Q01 198.1 [Sphingomonas paucimobilisl
short-chain dehydrogenase/reductase SDR LigD [Novosphingobium aromaticivorans DSM
12444] >gb|ABD24653.1 | short-chain
dehydrogenase/reductase SDR
[Novosphingobium aromaticivorans DSM
779 780 YP 495487.1 124441
short-chain dehydrogenase/reductase SDR LigD [Novosphingobium sp. PP1Y]
>emb|CCA92080.1 | short-chain
dehydrogenase/reductase SDR
781 782 YP 004533898.1 [Novosphingobium sp. PP1Y1
Calpha-dehydrogenase [Sphingobium sp. LigD
783 784 BAH56687.1 SYK-61
short-chain dehydrogenase/reductase SDR LigD [Novosphingobium sp. PP1Y]
>emb|CCA92103.1 | short-chain
dehydrogenase/reductase SDR
785 786 YP 004533921.1 [Novosphingobium sp. PP1Y1
short-chain dehydrogenase/reductase SDR LigD [Novosphingobium aromaticivorans DSM
12444] >gb|ABD25238.1 | short-chain
dehydrogenase/reductase SDR
[Novosphingobium aromaticivorans DSM
787 788 YP 496072.1 124441
Chain A, Structure Of Putative Short-Chain LigD Dehydrogenase (Saro_0793) From
Novosphingobium Aromaticivorans
>pdb|3IOY|B Chain B, Structure Of Putative Short-Chain Dehydrogenase (Saro_0793)
789 790 3IOY A From Novosphingobium Aromaticivorans PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO:
NO: NO:
short-chain dehydrogenase/reductase SDR LigD [Novosphingobium aromaticivorans DSM
12444] >gb|ABD25239.1 | short-chain
dehydrogenase/reductase SDR
[Novosphingobium aromaticivorans DSM
791 792 YP 496073.1 124441
Calpha-dehydrogenase [Sphingobium sp. LigD
793 794 BAH56683.1 SYK-61
short-chain dehydrogenase/reductase SDR LigD [Novosphingobium sp. PP1Y]
>emb|CCA92102.1 | short-chain
dehydrogenase/reductase SDR
795 796 YP 004533920.1 [Novosphingobium sp. PP1Y1
short-chain dehydrogenase/reductase SDR LigD [Caulobacter segnis ATCC 21756]
>gb|ADG10214.1 | short-chain
dehydrogenase/reductase SDR [Caulobacter
797 798 YP 003592832.1 segnis ATCC 217561
short-chain dehydrogenase/reductase SDR LigD [Novosphingobium aromaticivorans DSM
12444] >gb|ABD25150.1 | short-chain
dehydrogenase/reductase SDR
[Novosphingobium aromaticivorans DSM
799 800 YP 495984.1 124441
short-chain dehydrogenase/reductase SDR LigD [Novosphingobium aromaticivorans DSM
12444] >gb|ABD26315.1 | short-chain
dehydrogenase/reductase SDR
[Novosphingobium aromaticivorans DSM
801 802 YP 497149.1 124441
short-chain dehydrogenase/reductase SDR LigD [Caulobacter segnis ATCC 21756]
>gb|ADG10212.1 | short-chain
dehydrogenase/reductase SDR [Caulobacter
803 804 YP 003592830.1 segnis ATCC 217561
short-chain dehydrogenase/reductase SDR LigD [Sphingomonas wittichii RW1]
>gb|ABQ66748.1 | short-chain
dehydrogenase/reductase SDR
805 806 YP 001260886.1 [Sphingomonas wittichii RW11 PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO:
NO: NO:
short-chain dehydrogenase/reductase SDR LigD [Parvibaculum lavamentivorans DS-1]
>gb|ABS64322.1 | short-chain
dehydrogenase/reductase SDR
807 808 YP 001413979.1 [Parvibaculum lavamentivorans DS-1]
short-chain dehydrogenase/reductase SDR LigD [Parvibaculum lavamentivorans DS-1]
>gb|ABS62643.1 | short-chain
dehydrogenase/reductase SDR
809 810 YP 001412300.1 [Parvibaculum lavamentivorans DS-11
short-chain dehydrogenase/reductase SDR LigD [Parvibaculum lavamentivorans DS-1]
>gb|ABS62642.1 | short-chain
dehydrogenase/reductase SDR
81 1 812 YP 001412299.1 [Parvibaculum lavamentivorans DS-1]
Calpha-dehydrogenase [Sphingobium sp. LigD
813 814 BAH56685.1 SYK-61
short chain dehydrogenase [Mycobacterium LigD avium subsp. paratuberculosis K-10]
>ref|YP_880159.1 | short chain
dehydrogenase [Mycobacterium avium 104] >ref|ZP_05215302.1 | short chain
dehydrogenase [Mycobacterium avium
subsp. avium ATCC 25291]
>gb|AAS03027.1 | hypothetical protein
MAP_0710c [Mycobacterium avium subsp.
paratuberculosis K-10] >gb|ABK67661.1 | short chain dehydrogenase [Mycobacterium avium 104] >gb|EGO40035.11 short-chain alcohol dehydrogenase [Mycobacterium
815 816 NP 959644.1 avium subsp. paratuberculosis S3971
short chain dehydrogenase [Mycobacterium LigD colombiense CECT 3035] >gb|EGT85268.1 | short chain dehydrogenase [Mycobacterium
817 818 ZP 08717023.1 colombiense CECT 30351 PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO:
NO: NO:
oxidoreductase, short chain LigD dehydrogenase/reductase family protein
[gamma proteobacterium NOR5-3]
>gb|EED33994.1 | oxidoreductase, short chain dehydrogenase/reductase family
819 820 ZP 05127447.1 protein [gamma proteobacterium NOR5-31
Estradiol 17-beta-dehydrogenase LigD [Sphingobium chlorophenolicum L-1]
>gb|AEG50913.1 | Estradiol 17-beta- dehydrogenase [Sphingobium
821 822 YP 004555419.1 chlorophenolicum L- 1
short-chain dehydrogenase/reductase SDR LigD [Burkholderia sp. CCGE1001]
>gb|ADX57778.1 | short-chain
dehydrogenase/reductase SDR
823 824 YP 004230838.1 [Burkholderia sp. CCGE10011
putative oxidoreductase [Acidiphilium LigD multivorum AIU301] >dbj|BAJ81707.11
putative oxidoreductase [Acidiphilium
825 826 YP 004284589.1 multivorum AIU3011
hypothetical protein Acry_21 15 [Acidiphilium LigD cryptum JF-5] >gb|ABQ31314.1 | short-chain dehydrogenase/reductase SDR [Acidiphilium
827 828 YP 001235233.1 cryptum JF-51
hypothetical protein GP2143_09415 [marine LigD gamma proteobacterium HTCC2143]
>gb|EAW30413.1 | hypothetical protein
GP2143_09415 [marine gamma
829 830 ZP 01617820.1 proteobacterium HTCC21431
short-chain dehydrogenase/reductase LigD [Bradyrhizobiaceae bacterium SG-6C]
>gb|EGP07476.1 | short-chain
dehydrogenase/reductase
831 832 ZP 08629833.1 [Bradyrhizobiaceae bacterium SG-6C1 PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO:
NO: NO:
short-chain type dehydrogenase/reductase LigD [Mycobacterium marinum M]
>gb|ACC43159.1 | short-chain type
dehydrogenase/reductase [Mycobacterium
833 834 YP 001853014.1 marinum Ml
short-chain dehydrogenase/reductase SDR LigD [Collimonas fungivorans Ter331]
>gb|AEK63634.1 | short-chain
dehydrogenase/reductase SDR [Collimonas
835 836 YP 004754457.1 fungivorans Ter331l
short-chain dehydrogenase/reductase SDR LigD [gamma proteobacterium NOR5-3]
>gb|EED30944.1 | short-chain
dehydrogenase/reductase SDR [gamma
837 838 ZP 05129129.1 proteobacterium NOR5-31
short chain dehydrogenase [Mycobacterium LigD
839 840 ZP 05223648.1 intracellular ATCC 139501
short-chain dehydrogenase/reductase SDR LigD [Sphingobium chlorophenolicum L-1]
>gb|AEG50877.1 | short-chain
dehydrogenase/reductase SDR
841 842 YP 004555383.1 [Sphingobium chlorophenolicum L- 1
PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO:
NO: NO:
short chain dehydrogenase [Mycobacterium LigD bovis BCG str. Pasteur 1 173P2]
>ref|YP_002643932.1 | short-chain
dehydrogenase [Mycobacterium bovis BCG str. Tokyo 172] >ref|ZP_06432004.11 short- chain type dehydrogenase/reductase
[Mycobacterium tuberculosis T46]
>ref|ZP_06449040.1 | short-chain type
dehydrogenase/reductase [Mycobacterium tuberculosis T17] >ref|ZP_06453700.11 short chain type dehydrogenase/reductase
[Mycobacterium tuberculosis K85]
>ref|ZP_06508748.1 | short-chain type
dehydrogenase/reductase [Mycobacterium tuberculosis T92] >ref|ZP_06512283.1 | short chain dehydrogenase [Mycobacterium
tuberculosis EAS054] >ref|YP_004722558.11 short-chain type dehydrogenase/reductase
[Mycobacterium africanum GM041182]
>emb|CAL70889.1 | Putative short-chain type dehydrogenase/reductase [Mycobacterium bovis BCG str. Pasteur 1 173P2]
>dbj|BAH25164.1 | short-chain
dehydrogenase [Mycobacterium bovis BCG str. Tokyo 172] >gb|EFD12419.11 short- chain type dehydrogenase/reductase
[Mycobacterium tuberculosis T46]
>gb|EFD42482.1 | short-chain type
dehydrogenase/reductase [Mycobacterium
843 844 YP 976997.1 tuberculosis K851 >gb|EFD46215.1 | short-
Short-chain dehydrogenase/reductase SDR LigD [Congregibacter litoralis KT71]
>gb|EAQ98875.1 | Short-chain
dehydrogenase/reductase SDR
845 846 ZP 01101659.1 [Congregibacter litoralis KT711
short chain dehydrogenase [marine gamma LigD proteobacterium HTCC2143]
>gb|EAW32447.1 | short chain
dehydrogenase [marine gamma
847 848 ZP 01615364.1 proteobacterium HTCC21431 PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO:
NO: NO:
short-chain type dehydrogenase/reductase LigD [Mycobacterium tuberculosis CPHL_A]
>gb|EFD16575.1 | short-chain type
dehydrogenase/reductase [Mycobacterium
849 850 ZP 06436160.1 tuberculosis CPHL Al
short chain dehydrogenase [Mycobacterium LigD bovis AF2122/97] >emb|CAD93736.11
PUTATIVE SHORT-CHAIN TYPE
DEHYDROGENASE/REDUCTASE
851 852 NP 854532.1 [Mycobacterium bovis AF2122/971
putative short-chain type LigD dehydrogenase/reductase [Mycobacterium canettii CIPT 140010059]
>emb|CCC43191.1 | putative short-chain type dehydrogenase/reductase
853 854 YP 004744317.1 [Mycobacterium canettii CIPT 1400100591
short-chain dehydrogenase/reductase sdr LigD [Paenibacillus polymyxa SC2]
>gb|AD057345.1 | Short-chain
dehydrogenase/reductase SDR
855 856 YP 003947586.1 [Paenibacillus polymyxa SC21
short-chain dehydrogenase/reductase LigD [Stigmatella aurantiaca DW4/3-1]
>gb|AD069364.1 | Short-chain
dehydrogenase/reductase SDR [Stigmatella
857 858 YP 003951 191.1 aurantiaca DW4/3-11
hypothetical protein Rmet_1846 LigD [Cupriavidus metallidurans CH34]
>gb|ABF08725.1 | conserved hypothetical
859 860 YP 583994.1 protein [Cupriavidus metallidurans CH341
Figure imgf000126_0001
PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO:
NO: NO:
short-chain dehydrogenase/reductase family LigD oxidoreductase [Mycobacterium
parascrofulaceum ATCC BAA-614]
>gb|EFG75472.1 | short-chain
dehydrogenase/reductase family
oxidoreductase [Mycobacterium
865 866 ZP 06851131.1 parascrofulaceum ATCC BAA-6141
3-oxoacyl-[acyl-carrier-protein] reductase (3- LigD ketoacyl-acyl carrier protein reductase)
[Paenibacillus polymyxa E681]
>gb|ADM70831.11 3-oxoacyl-[acyl-carrier- protein] reductase (3-ketoacyl-acyl carrier protein reductase) [Paenibacillus polymyxa
867 868 YP 003871369.1 E6811
oxidoreductase, short chain LigD dehydrogenase/reductase family [marine gamma proteobacterium HTCC2148]
>gb|EEB78920.1 | oxidoreductase, short chain dehydrogenase/reductase family
[marine gamma proteobacterium
869 870 ZP 05094873.1 HTCC21481
probable oxidoreductase dehydrogenase LigD signal peptide protein [marine gamma
proteobacterium HTCC2207]
>gb|EAS47242.1 | probable oxidoreductase dehydrogenase signal peptide protein
[marine gamma proteobacterium
871 872 ZP 01224235.1 HTCC22071
short chain dehydrogenase [Myxococcus LigD xanthus DK 1622] >gb|ABF86178.11
oxidoreductase, short chain
dehydrogenase/reductase family
873 874 YP 634033.1 [Myxococcus xanthus DK 16221
short-chain dehydrogenase/reductase LigD
875 876 ABL97174.1 [uncultured marine bacterium EB0 49D071 PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO:
NO: NO:
short chain dehydrogenase [Mycobacterium LigD tuberculosis CDC1551]
>ref|ZP_07413312.2| short-chain type
dehydrogenase/reductase [Mycobacterium tuberculosis SUMu001]
>ref|ZP_07668817.1 | short-chain type
dehydrogenase/reductase [Mycobacterium tuberculosis SUMu010]
>ref|ZP_07669069.1 | short-chain type
dehydrogenase/reductase [Mycobacterium tuberculosis SUMu01 1] >gb|AAK45115.11
oxidoreductase, short-chain
dehydrogenase/reductase family
[Mycobacterium tuberculosis CDC1551]
>gb|EFO75870.1 | short-chain type
dehydrogenase/reductase [Mycobacterium tuberculosis SUMu001] >gb|EFP48221.1 | short-chain type dehydrogenase/reductase
[Mycobacterium tuberculosis SUMu010]
>gb|EFP52129.1 | short-chain type
dehydrogenase/reductase [Mycobacterium
877 878 NP 335301.1 tuberculosis SUMu01 11
short-chain dehydrogenase/reductase SDR LigD [marine gamma proteobacterium
HTCC2080] >gb|EAW39988.1 | short-chain dehydrogenase/reductase SDR [marine
879 880 ZP 01627272.1 gamma proteobacterium HTCC20801
short chain dehydrogenase [Brevibacillus LigD brevis NBRC 100599] >dbj|BAH46 43.11
probable short chain dehydrogenase
881 882 YP 002774647.1 [Brevibacillus brevis NBRC 1005991
short-chain dehydrogenase/reductase SDR LigD [Novosphingobium sp. PP1Y]
>emb|CCA92091.1 | short-chain
dehydrogenase/reductase SDR
883 884 YP 004533909.1 [Novosphingobium sp. PP1Y1 PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO:
NO: NO:
short chain dehydrogenase [Mycobacterium LigD
885 886 ZP 04751842.1 kansasii ATCC 124781
short-chain dehydrogenase/reductase SDR LigD [gamma proteobacterium IMCC3088]
>gb|EGG29327.1 | short-chain
dehydrogenase/reductase SDR [gamma
887 888 ZP 08271356.1 proteobacterium IMCC30881
short chain dehydrogenase [Myxococcus LigD fulvus HW-1] >gb|AEI65260.1 | short chain
889 890 YP 004666338.1 dehydrogenase [Myxococcus fulvus HW-11
putative short chain LigD dehydrogenase/reductase [Mycobacterium abscessus ATCC 19977]
>emb|CAM63993.1 | Putative short chain dehydrogenase/reductase [Mycobacterium
891 892 YP 001704647.1 abscessusl
cis-2,3-dihydrobiphenyl-2,3-diol LigD dehydrogenase [Streptomyces sp. AA4]
>gb|EFL12318.1 | cis-2,3-dihydrobiphenyl- 2,3-diol dehydrogenase [Streptomyces sp.
893 894 ZP 07283949.1 AA41
hypothetical protein RALTA_A1476 LigD [Cupriavidus taiwanensis LMG 19424]
>emb|CAQ69425.1 | putative
OXIDOREDUCTASE DEHYDROGENASE
895 896 YP 002005492.1 [Cupriavidus taiwanensis LMG 194241
SDR-family protein [Sphingobium japonicum LigD UT26S] >dbj|BAI95093.1 | SDR-family
897 898 YP 003543705.1 protein [Sphingobium japonicum UT26S1
short chain dehydrogenase/reductase family LigD oxidoreductase [Hyphomonas neptunium
ATCC 15444] >gb|ABI75402.11
oxidoreductase, short chain
dehydrogenase/reductase family
899 900 YP 759628.1 [Hyphomonas neptunium ATCC 154441 PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO:
NO: NO:
short-chain dehydrogenase/reductase SDR LigD [Comamonas testosteroni KF-1]
>gb|EED68191.1 | short-chain
dehydrogenase/reductase SDR
901 902 ZP 03543905.1 [Comamonas testosteroni KF-1]
hypothetical protein SCAB_14801 LigD [Streptomyces scabiei 87.22]
>emb|CBG68626.1 | putative PROBABLE
SHORT-CHAIN TYPE
DEHYDROGENASE/REDUCTASE
903 904 YP 003487191.1 [Streptomyces scabiei 87.221
3-oxoacyl-[acyl-carrier-protein] reductase LigD
905 906 AEG69105.1 [Ralstonia solanacearum Po821
short-chain dehydrogenase/reductase SDR LigD [Clostridium cellulovorans 743B]
>ref|ZP_07630916.1 | short-chain
dehydrogenase/reductase SDR [Clostridium cellulovorans 743B] >gb|ADL50229.11 short- chain dehydrogenase/reductase SDR
907 908 YP 003841993.1 [Clostridium cellulovorans 743B1
hypothetical protein Rpic_1437 [Ralstonia LigD pickettii 12J] >gb|ACD26578.1 | short-chain dehydrogenase/reductase SDR [Ralstonia
909 910 YP 001899010.1 pickettii 12J1
short chain dehydrogenase [Segniliparus LigD rugosus ATCC BAA-974] >gb|EFV13275.11 short chain dehydrogenase [Segniliparus
91 1 912 ZP 07965490.1 rugosus ATCC BAA-9741 PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO:
NO: NO:
short-chain dehydrogenase [Pseudomonas LigD aeruginosa PA01] >ref|ZP_01364886.1 | hypothetical protein PaerPA_01001998
[Pseudomonas aeruginosa PACS2]
>ref|YP_002441374.1 | putative short-chain dehydrogenase [Pseudomonas aeruginosa LESB58] >ref|ZP_04933207.1 | hypothetical protein PA2G_00514 [Pseudomonas
aeruginosa 2192]
>gb|AAG04926.1 |AE004582_4 probable short-chain dehydrogenase [Pseudomonas aeruginosa PA01] >gb|EAZ57326.1 |
hypothetical protein PA2G_00514
[Pseudomonas aeruginosa 2192]
>emb|CAW28518.1 | probable short-chain dehydrogenase [Pseudomonas aeruginosa LESB58] >gb|EGM 16253.11 putative short- chain dehydrogenase [Pseudomonas
913 914 NP 250228.1 aeruginosa 1382441
hypothetical protein Mpe_A1784 LigD [Methylibium petroleiphilum PM1]
>gb|ABM94743.1 | putative oxidoreductase dehydrogenase signal peptide protein
915 916 YP 001020978.1 [Methylibium petroleiphilum PM11
oxidoreductase dehydrogenase [Ralstonia LigD solanacearum CFBP2957]
>emb|CBJ43067.1 | putative oxidoreductase dehydrogenase [Ralstonia solanacearum
917 918 YP 003745682.1 CFBP29571
919 920 ADD82954.1 BatM [Pseudomonas fluorescens] LigD short-chain dehydrogenase/reductase family LigD oxidoreductase [Mycobacterium
parascrofulaceum ATCC BAA-614]
>gb|EFG80090.1 | short-chain
dehydrogenase/reductase family
oxidoreductase [Mycobacterium
921 922 ZP 06846575.1 parascrofulaceum ATCC BAA-6141 PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO:
NO: NO:
oxidoreductase, short chain LigD dehydrogenase/reductase family
[Alcanivorax sp. DG881] >gb|EDX89108.11 oxidoreductase, short chain
dehydrogenase/reductase family
923 924 ZP 05041687.1 [Alcanivorax sp. DG8811
hypothetical protein H16_A1536 [Ralstonia LigD eutropha H16] >emb|CAJ92668.11
conserved hypothetical protein [Ralstonia
925 926 YP 726036.1 eutropha H161
Hypothetical Protein IMCC9480_775 LigD [Oxalobacteraceae bacterium IMCC9480]
>gb|EGF30787.1 | Hypothetical Protein
IMCC9480_775 [Oxalobacteraceae
927 928 ZP 08275744.1 bacterium IMCC94801
putative short-chain dehydrogenase LigD [Pseudomonas aeruginosa UCBPP-PA14]
>ref|ZP_06879570.1 | putative short-chain dehydrogenase [Pseudomonas aeruginosa PAb1] >ref|ZP_07792770.1 | putative short- chain dehydrogenase [Pseudomonas
aeruginosa 39016] >gb|ABJ10717.1 |
putative short-chain dehydrogenase
[Pseudomonas aeruginosa UCBPP-PA14]
>gb|EFQ37866.1 | putative short-chain
dehydrogenase [Pseudomonas aeruginosa 39016] >gb|EGM15719.1 | putative short- chain dehydrogenase [Pseudomonas
929 930 YP 791716.1 aeruginosa 152504]
oxidoreductase dehydrogenase protein LigD
931 932 CAQ35702.1 [Ralstonia solanacearum MolK2]
short chain dehydrogenase [Segniliparus LigD rugosus ATCC BAA-974] >gb|EFV12481.11 short chain dehydrogenase [Segniliparus
933 934 ZP 07966320.1 rugosus ATCC BAA-9741 PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO:
NO: NO:
hypothetical protein Rpic12D_1478 LigD [Ralstonia pickettii 12D] >gb|ACS62765.1 | short-chain dehydrogenase/reductase SDR
935 936 YP 002981437.1 [Ralstonia pickettii 12D1
C alpha-dehydrogenase LigD [Cupriavidus LigD necator N-1] >gb|AEI76910.11 C alpha- dehydrogenase LigD [Cupriavidus necator N-
937 938 YP 004685391.1 11
Hypothetical Protein RRSL_01608 LigD [Ralstonia solanacearum UW551]
>ref| YP_002259522.11 oxidoreductase
dehydrogenase protein [Ralstonia
solanacearum IPO1609] >gb|EAP71895.1 | Hypothetical Protein RRSL_01608
[Ralstonia solanacearum UW551]
>emb|CAQ61454.1 | oxidoreductase
dehydrogenase protein [Ralstonia
939 940 ZP 00945631.1 solanacearum IPO16091
hypothetical protein RSc1769 [Ralstonia LigD solanacearum GMI1000]
>emb|CAD15471.11 probable
oxidoreductase dehydrogenase signal
peptide protein [Ralstonia solanacearum
941 942 NP 519890.1 GMI10001
oxidoreductase dehydrogenase signal LigD peptide protein [Ralstonia sp. 5_7_47FAA] >gb|EFP64736.1 | oxidoreductase
dehydrogenase signal peptide protein
943 944 ZP 07676733.1 [Ralstonia sp. 5 7 47FAA1
oxidoreductase dehydrogenase [Ralstonia LigD solanacearum PSI07] >emb|CBJ51 176.1 | putative oxidoreductase dehydrogenase
945 946 YP 003752456.1 [Ralstonia solanacearum PSI071 PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO:
NO: NO:
hypothetical protein PP1Y_AT3242 LigD [Novosphingobium sp. PP1Y]
>emb|CCA91281.1 | conserved hypothetical
947 948 YP 004533099.1 protein [Novosphingobium sp. PP1Y1
hypothetical protein Daci_3363 [Delftia LigD acidovorans SPH-1] >gb|ABX36001.1 | short- chain dehydrogenase/reductase SDR
949 950 YP 001564386.1 [Delftia acidovorans SPH-1]
short-chain dehydrogenase/reductase SDR LigD [Delftia sp. Cs1-4] >gb|AEF90398.1 | short- chain dehydrogenase/reductase SDR
951 952 YP 004488753.1 [Delftia sp. Cs1-41
short-chain dehydrogenase/reductase SDR LigD [Pseudomonas mendocina ymp]
>gb|ABP85377.1 | short-chain
dehydrogenase/reductase SDR
953 954 YP 001 188109.1 [Pseudomonas mendocina ymp]
short-chain dehydrogenase/reductase SDR LigD
955 956 ADP99633.1 [Marinobacter adhaerens HP15]
short-chain dehydrogenase/reductase family LigD protein [Alcanivorax borkumensis SK2]
>emb|CAL17366.11 short-chain
dehydrogenase/reductase family
957 958 YP 693638.1 [Alcanivorax borkumensis SK21
short-chain dehydrogenase/reductase SDR LigD [Cupriavidus metallidurans CH34]
>gb|ABF10471.11 short-chain
dehydrogenase/reductase SDR [Cupriavidus
959 960 YP 585740.1 metallidurans CH34]
short-chain dehydrogenase/reductase SDR LigD [Comamonas testosteroni CNB-2]
>gb|ACY32473.1 | short-chain
dehydrogenase/reductase SDR
961 962 YP 003277769.1 [Comamonas testosteroni CNB-21 PROTEIN GENE GENBANK DESCRIPTION: TYPE SEQ ID SEQ ID ACCESSION NO:
NO: NO:
hypothetical protein HGFM 131 1 LigD [Hylemonella gracilis ATCC 19624]
>gb|EGI76405.1 | hypothetical protein
HGR_1 131 1 [Hylemonella gracilis ATCC
963 964 ZP 08406457.1 196241
short-chain dehydrogenase/reductase SDR LigD [Clostridium cellulovorans 743B]
>ref|ZP_07632312.1 | short-chain
dehydrogenase/reductase SDR [Clostridium cellulovorans 743B] >gb|ADL50757.11 short- chain dehydrogenase/reductase SDR
965 966 YP 003842521.1 [Clostridium cellulovorans 743B]
short-chain dehydrogenase/reductase SDR LigD [Comamonas testosteroni S44]
>gb|EFI62855.1 | short-chain
dehydrogenase/reductase SDR
967 968 ZP 07043693.1 [Comamonas testosteroni S44l
hypothetical protein Reut_A1415 [Ralstonia LigD eutropha JMP134] >gb|AAZ60785.1 | Short- chain dehydrogenase/reductase SDR
969 970 YP 295629.1 [Ralstonia eutropha JMP1341
putative oxidoreductase dehydrogenase LigD
971 972 CBJ37979.1 [Ralstonia solanacearum CMR15]
short-chain dehydrogenase/reductase sdr LigD [Variovorax paradoxus EPS]
>gb|ADU37360.1 | short-chain
dehydrogenase/reductase SDR [Variovorax
973 974 YP 004155471.1 paradoxus EPSl
hypothetical protein mma_1991 LigD [Janthinobacterium sp. Marseille]
>gb|ABR91341.1 | short-chain
dehydrogenase/reductase SDR
975 976 YP 001353681.1 [Janthinobacterium sp. Marseille] 59] Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, that there are many equivalents to the specific embodiments described herein that have been described and enabled to the extent that one of skill in the art can practice the invention well-beyond the scope of the specific embodiments taught herein. Such equivalents are intended to be encompassed by the following claims. In addition, there are numerous lists and Markush groups taught and claimed herein. One of skill will appreciate that each such list and group contains various species and can be modified by the removal, or addition, of one or more of species, since every list and group taught and claimed herein may not be applicable to every embodiment feasible in the practice of the invention. As such, components in such lists can be removed and are expected to be removed to reflect some embodiments taught herein. All publications, patents, patent applications, other references, accession numbers, ATCC numbers, etc., mentioned in this application are herein incorporated by reference into the specification to the same extent as if each was specifically indicated to be herein incorporated by reference in its entirety.

Claims

WE CLAIM
1 . An isolated recombinant polypeptide, comprising:
an amino acid sequence having at least 95% identity to SEQ ID NO:101 , the amino acid sequence conserving residues 1 , 2, 4-8, 10-12, 14, 17, 19-22, 24, 25, 27-37, 39, 41 -54, 57, 58, 60, 62-67, 69-73, 75, 77-80, 82-87, 89, 100, 102, 103, 104, 105, 107, 1 10-1 14, 1 17, 212, 122, 124-130, 133, 134, 137-139, 148, 149, 151 -156, 159, 160, 166-168, 170, 173, 174, 178-181 , 184, 185, 187-189, 198-201 , 204, 205, 207, 210-216, 219, 222, 223, 226-232, 235-239, 242-246, 249, 251 , 254, 257, 264, 266, 267, 270, 275, and 278 of SEQ ID NO:101 ;
wherein, an amino acid substitution outside of the conserved residues is a conservative substitution; and,
the amino acid sequence functions to cleave a beta-aryl ether.
2. An isolated recombinant polypeptide, comprising:
an amino acid sequence having at least 95% identity to SEQ ID NO:101 , the amino acid sequence conserving residues 19-22, 24, 25, 27-30, 33-36, 39-45, 47, 48, 50-54; 100, 101 , 104, 1 1 1 , 1 12, 1 15, 1 16, 166, 107, 184, 187, 188, 191 , 192, and 195 of SEQ ID:101 ;
wherein an amino acid substitution outside of the conserved residues is a conservative substitution.
3. The isolated recombinant polypeptide of claim 2, wherein the amino acid sequence functions to cleave a beta-aryl ether.
4. An isolated recombinant polypeptide, comprising:
SEQ ID NO:101 ; or conservative substitutions thereof outside of conserved residues 19- 22, 24, 25, 27-30, 33-36, 39-45, 47, 48, 50-54; 100, 101 , 104, 1 1 1 , 1 12, 1 15, 1 16, 166, 107, 184, 187, 188, 191 , 192, and 195 of SEQ ID:101 .
5. A isolated recombinant glutathione S-transferase enzyme, comprising:
an amino acid sequence having at least 95% identity to SEQ ID NO:101 , the amino acid sequence conserving residues 19-22, 24, 25, 27-30, 33-36, 39-45, 47, 48, 50-54; 100, 101 , 104, 1 1 1 , 1 12, 1 15, 1 16, 166, 107, 184, 187, 188, 191 , 192, and 195 of SEQ ID:101 ;
wherein, the amino acid sequence functions to cleave a beta-aryl ether.
6. A isolated recombinant glutathione S-transferase enzyme, comprising:
an amino acid sequence having at least 95% identity to SEQ ID NO:101 ; wherein, the amino acid sequence functions to cleave a beta-aryl ether.
7. An isolated recombinant polypeptide, comprising:
a length ranging from about 279 to about 281 amino acids;
a first amino acid region consisting of residues 19-54 from SEQ ID NO:101 , or
conservative substitutions thereof outside of conserved residues 19-22, 24, 25, 27-30, 33-36, 39-45, 47, 48, and 50-54 of SEQ ID NO:101 ; and, a second amino acid region consisting of residues 98-221 from SEQ ID NO:101 , or conservative substitutions thereof outside of conserved residues 100, 101 , 104, 1 1 1 , 1 12, 1 15, 1 16, 166, 107, 184, 187, 188, 191 , 192, and 195 of SEQ ID:101 .
8. An isolated recombinant glutathione S-transferase enzyme, comprising:
a length ranging from about 279 to about 281 amino acids;
a first amino acid region having at least 95% identity to residues 19-54 from SEQ ID NO:101 while conserving residues 19-22, 24, 25, 27-30, 33-36, 39-45, 47, 48, and 50-54 of SEQ ID NO:101 ; wherein, the first amino acid region is located in the recombinant polypeptide from about residue 14 to about residue 59; and, a second amino acid region having at least 95% identity to residues 98-221 from SEQ ID NO:101 while conserving residues 100, 101 , 104, 1 1 1 , 1 12, 1 15, 1 16, 166, 107, 184, 187, 188, 191 , 192, and 195 of SEQ ID:101 ; wherein, the second amino acid region is located in the recombinant polypeptide from about residue 93 to about residue 226; and,
wherein, the recombinant glutathione S-transferase enzyme functions to cleave a beta- aryl ether.
9. The isolated recombinant polypeptide of claim 8, wherein an amino acid substitution outside of the conserved residues is a conservative substitution.
10. A method of cleaving a beta-aryl ether bond, comprising:
contacting a polypeptide comprising an amino acid sequence having at least 95%
identity to SEQ ID NO:101 , the amino acid sequence conserving residues 19-22, 24, 25, 27-30, 33-36, 39-45, 47, 48, 50-54; 100, 101 , 104, 1 1 1 , 1 12, 1 15, 1 16, 166, 107, 184, 187, 188, 191 , 192, and 195 of SEQ ID:101 , with a lignin-derived compound having (i) a beta-aryl ether bond and (ii) a molecular weight ranging from about 180 Daltons to about 3000 Daltons;
wherein, the contacting occurs in a solvent environment in which the lignin-derived
compound is soluble.
1 1 . The method of claim 10, wherein the lignin-derived compound has a molecular weight of about 180 Daltons to about 1000 Daltons.
12. The method of claim 10, wherein an amino acid substitution outside of the conserved residues is a conservative substitution.
13. The method of claim 10, wherein the solvent environment comprises water.
14. The method of claim 10, wherein the solvent environment comprises a polar organic solvent.
15. A method of cleaving a beta-aryl ether bond, comprising: contacting a polypeptide comprising an amino acid sequence having at least 95%
identity to SEQ ID NO:101 , the amino acid sequence conserving residues 19-22, 24, 25, 27-30, 33-36, 39-45, 47, 48, 50-54; 100, 101 , 104, 1 1 1 , 1 12, 1 15, 1 16, 166, 107, 184, 187, 188, 191 , 192, and 195 of SEQ ID:101 , with a lignin-derived compound having (i) a beta-aryl ether bond and (ii) a molecular weight ranging from about 180 Daltons to about 3000 Daltons;
wherein, the contacting occurs in a solvent environment in which the lignin-derived
compound is soluble.
16. The method of claim 15, wherein the lignin-derived compound has a molecular weight of about 180 Daltons to about 1000 Daltons.
17. The method of claim 15, wherein the solvent environment comprises water.
18. The method of claim 15, wherein the solvent environment comprises a polar organic solvent.
19. A system for bioprocessing lignin-derived compounds, comprising:
a polypeptide comprising an amino acid sequence having at least 95% identity to SEQ ID NO:101 , the amino acid sequence conserving residues 19-22, 24, 25, 27-30, 33-36, 39-45, 47, 48, 50-54; 100, 101 , 104, 1 1 1 , 1 12, 1 15, 1 16, 166, 107, 184, 187, 188, 191 , 192, and 195 of SEQ ID:101 ;
a lignin-derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; and,
a solvent in which the lignin-derived compound is soluble;
wherein, the system functions to cleave the beta-aryl ether bond by contacting the
polypeptide with the lignin-derived compound in the solvent.
20. The system of claim 19, wherein an amino acid substitution outside of the conserved residues is a conservative substitution.
21 . A recombinant polynucleotide comprising a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence having at least 95% identity to SEQ ID
NO:101 , the amino acid sequence conserving residues 19-22, 24, 25, 27-30, 33-36, 39-45, 47, 48, 50-54; 100, 101 , 104, 1 1 1 , 1 12, 1 15, 1 16, 166, 107, 184, 187, 188, 191 , 192, and 195 of SEQ ID:101 .
22. A recombinant polynucleotide comprising a nucleotide sequence that encodes a polypeptide comprising SEQ ID NO:101 ; or conservative substitutions thereof outside of conserved residues 19-22, 24, 25, 27-30, 33-36, 39-45, 47, 48, 50-54; 100, 101 , 104, 1 1 1 , 1 12, 1 15, 1 16, 166, 107, 184, 187, 188, 191 , 192, and 195 of SEQ ID:101 .
23. A vector comprising the polynucleotide of claim 21 .
24. A vector comprising the polynucleotide of claim 22.
25. A plasmid comprising the polynucleotide of claim 21 .
26. A plasmid comprising the polynucleotide of claim 22.
27. A host cell transformed by the vector of claim 23.
28. A host cell transformed by the vector of claim 24.
29. A method of cleaving a beta-aryl ether bond, comprising
culturing the host cell of claim 27 under conditions suitable to produce the polypeptide; recovering the polypeptide from the host cell culture; and,
contacting the polypeptide with a lignin-derived compound having (i) a beta-aryl ether bond and (ii) a molecular weight ranging from about 180 Daltons to about 3000 Daltons;
wherein, the contacting occurs in a solvent environment in which the lignin-derived
compound is soluble.
30. The method of claim 29, wherein the host cell is E. Coli.
31 . The method of claim 29, wherein the host cell is Azotobacter vinelandii.
32. The method of claim 29, wherein the lignin-derived compound has a molecular weight of about 180 Daltons to about 1000 Daltons.
33. The method of claim 29, wherein an amino acid substitution outside of the conserved residues is a conservative substitution.
34. The method of claim 29, wherein the solvent environment comprises water.
35. The method of claim 29, wherein the solvent environment comprises a polar organic solvent.
36. A method of cleaving a beta-aryl ether bond, comprising
culturing the host cell of claim 28 under conditions suitable to produce the polypeptide; recovering the polypeptide from the host cell culture; and,
contacting the polypeptide with a lignin-derived compound having (i) a beta-aryl ether bond and (ii) a molecular weight ranging from about 180 Daltons to about 3000 Daltons; wherein, the contacting occurs in a solvent environment in which the lignin-derived compound is soluble.
37. The method of claim 36, wherein the host cell is E. Coli.
38. The method of claim 36, wherein the host cell is Azotobacter vinelandii.
39. The method of claim 36, wherein the lignin-derived compound has a molecular weight of about 180 Daltons to about 1000 Daltons.
40. The method of claim 36, wherein the solvent environment comprises water.
41 . The method of claim 36, wherein the solvent environment comprises a polar organic solvent.
42. A system for bioprocessing lignin-derived compounds, comprising:
the transformed host cell of claim 27;
a lignin-derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; and,
a solvent in which the lignin-derived compound is soluble;
wherein, the system functions to cleave the beta-aryl ether bond by contacting the
polypeptide with the lignin-derived compound in the solvent.
43. The system of claim 42, wherein the transformed host cell comprises Azotobacter vinelandii.
44. The system of claim 42, wherein the transformed host cell expresses the polypeptide in the solvent in which the lignin-derived compound is soluble.
45. A system for bioprocessing lignin-derived compounds, comprising:
a transformant including a host cell transformed with the vector of claim 23, the
transformant expressing the polypeptide;
a lignin-derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; and,
a solvent in which the lignin-derived compound is soluble; wherein, the system functions to cleave the beta-aryl ether bond by contacting the polypeptide with the lignin-derived compound in the solvent.
46. The system of claim 45, wherein the transformant comprises E. Coli.
47. The system of claim 45, wherein the transformant comprises Azotobacter vinelandii.
48. The system of claim 45, wherein an amino acid substitution outside of the conserved residues is a conservative substitution.
49. The system of claim 45, wherein the transformed host cell expresses the polypeptide in the solvent in which the lignin-derived compound is soluble.
50. The system of claim 45, wherein the lignin-derived compound has a molecular weight ranging from about 180 Daltons to about 1000 Daltons.
51 . The system of claim 45, wherein the solvent environment comprises water.
52. The system of claim 45, wherein the solvent environment comprises a polar organic solvent.
53. A system for bioprocessing lignin-derived compounds, comprising:
a transformant including a host cell transformed with the vector of claim 24, the
transformant expressing the polypeptide;
a lignin-derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; and,
a solvent in which the lignin-derived compound is soluble;
wherein, the system functions to cleave the beta-aryl ether bond by contacting the
polypeptide with the lignin-derived compound in the solvent.
54. The system of claim 53, wherein the transformant comprises E. Coli.
55. The system of claim 53, wherein the transformant comprises Azotobacter vinelandii.
56. The system of claim 53, wherein the transformed host cell expresses the polypeptide in the solvent in which the lignin-derived compound is soluble.
57. The system of claim 53, wherein the lignin-derived compound has a molecular weight ranging from about 180 Daltons to about 1000 Daltons.
58. The system of claim 53, wherein the solvent environment comprises water.
59. The system of claim 53, wherein the solvent environment comprises a polar organic solvent.
60. A system for bioprocessing lignin-derived compounds, comprising:
a transformant including an Azotobacter vinelandii host cell transformed with the vector of claim 23, the transformant expressing the polypeptide;
a lignin-derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; and,
a solvent in which the lignin-derived compound is soluble;
wherein, the system functions to cleave the beta-aryl ether bond by contacting the
polypeptide with the lignin-derived compound in the solvent.
61 . The system of claim 60, wherein the transformed host cell expresses the polypeptide in the solvent in which the lignin-derived compound is soluble.
62. The system of claim 60, wherein the lignin-derived compound has a molecular weight ranging from about 180 Daltons to about 1000 Daltons.
63. The system of claim 60, wherein the solvent environment comprises water.
64. The system of claim 60, wherein the solvent environment comprises a polar organic solvent.
65. An isolated recombinant polypeptide, comprising:
an amino acid sequence having at least 95% identity to SEQ ID NO:541 , the amino acid sequence conserving residues 47-57, 63-76, 100, 101 , 104, 107, 1 1 1 , 1 12, 1 15, 1 16, 176, 194, 197, 198, 201 , 202, and 206.
66. The isolated recombinant polypeptide of claim 65, wherein an amino acid substitution outside of the conserved residues is a conservative substitution.
67. The isolated recombinant polypeptide of claim 65, wherein, the amino acid sequence functions to cleave a beta-aryl ether.
68. A isolated recombinant polypeptide, comprising:
SEQ ID NO:541 ; or conservative substitutions thereof outside of conserved residues 47- 57, 63-76, 100, 101 , 104, 107, 1 1 1 , 1 12, 1 15, 1 16, 176, 194, 197, 198, 201 , 202, and 206.
69. A isolated recombinant glutathione S-transferase enzyme, comprising:
an amino acid sequence having at least 95% identity to SEQ ID NO:541 , the amino acid sequence conserving residues conserved residues 47-57, 63-76, 100, 101 , 104, 107, 1 1 1 , 1 12, 1 15, 1 16, 176, 194, 197, 198, 201 , 202, and 206; wherein, the amino acid sequence functions to cleave a beta-aryl ether.
70. A isolated recombinant glutathione S-transferase enzyme, comprising:
an amino acid sequence having at least 95% identity to SEQ ID NO:541 ; wherein, the amino acid sequence functions to cleave a beta-aryl ether.
71 . An isolated recombinant polypeptide, comprising:
a length ranging from about 256 to about 260 amino acids;
a first amino acid region consisting of residues 47-57 from SEQ ID NO:541 , or
conservative substitutions thereof outside of conserved residues 47, 48, 49, 50, 52, 54, 55, 56, 57;
a second amino acid region consisting of 63-76 from SEQ ID NO:541 ; and,
a third amino acid region consisting of residues 99-230 from SEQ ID NO:541 , or
conservative substitutions thereof outside of conserved residues 100, 101 , 104, 107, 1 1 1 , 1 12, 1 15, 1 16, 176, 194, 197, 198, 201 , 202, and 206.
72. An isolated recombinant glutathione S-transferase enzyme, comprising:
a length ranging from about 279 to about 281 amino acids;
a first amino acid region having at least 95% identity to 47-57 from SEQ ID NO:541 , or conservative substitutions thereof outside of conserved residues 47, 48, 49, 50, 52, 54, 55, 56, 57; a second amino acid region consisting of 63-76 from SEQ ID NO:541 ; and, a third amino acid region having at least 95% identity to residues 99-230 from SEQ ID
NO:541 , or conservative substitutions thereof outside of conserved residues 100, 101 , 104, 107, 1 1 1 , 1 12, 1 15, 1 16, 176, 194, 197, 198, 201 , 202, and 206;
wherein, the recombinant glutathione S-transferase enzyme functions to cleave a beta- aryl ether.
73. The isolated recombinant polypeptide of claim 72, wherein an amino acid substitution outside of the conserved residues is a conservative substitution.
74. A method of cleaving a beta-aryl ether bond, comprising:
contacting an amino acid sequence having at least 95% identity to SEQ ID NO:541 , the amino acid sequence conserving residues 47-57, 63-76, 100, 101 , 104, 107, 1 1 1 , 1 12, 1 15, 1 16, 176, 194, 197, 198, 201 , 202, and 206 with a lignin-derived compound having (i) a beta-aryl ether bond and (ii) a molecular weight ranging from about 180 Daltons to about 3000 Daltons;
wherein, the contacting occurs in a solvent environment in which the lignin-derived
compound is soluble.
75. The method of claim 74, wherein the lignin-derived compound has a molecular weight of about 180 Daltons to about 1000 Daltons.
76. The method of claim 74, wherein an amino acid substitution outside of the conserved residues is a conservative substitution.
77. The method of claim 74, wherein the solvent environment comprises water.
78. The method of claim 74, wherein the solvent environment comprises a polar organic solvent.
79. A method of cleaving a beta-aryl ether bond, comprising:
contacting a polypeptide comprising SEQ ID NO:541 ; or conservative substitutions
thereof outside of conserved residues 47-57, 63-76, 100, 101 , 104, 107, 1 1 1 , 1 12, 1 15, 1 16, 176, 194, 197, 198, 201 , 202, and 206 with a lignin-derived compound having (i) a beta-aryl ether bond and (ii) a molecular weight ranging from about 180 Daltons to about 3000 Daltons;
wherein, the contacting occurs in a solvent environment in which the lignin-derived
compound is soluble.
80. The method of claim 79, wherein the lignin-derived compound has a molecular weight of about 180 Daltons to about 1000 Daltons.
81 . The method of claim 79, wherein the solvent environment comprises water.
82. The method of claim 79, wherein the solvent environment comprises a polar organic solvent.
83. A system for bioprocessing lignin-derived compounds, comprising:
a polypeptide having at least 95% identity to SEQ ID NO:541 , the amino acid sequence conserving residues 47-57, 63-76, 100, 101 , 104, 107, 1 1 1 , 1 12, 1 15, 1 16, 176, 194, 197, 198, 201 , 202, and 206;
a lignin-derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; and,
a solvent in which the lignin-derived compound is soluble;
wherein, the system functions to cleave the beta-aryl ether bond by contacting the
polypeptide with the lignin-derived compound in the solvent.
84. The system of claim 83, wherein an amino acid substitution outside of the conserved residues is a conservative substitution.
85. A recombinant polynucleotide comprising a nucleotide sequence that encodes the polypeptide of claim 65.
86. A recombinant polynucleotide comprising a nucleotide sequence that encodes the polypeptide of claim 68.
87. A vector comprising the polynucleotide of claim 65.
88. A vector comprising the polynucleotide of claim 68.
89. A plasmid comprising the polynucleotide of claim 65.
90. A plasmid comprising the polynucleotide of claim 68.
91 . A host cell transformed by the vector of claim 87.
92. A host cell transformed by the vector of claim 88.
93. A method of cleaving a beta-aryl ether bond, comprising
culturing the host cell of claim 91 under conditions suitable to produce the polypeptide; recovering the polypeptide from the host cell culture; and,
contacting the polypeptide with a lignin-derived compound having (i) a beta-aryl ether bond and (ii) a molecular weight ranging from about 180 Daltons to about 3000 Daltons;
wherein, the contacting occurs in a solvent environment in which the lignin-derived
compound is soluble.
94. The method of claim 93, wherein the host cell is E. Coli.
95. The method of claim 93, wherein the host cell is Azotobacter vinelandii.
96. The method of claim 93, wherein the lignin-derived compound has a molecular weight of about 180 Daltons to about 1000 Daltons.
97. The method of claim 93, wherein an amino acid substitution outside of the conserved residues is a conservative substitution.
98. The method of claim 93, wherein the solvent environment comprises water.
99. The method of claim 93, wherein the solvent environment comprises a polar organic solvent.
100. A method of cleaving a beta-aryl ether bond, comprising
culturing the host cell of claim 92 under conditions suitable to produce the polypeptide; recovering the polypeptide from the host cell culture; and, contacting the polypeptide with a lignin-derived compound having (i) a beta-aryl ether bond and (ii) a molecular weight ranging from about 180 Daltons to about 3000 Daltons;
wherein, the contacting occurs in a solvent environment in which the lignin-derived
compound is soluble.
101 . The method of claim 100, wherein the host cell is E. Coli.
102. The method of claim 100, wherein the host cell is Azotobacter vinelandii.
103. The method of claim 100, wherein the lignin-derived compound has a molecular weight of about 180 Daltons to about 1000 Daltons.
104. The method of claim 100, wherein the solvent environment comprises water.
105. The method of claim 100, wherein the solvent environment comprises a polar organic solvent.
106. A system for bioprocessing lignin-derived compounds, comprising:
the transformed host cell of claim 91 ;
a lignin-derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; and,
a solvent in which the lignin-derived compound is soluble;
wherein, the system functions to cleave the beta-aryl ether bond by contacting the
polypeptide with the lignin-derived compound in the solvent.
107. The system of claim 106, wherein the transformed host cell comprises Azotobacter vinelandii.
108. The system of claim 106, wherein the transformed host cell expresses the polypeptide of claim 65 in the solvent in which the lignin-derived compound is soluble.
109. A system for bioprocessing lignin-derived compounds, comprising:
a transformant including a host cell transformed with the vector of claim 87, the
transformant expressing the polypeptide; a lignin-derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; and,
a solvent in which the lignin-derived compound is soluble;
wherein, the system functions to cleave the beta-aryl ether bond by contacting the
polypeptide of with the lignin-derived compound in the solvent.
1 10. The system of claim 109, wherein the transformant comprises E. Coli.
1 1 1 . The system of claim 109, wherein the transformant comprises Azotobacter vinelandii.
1 12. The system of claim 109, wherein an amino acid substitution outside of the conserved residues is a conservative substitution.
1 13. The system of claim 109, wherein the transformed host cell expresses the polypeptide in the solvent in which the lignin-derived compound is soluble.
1 14. The system of claim 109, wherein the lignin-derived compound has a molecular weight ranging from about 180 Daltons to about 1000 Daltons.
1 15. The system of claim 109, wherein the solvent environment comprises water.
1 16. The system of claim 109, wherein the solvent environment comprises a polar organic solvent.
1 17. A system for bioprocessing lignin-derived compounds, comprising:
a transformant including a host cell transformed with the vector of claim 88, the
transformant expressing the polypeptide;
a lignin-derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; and,
a solvent in which the lignin-derived compound is soluble;
wherein, the system functions to cleave the beta-aryl ether bond by contacting the
polypeptide with the lignin-derived compound in the solvent.
1 18. The system of claim 1 17, wherein the transformant comprises E. Coli.
1 19. The system of claim 1 17, wherein the transformant comprises Azotobacter vinelandii.
120. The system of claim 1 17, wherein the transformed host cell expresses the polypeptide in the solvent in which the lignin-derived compound is soluble.
121 . The system of claim 1 17, wherein the lignin-derived compound has a molecular weight ranging from about 180 Daltons to about 1000 Daltons.
122. The system of claim 1 17, wherein the solvent environment comprises water.
123. The system of claim 1 17, wherein the solvent environment comprises a polar organic solvent.
124. A system for bioprocessing lignin-derived compounds, comprising:
a transformant including an Azotobacter vinelandii host cell transformed with the vector of claim 87, the transformant expressing the polypeptide;
a lignin-derived compound having a beta-aryl ether bond and a molecular weight ranging from about 180 Daltons to about 3000 Daltons; and,
a solvent in which the lignin-derived compound is soluble;
wherein, the system functions to cleave the beta-aryl ether bond by contacting the
polypeptide with the lignin-derived compound in the solvent.
125. The system of claim 124, wherein the transformed host cell expresses the polypeptide of claim 65 in the solvent in which the lignin-derived compound is soluble.
126. The system of claim 124, wherein the lignin-derived compound has a molecular weight ranging from about 180 Daltons to about 1000 Daltons.
127. The system of claim 124, wherein the solvent environment comprises water.
128. The system of claim 124, wherein the solvent environment comprises a polar organic solvent.
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