The present application includes as part of its description a sequence listing that includes 11 1 sequences and which was filed with this application in electronic form and this sequence listing is incorporated into the present application in its entirety.

TECHNICAL FIELD

[1] This disclosure relates to enzymatic synthesis of polymer precursors from carboxylic acids.

BACKGROUND OF THE ART

[2] Mono and dicarboxylic acids such as adipic, fumaric, glucaric, and succinic acids, diamines (cadaverine, putrescine, hexamethylenediamine), and diols (propanediols and butanediols) are the most common polymer precursors used in condensation polymerization reactions in the chemical industry. Polymeric materials find diverse application in a variety of industries, but most of them are still produced from petroleum.

[3] Adipic acid is the most important commercial aliphatic dicarboxylic acid used for the synthesis of Nylon-6,6 polyamide (~$ 6 billion global market). 2.6 Million metric tonnes per year of adipic acid is produced from petroleum-derived benzene but known chemical processes can produce toxic by-products such as nitrous oxide (N ₂ 0).

[4] Other important polymer precursors typically manufactured from petroleum include

1 ,4-butanediol, 1 ,6-hexanediol, 6-hydroxyhexanoic and 6-aminocaproic acids.

[5] There is a need for sustainable production of commodity chemicals from renewable biomass instead of petroleum due to growing concerns over climate change, energy security, and human health.

BRIEF SUMMARY

[6] In one aspect, there is provided a host microorganism in which exogenous nucleic acids are introduced, wherein said exogenous nucleic acids encode an enzyme having α,β- enoate reductase activity, wherein the enzyme comprises an amino acid sequence of SEQ ID NO: 1 or active fragment or homologue thereof. In one embodiment, the enzyme comprises amino acids (363) to (382) of SEQ ID NO: 1. In one embodiment, the enzyme comprises an amino acid sequence that is at least 80%, 85%, 90%, 95% or 100% identical to the amino acid sequence of SEQ ID NO: 1.

[7] In another aspect, there is provided a host microorganism in which exogenous nucleic acids are introduced, wherein said exogenous nucleic acids encode an enzyme having α,β-enoate reductase activity, wherein the enzyme comprises an amino acid sequence of SEQ ID NO: 2 or active fragment or homologue thereof.

[8] In one embodiment, the enzyme having α,β-enoate reductase activity is derived from a microorganism of the genus Bacillus, Clostridium, or Moorella. In one embodiment, the microorganism is Bacillus coagulans.

[9] In one embodiment, the host microorganism is Escherichia coli.

[10] Also provided is a process for producing adipic acid comprising culturing a host microorganism as described above under conditions and for a sufficient period of time to produce adipic acid.

[11] Also provided is a process for producing adipic acid comprising enzymatically converting a 6-carbon unsaturated dicarboxylic acid to adipic acid using a 2-enoate reductase. In one embodiment, the enzyme comprises the amino acid sequence of SEQ ID NO:1 or 2 or is a fragment or homologue of an enzyme comprising the amino acid sequence of SEQ ID NO: 1 or 2.

[12] In one embodiment, the unsaturated 6-carbon dicarboxylic acid is muconic acid or 2- hexenedioic acid. In one embodiment, the 6-carbon unsaturated dicarboxylic acid is produced from biosynthetic methods.

[13] In one embodiment, the process comprises culturing a host microorganism as described above under conditions and for a sufficient period of time to produce adipic acid.

[14] In one embodiment of the process, the culture medium is substantially aerobic.

[15] Also provided is a composition comprising a host microorganism as described above and muconic acid and/or 2-hexenedioic acid. [16] In another aspect, there is provided a host microorganism in which exogenous nucleic acids are introduced, wherein said exogenous nucleic acids encode an enzyme having carboxylate reductase activity, wherein the enzyme comprises an amino acid sequence of SEQ ID NO: 36 or active fragment or homologue thereof. In one embodiment, the enzyme comprises an amino acid sequence that is at least 80%, 85%, 90%, 95% or 100% identical to the amino acid sequence of SEQ ID NO:36. In one embodiment, the host microorganism is Escherichia coli.

[17] Also provided, is a host microorganism comprising exogenous nucleic acids encoding an enzyme having carboxylate reductase activity wherein the enzyme comprises an amino acid sequence of any one of SEQ ID NOs: 35, 36, 37, 38 or 70 or active fragment or homologue thereof. In one embodiment, the host microorganism further co-expresses a gene encoding a phosphopantetheinyl transferase.

[18] Also provided is a host microorganism comprising exogenous nucleic acids encoding an enzyme having aldehyde reductase activity, wherein the enzyme comprises an amino acid sequence of NOs:40-52, preferably an amino acid of one of SEQ ID NOs:47, 43, 50, 45, 46 or 52 or active fragment or homologue thereof.

[19] Also provided is a host microorganism comprising exogenous nucleic acids encoding an enzyme having aminotransferase activity, wherein the enzyme comprises an amino acid sequence of one of SEQ ID NOs:53-65, preferably one of SEQ ID NOs: 53, 59, 55, 58 or 60 or active fragment or homologue thereof.

[20] In another aspect, there is provided a process for producing a short chain aldehyde comprising enzymatically converting a carboxylic group of a C5-C8 saturated di- carboxylic acid to an aldehyde using a carboxylate reductase. In one embodiment, the carboxylate reductase comprises an amino acid sequence of any one of SEQ ID NOs: 35, 36, 37, 38 or 70 or active fragment or homologue thereof.

[21] The process may further include enzymatically converting the aldehyde group to a hydroxy group using an aldehyde reductase. In one embodiment, the aldehyde reductase comprises an amino acid sequence of one of SEQ ID NOs:40-52, preferably an amino acid of one of SEQ ID NOs:47, 43, 50, 45, 46 or 52 or active fragment or homologue thereof. [22] The process can further include enzymatically coverting a second carboxylic acid group to an aldehyde using a carboxylate reductase, and optionally enzymatically converting said aldehyde to a hydroxyl group using an aldehyde reductase.

[23] In another embodiment, the process further includes enzymatically converting the aldehyde to an amine using an aminotransferase. In one embodiment, the aminotransferase comprises an amino acid sequence of one of SEQ ID NOs:53-65, preferably one of SEQ ID NOs: 53, 59, 55, 58 or 60 or active fragment or homologue thereof. The process can further include enzymatically coverting a second carboxylic acid group to an aldehyde using a carboxylate reductase, and optionally enzymatically converting said aldehyde to an amine using an aminotransferase.

[24] In the processes described above, the di- carboxylic acid may be adipic acid.

[25] In one embodiment, the aldehyde is 6-oxohexanoic acid and the product of the enzymatic conversion is 6-hydroxyhexanoic acid.

[26] In one embodiment, the product is 1 ,6-hexanediol.

[27] In one embodiment, the product is 6-aminocaproic acid.

[28] In one embodiment, the product is hexamethylenediamine.

[29] In one embodiment, the di- carboxylic acid is adipic acid produced by a process described above.

[30] Also provided is a process for producing 6-hydroxyhexanoic acid comprising culturing a host microorganism as described above under conditions and for a sufficient period of time to produce 6-hydroxyhexanoic acid.

[31] Also provided is a process for producing 1 ,6-hexanediol comprising culturing a host microorganism as described above under conditions and for a sufficient period of time to produce 1 ,6-hexanediol. [32] Also provided is a process for producing 6-aminocaproic acid comprising culturing a host microorganism as described above under conditions and for a sufficient period of time to produce 6-aminocaproic acid.

[33] Also provided is a process for producing hexamethylenediamine comprising culturing a host microorganism as described above under conditions and for a sufficient period of time to produce hexamethylenediamine.

[34] Also provided is a process for producing 1 ,4-butanediol comprising culturing a host microorganism comprising exogenous nucleic acids encoding an enzyme having carboxylate reductase activity wherein the enzyme comprises an amino acid sequence of SEQ ID NO: 36 or active fragment or homologue thereof under conditions and for a sufficient period of time to produce 1 ,4-butanediol. In one embodiment, the enzyme comprises an amino acid sequence that is at least 80%, 85%, 90%, 95% or 100 % identical to the amino acid sequence of SEQ ID NO: 36.

BRIEF DESCRIPTION OF THE DRAWINGS

[35] Figure 1 shows chemocatalytic and biocatalytic hydrogenation of unsaturated six- carbon dicarboxylic acids into adipic acid using 2- enoate reductases (EREDs).

[36] Figure 2 shows enzymes and cascade enzymatic reactions for the bioconversion of carboxylic acids to 1 ,6-hexanediol, 6-hydroxyhexanoic and 6-aminocaproic acids.

[37] Figure 3 shows enzymes and cascade enzymatic reactions for the bioconversion of 4-hydroxybutyric acid to 1 ,4-butanediol and 4-aminobutanol.

[38] Figure 4 shows activity profiles of 25 Old Yellow Enzymes (OYEs; EC 1.6.99.1).

The cut-off value for enzyme activity of OYE is 0.05 U/mg protein. 1 mM of substrates, 0.25 mM of NADPH, and 2.5 μg of proteins were used in the reaction mixture (potassium phosphate 100 mM and pH 7.0). A mixture of cis- and trans- isomers of 2-hexenedioic acid was used as a substrate.

[39] Figure 5 shows SDS-PAGE analysis of the ERED expression in E. coli and protein purification, a) EREDCA, EREDCK, and EREDBC. b) EREDMT, EREDCL, and EREDCT. LC- MS analysis revealed that soluble proteins at 75 kDa in the E lane of EREDCT are hypothetical protein ECD_02181 (74.2 kDA, GenBank: ACT44004.1), heat shock protein 90 (71.4 kDa, ACT42323.1), and molecular chaperone DnaK (69.1 kDa, ACT41916.1) (data not shown). M: marker, E: purified ERED, S: supernatant (soluble fraction), P: pellet (insoluble fraction).

[40] Figure 6 shows time course of the anaerobic biotransformation of 2-hexenedioic acid into adipic acid by the E. coli cells expressing the recombinant EREDs. A mixture of cis- and trans- isomers of 2-hexenedioic acid was used as a substrate, and the results are means from at least two independent determinations. 20 mM 2-hexenedioic acid was used for the biotransformation.

[41] Figure 7 shows complete biotransformation of 2-hexenedioic acid into adipic acid by the E. coli cells expressing the recombinant a) EREDCL and b) EREDMT. 20 mM 2- hexenedioic acid was used for the biotransformation under anaerobic conditions.

[42] Figure 8 shows 24 h anaerobic biotransformation of c/ ^' s,c/ ^' s-muconic acid to adipic acid by the E. coli cells expressing the recombinant a) EREDBC, b) EREDCA, c) EREDMT, d) EREDCK and e) EREDCL. The saturated c/ ^' s,c/ ^' s-muconic acid solution (0.7 mM) was used for the biotransformation. Substrates and products were detected by LC-MS. 1 : c/ ^' s,c/ ^' s-muconic acid, 2: frans,frans-muconic acid, 3: 2-hexenedioic acid, 4: adipic acid, 5: 3-hexenedioic acidlike compound with m/z 143.0319.

[43] Figure 9 shows UV-visible absorption spectra of purified EREDBC and EREDCA. Purified protein was kept on ice in the presence of air (oxidation, Air lines) or 3mM NADH (reduction, NADH lines) under argon. Subsequent addition of 6 mM frans-cinnamic acid to the reduced protein resulted in partial re-oxidation (absorbance increase at 450 nm). The spectrophotometric cuvettes show brown-colored preparations of purified EREDBC and EREDCA used in these experiments.

[44] Figure 10 shows in vitro biochemical characterization of purified EREDBC. Reductase activity of EREDBC as a function of a) 2-hexenedioic acid, b) 2-cyclohexen-1-one, c) 3-methyl-2-hexenone, and d) frans-cinnamic acid concentration.

[45] Figure 11 shows in vitro biochemical characterization of purified EREDCA. Reductase activity of EREDCA as a function of a) frans-cinnamic acid concentration or b) 2- hexenedioic acid concentration in the presence of NADH. [46] Figure 12 shows in vitro biochemical characterization of purified EREDBC and EREDCA. Reductase activity as a function of 2-hexenedioic acid dissolved in a reaction mixture containing isopropanol in the presence of NADH.

[47] Figure 13 shows in vitro oxygen tolerance (residual activity) of purified a) EREDBC and b) EREDCA in the presence of 21 % of oxygen.

[48] Figure 14 shows multiple sequence alignment of EREDs studied. Multiple sequence alignment was performed and visualized by Cluster Omega and ESPript 3.0, respectively.

[49] Figure 15 shows whole-cell biotransformation of 2-hexenedioic acid (15 mM) into adipic acid by the E. coli cells expressing recombinant EREDBC (black) and EREDCA (white) under aerobic conditions. The cells were grown and the proteins were expressed anaerobically.

[50] Figure 16 shows substrate screening of purified carboxylate reductases (CARs): A - pimelic acid, suberic acid, azelaic acid (5mM each); B - crotonic acid, butyric acid, propionic acid (10mM each); C - benzoic acid (5mM) and cinnamic acid (10mM); D - adipic and 4- hydroxy butyric acid (5mM each). Reductase activity was measured spectrophotometrically by following the oxidation of NADPH depletion at 340 nm.

[51] Figure 17 shows saturation with NH ₄ CI for A - BSU31930 in presence of 1 mM NADH, 1 mM pyruvate. B- YOR375C in presence of 1 mM NADPH, 1 mM ketoglutarate.

[52] Figure 18 shows PP33160 double mutant (D222Q/H224N) saturation with NADPH and NADH cofactors in presence of 50mM formate.

[53] Figure 19 shows in vitro CARs coupled with aldehyde reductase (AR) PP_3370 conversion of 10mM adipic acid or 10mM 4-hydroxybutyric acid (12h). Reaction was supplied with ATP and NADPH -regenerating enzymes, supplied with 50mM formate and 5mM polyphosphate. A - graphical view of final product concentration. B - table of conversion efficiencies.

[54] Figure 20 shows in vivo conversion of 10 mM adipic acid or 10 mM 4- hydroxybutyric acid by E. coli expressing CARs. A - Time course of final 1 ,6-hexanediol and 6-hydroxyhexanoic acid formation. B - Time course of final 1 ,4-butanediol formation C - Table of conversion efficiencies. DETAILED DESCRIPTION

[55] As used herein "enzyme" includes proteins produced by a cell capable of catalyzing biochemical reactions. Further, unless context dictates otherwise, as used herein "enzyme" includes protein fragments that retain the relevant catalytic activity, and may include artificial enzymes synthesized to retain the relevant catalytic activity.

[56] In one aspect, the present disclosure provides novel enzymes for producing polymer precursors from renewable feedstocks and microorganisms for producing the same.

[57] In one aspect, the present disclosure provides novel enzymes capable of reducing C=C bonds of unsaturated dicarboxylic acids and microorganisms for producing the same.

[58] In one aspect, the present disclosure provides enzymes for converting hydroxycarboxylic acids, which may be produced from unsaturated dicarboxylic acids as described herein, to corresponding aldehydes, alcohols, and amines.

[59] In one aspect, the present disclosure provides processes for producing cells and organisms for the biochemical synthesis of adipic acid from unsaturated six-carbon dicarboxylic acids using biocatalysts having hydrogenation activity toward α,β-enoate. In one embodiment, adipic acid can be produced from muconic acid or 2-hexenedioc acid using 2-enoate reductases as illustrated in Figure 1.

[60] In one embodiment, the biochemical synthesis of adipic acid is performed in a substantially aerobic environment.

[61] In another aspect, the present disclosure provides processes for the enzymatic conversion of mono- and di- carboxylic acids to corresponding aldehydes, alcohols and amines.

[62] In one aspect, the present disclosure provides processes for the enzymatic conversion of short chain saturated mono- and di- carboxylic acids, in one embodiment C3 to C8 saturated mono- and di- carboxylic acids, to corresponding aldehydes, alcohols and amines. In one embodiment, the carboxylic acid is a C5 to C7 dicarboxylic acid. In one embodiment, the carboxylic acid is a C ₆ di- carboxylic acid, in one embodiment adipic acid. The product of the enzymatic conversion of adipic acid may be1-6-hexanediol, 6-hydroxyhexanoic and 6- aminocarpoic acids, as shown in Figure 2. [63] In another embodiment, there is described the enzymatic conversion of a mono- carboxylic acid, which may be substituted with a terminal hydroxy group, in one embodiment, the carboxylic acid is a C3 or C4 monoacid, in one embodiment 4-hydroxybutyric acid (4- hydroxybutanoic acid) as shown in Figure 3 to a corresponding aldehyde 4-hydroxybutanal, which may be enzymatically converted to 1 ,4-butanediol or 4-aminobutanol by aldehyde reductases and aminotransferases as described herein

[64] The enzymatic conversion of the carboxylic acids to corresponding aldehydes, alcohols and amines employ novel carboxylate reductases (CARs), aldehyde reductases (ARs) and/or aminotransferases (ATs). Also provided are processes for producing cells and organisms for the biochemical synthesis of these aldehydes, alcohols and amines.

[65] There have been tremendous efforts to develop sustainable production of commodity chemicals from renewable biomass instead of petroleum due to growing concerns over climate change, energy security, and human health.

[66] Production of polymer precursors using renewable feedstocks such as sugars, starch, lignin, cellulose and hemicellulose can help to overcome the depletion of fossil resources, without changing current technological processes of polymer synthesis. Recent development of engineered strains for dicarboxylic acids production using engineered shikimate [Curran K.A., Leavitt J.M., Karim A.S., Alper H.S. Metabolic engineering of muconic acid production in Saccharomyces cerevisiae. Metab. Eng. 15, 55-66 (2013)] or ketoadipate, reversed β-oxidation pathway [YuJ L, Xia X.X. , Zhong J.J., Qian Z.G. Direct biosynthesis of adipic acid from a synthetic pathway in recombinant Escherichia coli . Biotechnol Bioeng, 1 11 , 2580-2586 (2014)] enabled accumulating of fatty acids.

[67] Bio-based adipic acid has been produced from glucose via sequential chemical reactions i.e., oxidation of glucose into glucaric acid and hydrodeoxygenation of glucaric acid into adipic acid, which can be only catalyzed by chemical catalysts (US20100317823 A1). Bio- based production of adipic acid has been also attempted using metabolic engineering approaches. Industrial microorganisms such as E. coli or Saccharomyces cerevisiae with engineered aromatic amino acid biosynthesis pathway can produce c/ ^' s,c/ ^' s-muconic acid from glucose, which is then hydrogenated into adipic acid using chemical catalysts (see e.g. Niu, W., Draths, K.M. & Frost, J.W. Benzene-free synthesis of adipic acid. Biotechnology Progress 18, 201-21 1 (2002).) However, a biosynthetic pathway to produce adipic acid from 2-hexenedioic acid or muconic acid has not been experimentally demonstrated.

[68] The present disclosure provides for the biochemical synthesis of adipic acid from unsaturated six-carbon dicarboxylic acids using biocatalysts having hydrogenation activity toward α,β-enoate. In one embodiment, adipic acid is produced from muconic acid or 2- hexenedioc acid using 2-enoate reductases (ERED; EC 1.3.1.31). However, there are several known pathways to produce muconic acid and 2-hexenedioic acid starting from common renewable feedstocks, and in one embodiment, one or more of such pathways in suitably introduced into a host microorganism.

[69] The present disclosure also provides for the biochemical synthesis of aldehydes, alcohols and amines hydroxycarboxylic acids using biocatalysts using novel carboxylate reductases (EC 1.2.1.30), aldehyde reductases (EC 1.1.1.-), and/or aminotransferases (EC 2.6.1.48; EC 2.6.1.19). In one embodiment, 1-6-hexanediol is produced from 6-hydroxyhexanal using AR (EC 1.1.1.-). In one embodiment, 6-hydroxyhexanoic is produced from 6-oxohexanoic acid using AR (EC 1.1.1.-). In one embodiment, 6-aminocarpoic acid is produced from 6- oxohexanoic acid using AT (EC 2.6.1.48; EC 2.6.1.19).

[70] There have been efforts to produce 1 ,4-butanediol using the Carboxylic acid reductases as described in Burke et al. 2013 WO2013184602 A2, in which CARs from Nocardia iowensis, Mycobacterium smegmatis mc(2)155, Mycobacterium avium subspecies paratuberculosis K-10, Mycobacterium marinum M (designated 892) were identified.

[71] For the production of 1 ,4-butanediol, carboxylic reductases may be integrated into a 4-hydroxybutric acid producing host. 4 hydroxybuytric acid can be made either from 2- ketoglutarate through decarboxylation to succinate semialdehyde followed by reduction or from 4-aminobutyrate and 2-ketoglutarate via transamination resulting in 4-hydroxybutyrate and L- glutamate [Yim et al., Metabolic engineering of Escherichia coli for direct production of 1 ,4- butanediol. Nat Chem Biol. 2011 May 22;7(7):445-52.].

[72] The expression "derived from" in relation to an enzyme or (poly)peptide denotes that the enzyme or poly(peptide) was isolated from a (micro)organism or that it includes all or a biologically active part of the amino acid sequence of an enzyme or (poly)peptide isolated or characterized from such a (micro)organism. [73] In certain embodiments, EREDs as provided herein are derived from organisms of the genus Bacillus, Clostridium or Moorella. In one embodiment, the ERED is derived from the species Clostridium acetobutylicum. In one embodiment, the ERED is derived from the genus Bacillus. In one embodiment, the ERED is derived from the species Bacillus coagulans.

[74] In one embodiment, the ERED comprises or consists of the amino acid of SEQ ID NO: 1 or an active fragment or a homologue thereof.

[75] In another embodiment, the ERED comprises or consists of the amino acid of SEQ ID NO: 2 or an active fragment or a homologue thereof.

[76] In one aspect, the enzyme is at least 80%, 85%, 90%, 95% or 100% identical to the amino acid sequence of SEQ ID NO: 1 or SEQ ID NO: 2.

[77] In certain embodiments, CARs as provided herein are derived from organisms of the genus Mycobacterium. In one embodiment, the CAR is derived from the species Mycobacterium abscessus. In one embodiment, the CAR is derived from the species Mycobacterium paratuberculosis. In one embodiment, the CAR is derived from the species Mycobacterium smegmatis.

[78] In one embodiment, the CAR used comprises or consists of an amino acid of one of SEQ ID NOs: 35, 36, 37, 38 or 70 or an active fragment or a homologue thereof.

[79] In one aspect, the enzyme is at least 80%, 85%, 90%, 95% or 100% identical to the amino acid sequence of one of SEQ ID NOs: 35, 36, 37, 38 or 70.

[80] The present inventors surprisingly found that MAB_4714c from M. abscessus DSM444196 has high activity with respect to the conversion of both 4-hydroxybutyric acid and adipic acid to 4-hydroxybutanal and 6-oxohexanoic acid, respectively.

[81] In one embodiment, the CAR used comprises or consists of an amino acid of SEQ ID NO: 36 or an active fragment or a homologue thereof.

[82] In one embodiment, the enzyme is at least 80%, 85%, 90%, 95% or 100% identical to the amino acid sequence of SEQ ID NO: 36. [83] In one embodiment, an active fragment or homologue of a CAR as described herein includes the phosphopantetheine binding motif:

F-X(2)-L-G-G-D-S-X(2)-A wherein X(2) is any two amino acids.

[84] Previously it has been shown that post-translational phosphopantetheinylation of CARs is required for their activity [P. Venkitasubramanian et al. Reduction of Carboxylic Acids by Nocardia Aldehyde Oxidoreductase Requires a Phosphopantetheinylated Enzyme, January 5, 2007 The Journal of Biological Chemistry. 282, 478-485.]. Thus in one embodiment, CARs as described herein are co-expressed with a gene encoding a phosphopantetheinyl transferase. Suitable phosphopantetheinyl transferase genes will be known to those of skill in the art. Suitable phosphopantetheinyl transferase genes include e.g. BSU03570 and entD from Bacillus subtilis and E. coli K-12 genomic DNA.

[85] In certain embodiments, ARs as provided herein are derived from organisms of the genus Pseudomonas, Rhodococcus, Streptomyces or Thermotoga. In one embodiment, the AR is derived from the species Pseudomonas aeruginosa. In one embodiment, the AR is derived from the species Pseudomonas putida. In one embodiment, the AR is derived from the species Pseudomonas syringae. In one embodiment, the AR is derived from the species Rhodococcus jostii. In one embodiment, the AR is derived from the species Streptomyces coelicolor. In one embodiment, the AR is derived from the species Thermotoga maritima.

[86] In one embodiment, the AR comprises or consists of an amino acid of one of SEQ ID NOs: SEQ ID NOs:40-52 or an active fragment or a homologue thereof. In one aspect, the enzyme is at least 80%, 85%, 90%, 95% or 100% identical to the amino acid sequence of one of SEQ ID NOs: 40-52.

[87] In one embodiment, the AR comprises or consists of an amino acid of one of SEQ ID NOs: SEQ ID NOs:47, 43, 50, 45, 46 or 52 or an active fragment or a homologue thereof.

[88] In one aspect, the enzyme is at least 80%, 85%, 90%, 95% or 100% identical to the amino acid sequence of one of SEQ ID NOs: 47, 43, 50, 45, 46 or 52. [89] In one embodiment, an amino acid of SEQ ID NO: 43, 45, 47 or 50 is used for the enzymatic conversion of 6-oxohexanoic acid to 6-hydroxyhexanoic acid.

[90] In certain embodiments, ATs as provided herein are derived from organisms of the genus Escherichia, Sinorhizobium or Streptomyces In one embodiment, the AT is derived from the species Escherichia coli. In one embodiment, the AT is derived from the species Sinorhizobium meliloti. In one embodiment, the AT is derived from the species Streptomyces avermitilis. In one embodiment, the AT is derived from the species Sinorhizobium meliloti.

[91] In one embodiment, the AT comprises or consists of an amino acid of one of SEQ ID NOs: SEQ ID NOs:53-65 or an active fragment or a homologue thereof. In one aspect, the enzyme is at least 80%, 85%, 90%, 95% or 100% identical to the amino acid sequence of one of SEQ ID NOs: SEQ ID NOs:53-65

[92] In one embodiment, the AT comprises or consists of an amino acid of one of SEQ ID NOs: 53, 59, 55, 58 or 60 or an active fragment or a homologue thereof.

[93] In one aspect, the enzyme is at least 80%, 85%, 90%, 95% or 100% identical to the amino acid sequence of one of SEQ ID NOs: 53, 59, 55, 58 or 60.

[94] CARs adenylation domain uses 2 phosphates of ATP for substrate activation, forming acyl-AMP intermediate transferred to reducing domain, where one molecule of NADPH is oxidised for aldehyde release. Application of CARs together with ARs for full reduction of carboxylic group to alcohol needs 2 molecules of NADPH and 1 ATP. Full biotransformation of adipic acid to 1 ,6-hexanediol will cost in total 4 NADPH and 2 ATP molecules. In vitro application of cofactor dependent enzymes such as oxidoreductases or transferases needs enzymatic systems for regeneration of consumed cofactors to make the system cost-effective.

[95] In one embodiment, one or more of four enzymes commonly employed in the regeneration of ATP: pyruvate kinase (uses phosphoenolpyruvate), acetate kinase (uses acetylphosphate), creatine kinase (uses creatine phosphate), and polyphosphate kinase (uses polyphosphate) may be used. See Andexer and Richter, Emerging Enzymes for ATP Regeneration in Biocatalytic Process CHEMBIOCHEM 2015, 16, 380-386, for additional details. The majority of ATP-regenerating enzymes process only one step ADP phosphorylation. In one embodiment, polyphosphate kinases, in one embodiment, polyphosphate kinase family II; in one embodiment, for ATP regeneration SMc02148 from Sinorhizobium meliloti and PA3455 from Pseudomonas aeruginosa, may be used.

[96] CARs, ARs and amino-donor regenerating enzymes use pyridine nucleotides as cofactors. Several enzymatic methods have been developed for the regeneration of NAD(P)H, such as reduction with formate dehydrogenase, glucose dehydrogenase, glucose-6-phosphate dehydrogenase, and alcohol dehydrogenase. In one embodiment, the host microorganism can be engineered to increase co-factor pools of NADH and/or NADPH. In one embodiment, the microorganism can be engineered to express a formate dehydrogenase. In one embodiment, a formate dehydrogenase of SEQ ID NO: 108 or active fragment or homologue thereof.

[97] In one embodiment, if E. coli is to be used as the host organism, glucosephosphate isomerase (pgi) gene can be deleted to divert flux towards the pentose phosphate pathway to increase NADPH pools. Other strategies may involve switching the endogenous NADH- dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) to the host E. coli strain with an exogenous NADPH-dependent glyceraldehyde-3-phosphate dehydrogenase derived from Clostridium acetobutylicum. In another method, an NADH kinase (Pos5P) can be introduced from S. cerevisiae into the host E. coli strain. The latter was successfully used to increase several products that are produced through NADPH-dependent pathways [Lee, W.-H., Kim, M.- D., Jin, Y.-S., & Seo, J.-H. (2013). Engineering of NADPH regenerators in Escherichia coli for enhanced biotransformation. Applied Microbiology and Biotechnology. 97(7):2761-72]. As will be apparent to persons of skill in the art, if E. coli is chosen as the host organism, NADH pools can be increased by limiting competing pathways though the deletion of genes encoding NADH- dependent enzymes, including but not limited to: alcohol dehydrogenase (adhE), lactate dehydrogenase (IdhA) and pyruvate-formate lyase (pfIB).

[98] ATs disclosed herein consume alanine and/or glutamate as amino-group donors, which need to be regenerated. Accordingly, in one embodiment, a host microorganism can be engineered to increase the production of alanine and/or glutamate. In one embodiment, these host microorganism may be engineered to express a glutamate dehydrogenase or alanine dehydrogenase. Two enzymes were found suitable for this purposes - YOR375C, NADPH- dependent glutamate dehydrogenase from Saccharomyces cerevisiae, and BSU31930, NADH- dependent alanine dehydrogenase from Bacillus subtilis. [99] In various aspects, a homologue of each enzyme refers to a protein which has an identity of at least 25%, at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% with the amino acid sequence of SEQ ID NO corresponding to the enzyme and retains the activity of the enzyme. Algorithms for determining sequence identity are publicly available and include e.g. BLAST available through the National Center for Biotechnology Information (NCBI). One skilled in the art can determine if the sequences are similar to a degree that indicates homology and thus similar or identical function.

[100] A person skilled in the art can obtain a polynucleotide encoding a homologue of each enzyme by appropriately introducing substitution, deletion, insertion, and/or addition to the DNA of the enzyme which is composed of a nucleotide sequence disclosed herein, using methods such as site-specific mutagenesis (Nucleic Acid Res. 10, pp. 6487 (1982), Methods in Enzymol. 100, pp. 448 (1983), Molecular Cloning 2nd Edt., Cold Spring Harbor Laboratory Press (1989), PCR A Practical Approach IRL Press pp. 200 (1991)). The polynucleotide encoding a homologue of each enzyme can be introduced and expressed in a host to obtain the homologue.

[101] Enzymes as described herein may be produced by a non-naturally occurring microorganism.

[102] As used herein, the term "microorganism" is intended to mean any organism that exists as a microscopic cell and encompasses prokaryotic or eukaryotic cells or organisms having a microscopic size and includes bacteria, archaea and eubacteria of all species as well as eukaryotic microorganisms such as yeast and fungi. The term also includes cell cultures of any species that can be cultured for the production of a biochemical.

[103] As used herein, the term "non-naturally occurring" when used in reference to a microorganism refers to a microorganism that has at least one genetic alteration not normally found in a naturally occurring strain of the referenced species, including wild-type strains of the referenced species. Genetic alterations include, for example, modifications introducing expressible nucleic acids encoding metabolic polypeptides, other nucleic acid additions, nucleic acid deletions and/or other functional disruption of the microbial genetic material. Such modifications include, for example, coding regions and functional fragments thereof, for heterologous, homologous or both heterologous and homologous polypeptides for the referenced species. Additional modifications include, for example, non-coding regulatory regions in which the modifications alter expression of a gene or operon.

[104] The term "endogenous" refers to a referenced molecule or activity that originates in a host microorganism. Similarly, the term when used in reference to expression of an encoding nucleic acid refers to expression of an encoding nucleic acid contained within the microorganism.

[105] As used herein the term "exogenous" refers to molecules or activity that is introduced into a host microorganism. The molecule can be introduced, for example, by introduction of an encoding nucleic acid into the host genetic material such as by integration into a host chromosome or as non-chromosomal genetic material such as a plasmid. In reference to expression of an encoding nucleic acid the term refers to introduction of the encoding nucleic acid in an expressible form into the microorganism. When used in reference to a biosynthetic activity, the term refers to an activity that is introduced into a reference host organism. The source can be, for example, an encoding nucleic acid that expresses the activity following introduction into the host microorganism.

[106] The term "heterologous" refers to a molecule or activity derived from a source other than the referenced species whereas "homologous" refers to a molecule or activity derived from the host microbial organism. Accordingly, exogenous expression of an encoding nucleic acid can use either or both a heterologous or homologous encoding nucleic acid.

[107] As used herein, the term "isolated" when used in reference to a microorganism refers to an organism that is substantially free of at least one component as the referenced microorganism is found in nature. The term includes a microorganism that is removed from some or all components as it is found in its natural environment and includes substantially pure microbes and microbes cultured in a medium that is non-naturally occurring.

[108] As used herein, the term "operably linked" refers to a linkage between one or more expression control sequences and the coding region in a polynucleotide to be expressed in such a way that expression is achieved under conditions compatible with the expression control sequence. [109] In one embodiment, the microorganism used in a process as described herein is a microorganism which is genetically modified so as to contain a nucleic acid molecule encoding a 2-enoate reductase as described herein.

[1 10] Nucleic acid molecules encoding enzymes as described herein can be used alone or as part of a vector.

[1 1 1] In one embodiment, the enzyme comprises an amino acid sequence of SEQ I D NO: 1 or active fragment or homologue thereof. In one embodiment, the enzyme comprises an amino acid sequence that is at least 80%, 85%, 90%, 95% or 100% identical to the amino acid sequence of SEQ I D NO. 1 . In one aspect, the enzyme comprises amino acids (363) to (382) of SEQ I D NO: 1 . In one embodiment, the enzyme comprises an amino acid sequence of SEQ I D NO: 2 or active fragment or homologue thereof. In one embodiment, the enzyme comprises an amino acid sequence that is at least 80%, 85%, 90%, 95% or 100% identical to the amino acid sequence of SEQ ID NO. 2. In another aspect, the enzyme comprises amino acids (363) to (382) of SEQ ID NO: 2.

[1 12] In one embodiment, the enzyme comprises an 4Fe-4S cluster:

CXiSCX ₂ EGCMGRX ₃ QX ₄ YSX ₅ LX ₆ C

wherein

X is any amino acid, preferably a hydrophobic amino acid, preferably leucine or isoleucine, preferably leucine;

X ₂ is any amino acid, preferably a polar amino acid, preferably histidine or glutamine, preferably histidine;

X3 is any amino acid, preferably a hydrophobic amino acid preferably isoleucine or valine, preferably isoleucine;

X ₄ is any amino acid, preferably glutamic acid or histidine, preferably glutamic acid;

X5 is any amino acid, preferably a polar amino acid, preferably serine or methionine, preferably serine;

X(5 is any amino acid, preferably glycine or asparagine, preferably glycine. [113] In one embodiment, the enzyme comprises or substantially comprises (> 80%, > 85%, > 90%, > 95% or > 99%) of the consensus sequence as between SEQ ID NO: 1 and SEQ ID NO: 2.

[114] In one embodiment, the enzyme is substantially aerostable, which in one embodiment comprises an enzyme that retains at least 20, at least 25 or at least 30% of its activity when stored in air for 3 days.

[115] The nucleic acid molecules can further include expression control sequences operably linked to the polynucleotide comprised in the nucleic acid molecule. These expression control sequences may be suited to ensure transcription and synthesis of a translatable RNA in bacteria or fungi. Expression refers to the transcription of the heterologous DNA sequence, preferably into a translatable mRNA. Regulatory elements ensuring expression in bacteria, yeasts or fungi, cyanobacteria and algae are well known to those skilled in the art and encompass promoters, enhancers, termination signals, targeting signals and the like. Promoters for use in connection with the nucleic acid molecule may be homologous or heterologous with regard to its origin and/or with regard to the gene to be expressed. Suitable promoters are for instance promoters which lend themselves to constitutive expression. However, promoters which are only activated at a point in time determined by external influences can also be used. Artificial and/or chemically inducible promoters may be used.

[116] The polynucleotide introduced into a microorganism is expressed so as to lead to the production of a polypeptide having the enzymatic activity as described herein.

[117] An overview of different expression systems is for instance contained in Bitter et al. (Methods in Enzymology 153 (1987), 516-544) and in Sawers et al. (Applied Microbiology and Biotechnology 46 (1996), 1-9), Billman-Jacobe (Current Opinion in Biotechnology 7 (1996), 500-4), Hockney (Trends in Biotechnology 12 (1994), 456-463), Griffiths et al., (Methods in Molecular Biology 75 (1997), 427-440). An overview of yeast expression systems is for instance given by Hensing et al. (Antonie van Leuwenhoek 67 (1995), 261-279), Bussineau et al. (Developments in Biological Standardization 83 (1994), 13-19), Gellissen et al. (Antonie van Leuwenhoek 62 (1992), 79-93, Fleer (Current Opinion in Biotechnology 3 (1992), 486-496), Vedvick (Current Opinion in Biotechnology 2 (1991), 742-745) and Buckholz (Bio/Technology 9 (1991), 1067-1072). [118] Expression vectors have been widely described in the literature. Generally, they contain not only a selection marker gene and a replication-origin ensuring replication in the host selected, but also a bacterial or viral promoter, and in most cases a termination signal for transcription. Between the promoter and the termination signal there is in general at least one restriction site or a polylinker which enables the insertion of a coding DNA sequence. The DNA sequence naturally controlling the transcription of the corresponding gene can be used as the promoter sequence, if it is active in the selected host organism. However, this sequence can also be exchanged for other promoter sequences. It is possible to use promoters ensuring constitutive expression of the gene and inducible promoters which permit a deliberate control of the expression of the gene. Bacterial and viral promoter sequences possessing these properties are described in detail in the literature. Regulatory sequences for the expression in microorganisms, including E. coli and S. cerevisiae, are described in the literature known to those of skill in the art. Promoters permitting a particularly high expression of a downstream sequence are for instance the T7 promoter (Studier et al., Methods in Enzymology 185 (1990), 60-89), lacUV5, trp, trp-lacUV5 (DeBoer et al., in Rodriguez and Chamberlin (Eds), Promoters, Structure and Function; Praeger, New York, (1982), 462-481 ; DeBoer et al., Proc. Natl. Acad. Sci. USA (1983), 21-25), Ip1 , rac (Boros et al., Gene 42 (1986), 97-100).

[119] Inducible promoters which may provide higher polypeptide yields than constitutive promoters can be used. Suitably, in one embodiment, a two-stage process is used: the host cells are first cultured under optimum conditions up to a relatively high cell density; and transcription is then induced.

[120] Termination signals for transcription are also described in the literature.

[121] In addition, it is possible to insert different mutations into the polynucleotides by methods well known in molecular biology (see for instance Sambrook and Russell (2001), Molecular Cloning: A Laboratory Manual, CSH Press, Cold Spring Harbor, N.Y., USA), enabling the synthesis of polypeptides having modified biological properties. In one embodiment, point mutations are introduced at positions at which a modification of the amino acid sequence increases the catalytic activity or stability of the enzyme.

[122] Alternatively, the substrate preference of enzymes can also be changed using directed evolution. Enhancement in specific activity can be accomplished by using random mutagenesis over the whole length of the protein (Sheryl B. Rubin-Pitel et al. (2007), "Chapter 3: Directed Evolution Tools in Bioproduct and Bioprocess Development" in Bioprocessing for Value-Added Products from Renewable Resources, S.-T. Yang, Ed., Elsevier, Amsterdam, The Netherlands. )Protein solubility can be increased by site-directed mutagenesis to make hydrophobic to hydrophilic mutations on the protein surface (Saul R. Trevino et al. Journal of Molecular Biology 366 (2007), 449-460).

[123] Furthermore, genes can be subjected to codon optimization with techniques well known in the art to achieve optimized expression of the proteins.

[124] Appropriate modifications to a nucleic acid sequence to remove or include a targeting sequence can be incorporated into an exogenous nucleic acid sequence to impart desirable properties.

[125] As will be understood by those of skill in the art, when two or more exogenous encoding nucleic acids are to be co-expressed, both nucleic acids may be inserted, for example, into one expression vector or into separate expression vectors. For single vector expression, the encoding nucleic acids can be operationally linked to a common expression control sequence or linked to different expression control sequences, such as one inducible promoter and one constitutive promoter.

[126] It is to be understood that in one embodiment, a non-naturally occurring microorganism that produces a pathway intermediate or product, may be used in combination with another organism (or other organisms) expressing downstream or upstream pathway enzyme(s) to produce a desired product. For example, an engineered organism can be used to produce and accumulate adipic acid. The adipic acid can then be used as a substrate for another engineered organism expressing one or more of the pathway genes to convert adipic acid to 1 ,6-hexanediol, 6-hydroxyhexanoic or 6-aminocaproic acids.

[127] Host microorganisms can be selected from, and the non-naturally occurring microorganisms generated in, for example, bacteria, yeast, fungus or any of a variety of other microorganisms applicable to fermentation processes.

[128] Host microorganisms can be selected from, and the non-naturally occurring microorganisms generated in, for example, bacteria, yeast, fungus or any of a variety of other microorganisms may be used as a host organism. Suitable host microorganisms can be selected for example from Bacteria phylum like Proteobacteria, Firmicutes, Actinocacteria, Thermotogae, Bacteroides, Cyanobacteria. Archaea phyla Euryarchaeota, Fungi phylum Ascomycota and Zygomycota or Eukariota phylum like Chlorophyta, Dinoflagellata, Bacillariophyta, Eustigmatophyceae, Haptophyta and Heterokontophyta.

[129] Suitable bacterial and archaeal species include:

[130] Escherichia coli, Bacillus subtil is, Bacillus licheniformis, Bacillus cereus, Bacillus megaterium, Bacillus brevis, Bacillus pumilus, Corynebacterium glutamicum, Zymomonas mobilis, Clostridium acetobutylicum, Clostridium butylicum, Clostridium kluyveri, Clostridium autoethanogenum, Moorella thermoacetica, Clostridium aceticum, Clostridium beijerinckii, Clostridium ljungdahlii, Clostridium saccharoperbutylacetonicum, Clostridium perfringens, Clostridium difficile, Clostridium botulinum, Clostridium tyrobutyricum, Clostridium tetanomorphum, Clostridium tetani, Clostridium propionicum, Clostridium aminobutyricum, Clostridium subterminale, Clostridium sticklandii, Ralstonia eutropha, Mycobacterium bovis, Mycobacterium tuberculosis, Porphyromonas gingivalis, Pseudomonas fluorescens, Pseudomonas putida, Pseudomonas aeruginosa, Pseudomonas carboxidovorans (Oligotropha carboxidovorans), Pseudomonas stutzeri, Klebsiella pneumonia, Klebsiella oxytoca, Anaerobiospirillum succiniciproducens, Actinobacillus succinogenes, Mannheimia succiniciproducens, Rhizobium etli, Gluconobacter oxydans, Lactococcus lactis, Lactobacillus plantarum, Streptomyces coelicolor, Citrobacter freundii, Citrobacter amalonaticus, Acinetobacter calcoaceticus, Acinetobacter baylyi, Thermotoga maritima, Halobacterium salinarum, Serratia marcescens, Rhodospirillum rubrum, Ideonella sp., Rhodobacter capsulatus, Methylococcus capsulatus, Methylosinus trichosporium, Methylobacterium extorquens, Methylocystis GB25, Methylotrophus capsulatus, Methylomonas sp. 16a, Pyrococcus furiosus.

[131] Suitable yeasts or fungi include: Saccharomyces cerevisiae, Schizosaccharomyces pombe, Saccharomycopsis crataegensis, Kluyveromyces lactis, Kluyveromyces marxianus, Aspergillus terreus, Aspergillus niger, Pichia stipitis, Pichia pastoris, Rhizopus arrhizus, Rhizopus oryzae, Yarrowia lipolytica, Issatchenkia orientalis, Issatchenkia occidentalis, Candida lambica, Candida sorboxylosa, Candida zemplinina, Candida geochares, Pichia membranifaciens, Zygosaccharomyces kombuchaensis, Candida sorbosivorans, Candida vanderwaltii, Candida sorbophila, Zygosaccharomyces bisporus, Zygosaccharomyces lentus, Saccharomyces bayanus, Saccharomyces bulderi, Debaryomyces castellii, Candida boidinii, Candida etchellsii, Pichia jadinii, Pichia anomala, Penicillium chrysogenum, Candida tropicalis.

[132] In one embodiment, the host microorganism is an aerobic organism that can express an enzyme as described herein in an aerobic environment.

[133] Suitable cyanobacteria include: Acaryochloris marina MBIC1 1017, Anabaena sp. PCC 7120, Anabaena variabilis ATCC 29413, Agmenellum quadruplicatum, Chlorobium tepidu /77TLS, Cyanothece sp. ATCC 51142, Gloeobacter violaceus PCC 7421, Microcystis aeruginosa N I ES-843, Nostoc punctiforme ATCC 29133, Prochlorococcus marinus MED4, Prochlorococcus marinus Ml T9313, Prochlorococcus marinusSS^20, Prochlorococcus marinus str. AS9601, Prochlorococcus marinus str. MIT 9211, Prochlorococcus marinus str. MIT 9215, Prochlorococcus marinus str. MIT 9301, Prochlorococcus marinus str. MIT 9303, Prochlorococcus marinus str. MIT 9312, Prochlorococcus marinus str. MIT 9515, Prochlorococcus marinus str. NATL1A, Prochlorococcus marinus str.

NATL2A, Rhodopseudomonas palustris CGA009, Synechococcus elongatus PCC 6301, Synechococcus elongatus PCC 7942, Synechococcus sp. CC9311 , Synechococcus sp. CC9605, Synechococcus sp. CC9902, Synechococcus sp. JA-2-3BVa(2-

13), Synechococcus sp. JA-3-3Ab, Synechococcus sp. PCC 7002, Synechococcus sp. RCC307, Synechococcussp. WH 7803, Synechococcus sp. WH8102, Synechocystis sp. PCC 6803, Thermosynechococcus elongatus BP-1, Trichodesmium erythraeum IMS101.

[134] Suitable algae include: Botryococcus braunii, Chlamydomonas reinhardii, Chlorella sp., Crypthecodinium cohnii, Cylindrotheca sp., Dunaliella primolecta,

Isochrysis sp., Monallanthus salina, Nannochloris sp. , Nannochloropsis sp., Neochloris oleoabundans, Nitzschia sp., Phaeodactylum tricornutum, Schizochytrium sp., Tetraselmis sueica.

[135] In one embodiment, the host microorganism is an aerobic organism that can express an enzyme having α,β-enoate reductase activity in an aerobic environment. Expression of such an enzyme in an aerobic or a microaerobic environment may allow improved growth rate leading to improved productivity. Furthermore, this enzyme can be used to make chemicals from compounds that require aerobic biosynthesis pathways. [136] E. coli is a particularly useful host organism since it is a well characterized microorganism suitable for genetic engineering.

[137] Methods for constructing and testing the expression levels of a non-naturally occurring host can be performed by recombinant and detection methods, with techniques which are well known in the art. Such methods can be found described in, for example, Sambrook et al., Molecular Cloning: A Laboratory Manual, Third Ed., Cold Spring Harbor Laboratory, New York (2001); and Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1999). Specific methods for constructing and testing the expression levels of an E. coli host that produces one or more of the enzymes described herein are provided in the Examples.

[138] When reference is made to more than one exogenous nucleic acid being included in a microorganism, it is to be understood that this refers to the referenced encoding nucleic acids or biochemical activities and not the number of separate nucleic acids introduced into the host organism. As will be understood by those of skill in the art, such exogenous nucleic acids may be introduced into the host organism on separate nucleic acid molecules, on polycistronic nucleic acid molecules, or a combination thereof. For example, where two or more exogenous nucleic acids encoding different enzymatic activities are introduced into a host organism, the two or more exogenous nucleic acids can be introduced as a single nucleic acid, for example, on a single plasmid, on separate plasmids, can be integrated into the host chromosome at a single site or multiple sites, and still be considered as two or more exogenous nucleic acids.

[139] As will be apparent to persons of skill in the art, depending on the host microorganism selected, nucleic acids for the pathway enzyme(s) described can be introduced into the host organism. As will be apparent to persons of skill in the art, where a host microorganism expresses the pathway gene(s), the microorganism may be engineered such that the gene encoding the enzyme is overexpressed and/or genes encoding enzymes or proteins of competing pathways may be deleted.

[140] In one embodiment, methods are carried out with live cells. In another embodiment, the process is carried out in vitro with lysed cells or with partially or completely purified enzyme or with permeabilized cells. In one embodiment, the method is carried out in vitro and the enzyme is immobilized. Means and methods for immobilizing enzymes on different supports are well-known to the person skilled in the art. Such in vitro process can be similar to the processes described in ( 1) Dudley, Q.M., Karim, A.S., and Jewett, M.C. 2014. Cell-Free Metabolic Engineering: Biomanufacturing beyond the cell. Biotechnology Journal. 10:69-82., 2) Zhang Y-HP*. 2014. Production of biofuels and biochemicals by in vitro synthetic biosystems: opportunities and challenges. Biotechnology Advances, Epub, DOI: 10.1016/j.biotechadv.2014.10.009)

[141] In one embodiment, the methods are carried out in culture, with the host organism, producing the enzyme(s). The growth medium can include, for example, any inorganic or organic carbon source which can supply a source of carbohydrates or other precursors that the host organisms can naturally use or is engineered to use. In one embodiment, the host organism is provided with a feedstock of sugars. Such sources include, for example, sugars such as glucose, xylose, galactose, mannose, fructose and starch. Glucose can be obtained from various carbohydrate-containing sources including conventional biorenewable sources such as corn (maize), wheat, potato, cassava and rice as well as alternative sources such as energy crops, plant biomass, agricultural wastes, forestry residues, sugar processing residues and plant-derived household wastes.

[142] Sources of carbohydrate include renewable feedstocks and biomass, e.g. cellulosic biomass, hemicellulosic biomass and lignin feedstocks. Such biomass feedstocks contain, for example, carbohydrate substrates that can yield through biosynthetic pathways, unsaturated six-carbon dicarboxylic acids, muconic acid and 2-hexendioic acid. In addition, the enzyme can be incorporated in host microbes capable of using other substrates such as methanol, syngas, glycerol, C02 and producing muconic acid and 2-hexenedioic acid. Other renewable feedstocks and biomass will be known to persons of skill in the art.

[143] Biorenewable feedstock sources that may be used in accordance with the present invention include any renewable organic matter that includes a source of carbohydrates. These include, for example, grasses, trees (hardwood and softwood), vegetation and crop residues. Other sources can include, for example, organic waste materials (e.g., spent paper, green waste, municipal waste, etc.). Suitable carbohydrates, including glucose, may be isolated from biorenewable materials using methods that are known in the art. See, for example, Centi and van Santen, Catalysis for Renewables, Wiley-VCH, Weinheim 2007; Kamm, Gruber and Kamm, Biorefineries-lndustrial Processes and Products, Wiley-VCH, Weinheim 2006; Shang-Tian Yang, Bioprocessing for Value-Added Products from Renewable Resources New Technologies and Applications, Elsevier B. V. 2007; Furia, Starch in the Food Industry, Chapter 8, CRC Handbook of Food Additives 2 ^nd Edition CRC Press, 1973. See also chapters devoted to Starch, Sugar and Syrups within Kirk-Othmer Encyclopedia of Chemical Technology 5 ^th Edition, John Wiley and Sons 2001. Processes to convert starch to glucose are also well known in the art, see, for example, Schenck, "Glucose and Glucose containing Syrups" in Ullmann's Encyclopedia of Industrial Chemistry, Wiley-VCH 2009. Furthermore, methods to convert cellulose to glucose are known in the art, see, for example, Centi and van Santen, Catalysis for Renewables, Wiley-VCH, Weinheim 2007; Kamm, Gruber and Kamm, Biorefineries-lndustrial Processes and Products, Wley-VCH, Weinheim 2006; Shang-Tian Yang, Bioprocessing for Value-Added Products from Renewable Resources New Technologies and Applications, Elsevier B. V. 2007.

[144] In one embodiment, the processes as provided may be carried out in a fermenter.

[145] The engineered organism can be cultivated in a variety of reactors systems, and the process can be carried out in different modes of operations. The most commonly used bioreactor is a stirred tank bioreactor or aerated fermenter. The fermenter is equipped with sterile air supply, the mixing of bubble dispersion is achieved by mechanical agitation, and the temperature may be maintained using a jacket or coil that circulates steam or cooling water. For aerated vessels, high height/diameter ratio (>3) may be chosen to increase the contact time between the bubbles and liquid phase. Other variations of bioreactors are airlift bioreactor where mixing is achieved without mechanical agitation, and packed bed or fluidized bed bioreactors which are used when the biocatalyst is immobilized.

[146] The fermentation can be carried out in three different modes: batch, fed-batch and continuous mode. A standard batch bioreactor is considered a "closed" system. In batch mode, all the media components are added to bioreactor while ensuring the sterility. Once the medium has been prepared, the bioreactor is inoculated with an appropriate inoculum and the fermentation is allowed to proceed until the end without any changes to the medium, i.e., without feeding of any additional components. Components such as acid and/or base can, however, be added to maintain the pH, and air/oxygen can be added to maintain the dissolved oxygen levels. In batch fermentation biomass and product concentration change over time until the fermentation is complete. The cells undergo classical lag-phase, exponential growth-phase, stationary phase growth, followed by death phase.

[147] A variation of the batch mode is fed-batch mode where the nutrients including the carbon source is added to the fermenter as the process progresses.

[148] In addition to batch or fed-batch mode, continuous mode of fermentation can also be used. A continuous system is considered to be "open" system in contrast to the batch mode. In continuous mode, defined production medium is added continuously to the bioreactor and equal amounts of bioreactor contents are removed at the same rate. Continuous operation can be carried out in a chemostat where the vessel contents, including the cells are removed, or in a bioreactor that uses perfusion culture, which allows recycling of the viable cells back to the bioreactor, allowing high cell densities to be achieved.

[149] The commonly used fermenter designs and different operation modes are very well- established in the literature [Biochemical Engineering Fundamentals, 2 ^nd Ed. J. E. Bailey and D. F. Ollis, McGraw Hill, New York, 1986; Development of Sustainable Bioprocesses: Modeling and Assessment, E. Heinzle, A. P. Biwer and C. L. Cooney, John Wiley & Sons, Ltd., 2006; Bioprocess Engineering: Basic Concepts, 2 ^nd Ed., M. L. Shuler and F. Kargi, Prentice Hall, 2001].

[150] Batch, fed-batch or continuous fermentation procedures may be employed.

[151] The organisms can be grown in any suitable medium for growth such as Luria- Bertani broth, Terrific broth or yeast extract-peptone-dextrose (YPD) medium. For production, depending up on the choice of the host, synthetic minimal media such as M9 minimal medium, yeast synthetic minimal medium, yeast nitrogen base, BG-1 1 , or variations thereof can be used. A suitable minimal medium may contain at least one carbon source, at least one nitrogen source, salts, cofactors, buffers, and other components required to grow and maintain the recombinant microorganism. The carbon source can be one or more of the carbon sources described previously, the nitrogen source can be an ammonium salt or nitrate salt including but not limited to (NH ₄ )2S0 ₄ , NH ₄ CI, (NH ₄ )2HP0 ₄ , NH OH, KN0 ₃ , NaN0 ₃ . The medium may be supplemented with complex or organic nitrogen sources such as urea, yeast extract, casamino acids, peptone, tryptone, soy flour, corn steep liquor, or casein hydrolysate. Additionally, the minimal medium can be supplied with trace metals including but not limited to H ₃ B0 ₃ , MnCI ₂ , ZnS0 ₄ , Na ₂ Mo0 , CuS0 , Co(N0 ₃ ) ₂ , CuCI ₂ , ZnCI ₂ , CoCI ₂ , FeCI ₃ , Kl. The minimal medium may be supplemented with vitamins and/or non-vitamin compounds including but not limited to biotin, pantothanate, folic acid, inositol, nicotinic acid, p-aminobenzoic acid, pyridoxine, riboflavin, thiamine, cyanocobalamin, citric acid, ethylenediamine tetraacetic acid (EDTA), ferric ammonium citrate. The medium can be supplied by carbon dioxide either by direct sparging or in the form of NaHC0 ₃ , or Na ₂ C0 ₃ .

[152] In one embodiment, the processes are conducted under substantially aerobic conditions.

[153] As used herein the term "substantially aerobic" when used in reference to a culture or growth condition means, in one embodiment, that the amount of oxygen is equal to or greater than about 10% of saturation for dissolved oxygen in liquid media. In one embodiment, the term includes sealed chambers of liquid or solid medium maintained with an atmosphere greater than about 1 % oxygen.

[154] In one embodiment, the processes as described herein may suitably be performed at a pH range of between about 4 to about 8.

[155] While in one embodiment, the temperature at which the methods as described herein are performed is not particularly restricted, generally, the processes as described herein may be performed at temperatures of between about 20°C and about 60°C.

[156] A person skilled in the art will be readily able to determine an effective amount of enzyme to be used per quantity of substrate and, in one embodiment, the effective amount is not particularly restricted. The present inventors have found that an enzyme ratio of 1 μg of enzyme per 200 μg of substrate effective, although higher (e.g. 1 : 100) and lower (e.g. 1 : 1000) ratios of enzyme to substrate may be effective and an appropriate ratio can be readily determined by a person of skill in the art in relation to the specific reaction conditions.

[157] The amount of product in the medium can be determined using methods known in the art such as High Performance Liquid Chromatography (HPLC), Gas Chromatography (GC), Liquid Chromatography-Mass Spectrometry (LC-MS), Gas Chromatography-Mass Spectrometry (GC-MS). [158] Methods of assaying for the production of the polymer precursors described herein are known to those of skill in the art and further are exemplified below. For example, product, intermediate and byproduct formation can be analyzed by methods such as HPLC (High Performance Liquid Chromatography), GC-MS (Gas Chromatography-Mass Spectroscopy) and LC-MS (Liquid Chromatography-Mass Spectroscopy). Individual enzymatic activities from the exogenous DNA sequences can also be assayed using methods well known in the art.

[159] In some embodiments, processes as disclosed herein further include purifying the product of the processes products of the methods described herein. Such methods of purification are known to those of skill in the art and include e.g. by filtration, distillation or evaporation. Isolation of compound from the fermentation broth depends on the final purity of the compound required. The separation techniques may include: centrifugation, microfiltration, ultrafiltration, nano-filtration, evaporation, crystallization, distillation, and ion-exchange. Typical downstream processing operation would include a series of processes including separation of cells using centrifugation or microfiltration, removal of additional solids in the broth using ultrafiltration, removal of salts from the broth using nanofiltration, ion-exchange, or evaporative crystallization, and finally purification of adipic acid using distillation.

Industrial Applicability

[160] Adipic acid has various uses as will be known to those of skill in the art. The majority of adipic acid produced is used as a monomer for the production of nylon by a polycondensation reaction with hexamethylene diamine forming 6,6-nylon. Other major applications also involve polymers: it is a monomer for production of polyurethane and its esters are used as plasticizers, especially in polyvinyl chloride (PVC).

[161] The polymer precursors 1 ,4-butanediol, 1 ,6-hexanediol, 6-hydroxyhexanoic acid and 6-aminocaproic acid have diverse industrial uses.

[162] 1 ,4-Butanediol is used industrially as a solvent and in the manufacture of some plastics, elastic fibers and polyurethanes. 1 ,4-butanediol is also used for the synthesis of v- butyrolactone (GBL) and in the presence of phosphoric acid and high temperature, it dehydrates to the solvent tetrahydrofuran. [163] 1 ,6-Hexanediol is widely used for industrial polyester and polyurethane production. It is also an intermediate to acrylics, adhesives, and dyestuffs.

[164] Aminocaproic acid is an intermediate in the polymerization of Nylon-6, where it is formed by ring-opening hydrolysis of caprolactam. It also finds uses in pharmaceutical and applications.

[165] All documents referenced herein are incorporated by reference, however, it should be appreciated that any patent, publication, or other disclosure material, in whole or in part, that is incorporated by reference herein is incorporated only to the extent that the incorporated material does not conflict with definitions, statements, or other disclosure material set forth in this disclosure. As such, and to the extent necessary, the disclosure as explicitly set forth herein supersedes any conflicting material incorporated herein by reference.

[166] It will be understood that numerous modifications thereto will appear to those skilled in the art. Accordingly, the above description and accompanying drawings should be taken as illustrative of the invention and not in a limiting sense. It will further be understood that it is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure as come within known or customary practice within the art to which the invention pertains and as may be applied to the essential features herein before set forth, and as follows in the scope of the appended claims.

[167] The embodiments of the invention described above are intended to be exemplary only. The scope of the invention is therefore intended to be limited solely by the scope of the appended claims.

Examples

[168] The two families of flavoenzymes, Old Yellow Enzymes (OYEs; EC 1.6.99.1) and 2- enoate reductases (EREDs; EC 1.3.1.31) have been studied for biocatalytic hydrogenation of alkenes and exhibited a broad substrate specificity toward α,β-unsaturated substrates bearing an electron-withdrawing group such as aldehyde, ketone, and carboxylic acid. The C=C reducing activity of OYEs and EREDs from different organisms was analyzed. Example 1 - Cloning, expression, and purification of proteins

[169] Genes encoding the selected OYE and ERED proteins were PCR-amplified from genomic DNAs and cloned into p15Tv-Lic plasmid via a ligation-independent method as described in D. Bonsor, S. F. Butz, J. Solomons, S. Grant, I. J. S. Fairlamb, M. J. Fogg, G. Grogan, Organic and Biomolecular Chemistry 2006, 4, 1252-1260

[170] Recombinant ERED plasmids were transformed into the E. coli BL21 (DE3) AiscR strain for the overexpression of iron-sulfur containing proteins (per methods described in M. K. Akhtar, P. R. Jones, Applied Microbiology and Biotechnology 2008, 78, 853-862). E. coli transformants were cultured aerobically at 37°C in Terrific Broth (TB) medium (1 L) supplemented with 100 μg/mL ampicillin until the optical density (OD 600nm) reached 0.6-0.8. At this point cultures were transferred to tightly-closed flasks with a magnetic stir bar and protein expression was induced with 0.4 mM IPTG after a 30 min-anaerobic pre-cultivation in the closed flasks. Cultures were also incubated with DMSO (50 mM) as the final electron acceptor for 15-19 h at room temperature on a magnetic stir plate. E. coli cells were harvested by centrifugation (9,000g) and the cell pellets were stored in liquid N ₂ protein purification. For the whole-cell biotransformation cells were used immediately. Protein purification was performed in an anaerobic glove-box (Coy Laboratory Products, Grass Lake, Ml, USA) under an atmosphere of 80% N ₂ , 10% H ₂ , and 10% C0 ₂ . All buffers were degassed and sparged with Ar before use. Cell pellets were resuspended in lysis buffer (400 mM NaCI, 50 mM HEPES, pH 7.5, 5% glycerol, 5 mM imidazole, 0.05% Tween-20, 1 mg/mL lysozyme, 3 U/mL benzonase, 0.5 mM EDTA, and 1 mM DTT) and incubated at room temperature for 30 min. Cell lysates were cleared by centrifugation and the supernatant was incubated with Ni-affinity resin (Qiagen, Valencia, CA, USA) at 4°C for 1 h. The resin was then washed with 100 mL of washing buffer (400 mM NaCI, 50 mM HEPES, pH 7.5, 5% glycerol, 30 mM imidazole, 0.5 mM EDTA, and 1 mM DTT) and eluted with elution buffer (400 mM NaCI, 50 mM HEPES, pH 7.5, 5% glycerol, 250 mM imidazole, 0.5 mM EDTA, and 1 mM DTT). Purified EREDs were frozen and stored in liquid N ₂ . Protein concentration was determined using Bradford assay and protein purity was evaluated on 10% SDS-PAGE gels.

[171] Recombinant OYE plasmids were transformed into the E. coli BL21-Gold (DE3) strain (Stratagene, La Jolla, CA, USA). E. coli transformants were cultured at 37°C in TB medium supplemented with 100 μg/mL of ampicillin until the OD at 600nm reached 0.6-0.8. Protein expression was induced with 0.4 mM IPTG and the E. coli cells were grown overnight at 16°C. The E. coli cells were harvested by centrifugation (9,000g) and the pellets were resuspended in lysis buffer (400 mM NaCI, 50 mM HEPES, pH 7.5, 5% glycerol, and 5 mM imidazole) followed by sonication to break cells. Lysates were cleared by centrifugation and the supernatant was incubated with Ni-affinity resin at 4°C for 30 min. The resin was then washed with washing buffer (400 mM NaCI, 50 mM HEPES, pH 7.5, 5% Glycerol, and 30 mM imidazole) and eluted with elution buffer (400 mM NaCI, 50 mM HEPES, pH 7.5, 5% Glycerol, and 250 mM imidazole). Purified OYEs were frozen in liquid N ₂ and stored at -80°C.

Example 2 - Comparative Example

[172] All results in this study are means from at least two independent determinations. Control experiments were performed in parallel to correct substrate-independent oxidation of cofactors for OYEs. All buffers and reagents used in anaerobic reactions were rigorously sparged with Ar to remove traces of oxygen before use.

[173] OYEs do not contain an iron-sulfur cluster, but they can catalyze hydrogenation of activated alkenes by hydride transfer from NAD(P)H to FMN in a similar way to EREDs. 25 putative OYE genes (Table 1) were cloned based on the Pfam domain of the FMN oxidoreductase family PF00724. Purified OYEs were screened for hydrogenation activity against acrolein, 2-cyclohexn-1-one, c/ ^' s,c/ ^' s-muconic acid, frans.frans-muconic acid, and 2- hexendioic acid. Substrate specificity was measured spectrophotometrically in 96-well plates by following incubation for 20 min at room temperature in the anaerobic chamber. Buffers and reagents were also degassed and sparged with Ar. Reaction mixtures contained potassium phosphate (50 mM and pH 7.0), NaCI (10 mM), NADPH (0.25 mM), various substrates (1 mM) and protein (2.5 μg) in a final volume of 200 μΙ_. Enzyme reactions were monitored by following the decrease in absorbance at 340 nm (ε340 nm = 6,200/M ^« cm) as a measure of the conversion of the cofactor NADPH to NADP+.

Table 1. The OYE proteins tested for biocatalytic hydrogenation

Protein ID SEQ ID NO GenBank ID Microorganism Activity [U/mg protein]* acrolein 2-cyclohexen

-1 -one

BH1481 Bacillus halodurans C-125 ND 0.13

BSU2381 Bacillus subtiHs subsp. subtilis str. 168 ND 0.21

CV3501 9 Chromobacterium violaceum ATCC 12472 ND 0.07

EC5625 10 Escherichia coli K12 ND 0.18

LM02471 11 Listeria monocytogenes EGD-e ND 0.08

NE2398 12 Nitrosomonas europaea ATCC 19718 ND 0.19

PA2932 13 Pseudomonas aeruginosa PA01 ND 13

PA4356 14 Pseudomonas aeruginosa PA01 ND .15

PP091 1 15 Pseudomonas putida KT2440 ND 0.15

PP1244 16 Pseudomonas putida KT2440 0.06 0.25

PP1466 17 Pseudomonas putida KT2440 ND 0.14

PS1 143 18 Pseudomonas syringae pv. tomato str. ND 0.18

DC3000

PS2358 19 Pseudomonas syringae pv. tomato str. ND 0.13

DC3000

PS4251 20 Pseudomonas syringae pv. tomato str. ND 0.09

DC3000

PSPH1060 21 Pseudomonas syringae pv. phaseolicola ND 0.14

1448A

PSPH1370 22 Pseudomonas syringae pv. phaseolicola ND 0.18

1448A

PSPH4058 23 Pseudomonas syringae phaseolicola ND 0.22

1448A

RHA03305 24 Rhodococcus sp. RHA1 0.08 ND RHA09668 25 Rhodococcus sp. RHA1 ND ND SA0956 26 Staphylococcus aureus subsp. aureus ND ND Mu50

SAV151 1 27 BAC69220.1 Streptomyces avermitilis MA-4680 0.05 0.23 SM4273 28 AAK65532.1 Sinorhizobium meliloti 1021 ND ND S04153 29 AAN57126.1 Shewanella oneidensis MR-1 ND ND XCC0307 30 AAM39626.1 Xanthomonas campestris pv. campestri 0.15 str. ATCC 33913

YST4373 31 AAA83386.1 Saccharomyces cerevisiae 0.17 0.23

The cut-off value for enzyme activity of OYE is 0.05 U/mg protein. ND = not detected.

[174] 25 putative OYEs were overexpressed in E. coli and purified using Ni-NTA resin. OYE activity of purified proteins was tested with typical substrates of OYEs, i.e., acrolein and 2- cyclohexen-1-one, and 21 out of 25 proteins showed OYE activity (Table 1). However, no purified OYEs could hydrogenate 2-hexenedioic acid or muconic acid. Similarly, whole-cell biotransformations with three E.coli strains over-expressing OYEs: EC5625 (SEQ ID NO: 10) from E. coli (YST4373 (SEQ ID NO: 31) from S. cerevisiae, and BSU2381 (SEQ ID NO: 8) from Bacillus subtillis, revealed no hydrogenation of 2-hexenedioic acid into adipic acid. This results are consistent with previous reports that OYEs cannot easily reduce α,β-unsaturated carboxylic acids without additional electron-withdrawing groups such as second acid- or -ester, a halogen or nitrile.

Example 3 - Enzyme screening: ERED family (EC 1.3.1.31)

[175] All results in this study are means from at least two independent determinations. Control experiments were performed in parallel to correct substrate-independent oxidation of cofactors and EREDs. All buffers and reagents used in anaerobic reactions were rigorously sparged with Ar to remove traces of oxygen before use.

[176] The C=C reducing activity of EREDs was examined. Enzyme activity of purified EREDs was measured spectrophotometrically in 96-well plates by following incubation for 3-5 min at 30°C in the anaerobic chamber as described in M. Buhler, H. Simon, Hoppe-Seyler's Zeitschrift fur Physiologische Chemie 1982, 363, 609-625. Buffers and reagents were degassed and sparged with Ar. Reaction mixture contained potassium phosphate (100 mM and pH 7.0), NADH (0.5 mM), indicated substrates, and proteins (0.1-50 μg) in a final volume of 200 μΙ_. Enzyme reactions were monitored by following the decrease in absorbance at 340 nm (ε340 nm = 6,220/M ^« cm) due to oxidation of NADH to NAD+.

[177] It is known that ERED from C. tyrobutyricum (EREDCT, SEQ ID NO: 5 CAA71086.1) exhibits a broad substrate specificity toward α,β-unsaturated carboxylates in vivo. (Buhler and Simon 1982) EREDCT shows 50 ~ 82 % sequence identity to EREDs (Figure 14) from Bacillus coagulans 36D1 (EREDBC, SEQ ID NO: 1), C. acetobutylicum (EREDCA, SEQ ID NO: 2), C. kluveri (EREDCK, SEQ ID NO: 3), C. Ijungdahlii (EREDCL, SEQ ID NO: 4) and Moorella thermoacetica (EREDMT, SEQ ID NO: 6). Whole-cell anaerobic biotransformation of 2-hexenedioic acid (20mM) using these EREDs expressed in E.coli BL21 (DE3) AiscR (Figure 3) revealed production of adipic acid by all EREDs (except EREDCT) (Figure 6). EREDBC, EREDCA and EREDCK catalyzed a complete conversion of 2-hexenedioic acid to adipic acid within 3hr, while EREDMT and EREDCL showed complete hydrogenation of 2-hexenedioic acid after 6 and 48h, respectively (Figure 7) The inactivity of EREDCT can be attributed to its low expression in E. coli (Figure 5b), which can be improved using the established methods of codon optimization for recombinant protein expression in E. coli. Although the studied EREDCT is known to be an oxygen sensitive enzyme (Buhler, M. & Simon, H. On the kinetics and mechanism of enoate reductase. Hoppe-Seyler's Zeitschrift fur Physiologische Chemie 363, 609-625 (1982)), for anaerobically grown EREDBC (SEQ ID NO: 1) and EREDCA (SEQ ID NO: 2) aerobic biotransformation of 2-hexenedioic acid (15 mM) was performed. All used buffers and solvents were prepared and stored under aerobic conditions. Under aerobic incubation conditions, both cultures catalyzed full conversion of 2-hexenedioic acid to adipic acid within 20 minutes (Figure 15). This result can be explained by high cell density used for biotransformation (average - 100 mg of dry cell biomass per ml) and E.coli high respiration rates in E. coli cells maintaining anaerobic conditions inside the cells.

Table 2. The ERED proteins tested for biocatalytic hydrogenation

Protein ID GenBank ID Microorganism

EREDBC (SEQ ID NO: 1) AE099944.1 Bacillus coagulans 36D1

EREDCA (SEQ ID NO: 2) AEI32805.1 Clostridium acetobutylicum DSM 1731

EREDCK (SEQ I D NO: 3) EDK32796.1 Clostridium kluyveri DSM 555 EREDCL (SEQ ID NO: 4) ADK16394.1 Clostridium ljungdahlii DSM 13528 EREDCT (SEQ ID NO: 5) CAA71086.1 Clostridium tyrobutyricum

EREDMT (SEQ ID NO: 6) ABC20352.1 Moorella thermoacetica ATCC 39073

[178] Whole-cell biotransformation of cis,cis- and frans,frans-isomers of muconic acid (0.7 mM) revealed that EREDBC, EREDCA, and EREDMT also hydrogenated these substrates to adipic acid. After a 24-hr incubation, no muconic acid or 2-hexenedioic acid were detected in the culture, and a 99% yield of adipic acid was obtained (Figures 8a, 8b, and 8c). EREDCK and EREDCL also exhibited a 99% yield of adipic acid from frans,frans-muconic acid, but a lower yield (< 35%) from the c/ ^' s,c/ ^' s-isomer (Figures 8d and 8e). Interestingly, with the latter substrate these EREDs produced three additional products identified as frans,frans-muconic acid, 2-hexenedioic acid, and 3-hexenedioic acid-like compound with m/z 143.0319 (Figures 8d and 8e). The formation of frans,frans-muconic acid from a c/ ^' s,c/ ^' s-isomer suggests the presence of cis-trans isomerase activity in EREDCK and EREDCL. The 3-hexenedioic acid-like compound appears to be an inefficient substrate for these EREDS. This is similar to the mutated 2,4-dienoyl-CoA reductases from E. coli, which catalyze hydrogenation of 2,4-dienoyl CoA into 3-enoyl CoA (Tu, X., Hubbard, P.A., Kim, J. J. P. & Schulz, H. Two distinct proton donors at the active site of Escherichia coli 2,4-dienoyl-CoA reductase are responsible for the formation of different products. Biochemistry 47, 1167-1175 (2008).). Thus, the results indicate that the studied EREDs can catalyze the sequential hydrogenations of two C=C bonds of the six-carbon dicarboxylic acids, but appear to have different isomeric preferences.

Example 4 - Biochemical characterization of EREDCA and EREDBC

[179] Anaerobic over-expression and affinity purification of six cloned EREDs produced significant amounts of soluble protein for EREDBC, EREDCA, and EREDCK (> 5 mg/L), whereas the other three EREDs showed lower expression (Figure 5). Purified EREDBC and EREDCA exhibited a brown colour in solution and an absorption spectrum with a shoulder at 380 nm and flavin-like maximum at 450 nm (Figure 9). Both the brown colour of purified EREDBC and EREDCA and the 380 nm shoulder in its absorption spectrum suggest the presence of a functional [4Fe-4S] cluster. Our spectral studies revealed that purified EREDBC and EREDCA can be completely oxidized by oxygen (in the presence of air), reduced with an excess of NADH (3 mM), and then partially re-oxidized by substrate addition (i.e. 6 mM frans- cinnamic acid).

[180] For in vitro biochemical characterization, enzyme activities of purified EREDs were measured with 2-hexenedioic acid, cis-cis-muconic acid, trans-trans muconic acid, frans- cinnamic acid, frans-2-methyl-2-butenoic acid, frans-2-butenoic acid, acrolein, 2-cyclohexen-1- one, and 3-methyl-2-cyclohexenone. Purified EREDBC and EREDCA showed NADH- dependent reductase activity, while the other purified EREDs were inactive with the tested substrates, probably , due to the loss of the iron-sulfur cluster, or flavin cofactors, or different substrate preference. [Feng, J. et al. Discovery and Characterization of BlsE, a Radical S- Adenosyl-L-methionine Decarboxylase Involved in the Blasticidin S Biosynthetic Pathway. PLoS ONE 8 (2013).]. In the EREDBC and EREDCA spectra shown in Figure 9, the peaks for the associated flavine and FeS cluster cofactors are clearly visible, which can help to differentiate between the active and inactive enzymes (while purifying).

[181] Enzymatic assays under anaerobic conditions revealed that purified EREDCA has high hydrogenation activity against frans-cinnamic acid (3.5 U/mg protein) and low activity with frans-2-butenoic acid (0.008 U/mg protein). The kinetic constants (k _cat and K _m ) for frans- cinnamic acid were 5.2 s ^"1 and 0.17 mM respectively, and its specific activity was comparable to that of cinnamate reductase from C. sporogenes (5 U/mg protein). EREDCA exhibited substrate inhibition by frans-cinnamic acid at substrate concentrations higher than 0.5 mM with an inhibition constant ( <,) of 1.2 mM (Figure 11 a). Purified EREDCA was also active against 2- hexenedioic acid (up to 0.05U/mg protein), but showed no saturation by this substrate in the concentration range from 4 to 28 mM (Figure 1 1 b).

[182] Purified EREDBC exhibited significant reductase activity against 2-hexenedioic acid (0.09 U/mg protein), 2-cyclohexen-1-one (0.08 U/mg protein), 3-methyl-2-cyclohexenone (0.13 U/mg protein), and frans-cinnamic acid (0.39 U/mg protein) and detectable activity against frans-2-butenoic acid (crotonic acid, 0.036 U/mg protein) and acrolein (0.037 U/mg protein). EREDBC had a broad substrate specificity compared to EREDCA (Table 3). A biocompatible palladium catalyst was proposed for non-enzymatic hydrogenation of alkene metabolites in growth media including cinnamic acid variants and dicarboxylic acids. EREDBC exhibited a comparable substrate spectrum to that of the palladium catalyst (Sirasani, G., Tong, L. & Balskus, E.P. A biocompatible alkene hydrogenation merges organic synthesis with microbial metabolism. Angew. Chem. Int. Ed. (2014), providing evidence that EREDBC can be a good substitute for alkene hydrogenation in microbial production of biochemicals.

Table 3. In vitro C=C reductase activity of EREDBC against unsaturated carbonyl substrates.

Substrates Activity [U/mg protein]

2-Hexenedioic acid ^[al

[35 mM] 2.3 ± 0.04 frans-Cinnamic acid [1.0 mM] ^[b] 0.39 ± 0.001

T

3-Methyl-2-cyclohexenone [200 mM] 0.13 ± 0.03

1

2-Cyclohexen-1-one [200

Acrolein [15 mM] ^JJ 0.036 ± 0.005 frans-2-Butenoic acid [50 mM] ^{0 037 ± 0 0 0}

Muconic acid [0.7 mM] c/s,c/s-isomer ND ^[cl

frans,frans-isomer ND ^[cl

^[al 2-Hexendioic acid was dissolved in aqueous buffer (29 mM) or in 0.25 mM isopropanol (35 mM).

[b] frans-Cinnamic acid titrated with 1 N NaOH was used for enzyme assay. ^[cl ND: not detected.

[183] Kinetic studies of purified EREDBC were performed using 2-hexenedioic acid, 2- cyclohexen-1 -one, 3-methyl-2-cyclohexenone, and frans-cinnamic acid as substrates (Figure 10). EREDBC showed no saturation by 2-hexenedioic acid, 2-cyclohexen-1-one, and 3-methyl- 2-cyclohexenone, but saturation kinetics was observed for frans-cinnamic acid (Figure 10d). The kinetic constants (k _cat and K _m ) for frans-cinnamic acid were 0.50 s ^"1 and 0.51 mM, respectively. EREDBC also exhibited moderate substrate inhibition by frans-cinnamic acid at substrate concentrations higher than 1 .0 mM with the inhibition constant , 1.4 mM. In contrast to frans-cinnamic acid, EREDBC showed a sigmoid-like profile for 2-hexenedioic acid dissolved in aqueous buffer solution but no saturation was observed despite its significant in vitro activity (0.09 U/mg protein) (Figure 10a), which might be due to limited solubility of 2-hexenedioic acid in aqueous solutions.

[184] To increase the dissolved substrate concentration, 2-hexenedioic acid was dissolved in a reaction mixture containing 0.25 mM (final concentration) isopropanol, and kinetic constants of EREDBC and EREDCA were determined. Both ERED enzymes showed sigmoidal kinetics in the concentration range from 2.5 to 35 mM (Figure 12). Compared to EREDCA, EREDBC exhibited a higher turnover rate (k _caU 1 .86 vs. 0.138 s ^"1 ) and similar affinity ( _m , 18.9 vs. 20.47 mM) for 2-hexenedioic acid, resulting in a 14.6-fold higher catalytic efficiency of EREDBC compared to EREDCA (k _cat IK _m , 0.984 vs. 0.0674 s ^"1 mM ^"1 ).

Example 5 - Oxygen Tolerance

[185] It is known that EREDs are oxygen-sensitive enzymes, which are rapidly inactivated by oxygen due to the presence of an oxygen sensitive [4Fe-4S] iron-sulfur cluster coordinated by four cysteine residues in strictly conserved motif C-2X-C-3X-C-1 1X-C (Figure 14) [Gall, M. et al. Enzymatic conversion of flavonoids using bacterial chalcone isomerase and enoate reductase. Angewandte Chemie International Edition 53, 1439-1442 (2014).]. However, in the present experiments purified EREDBC exhibited significant resistance to inactivation by oxygen, whereas EREDCA was inactivated only after two days of incubation under air (Figure 13).

[186] Purified EREDs were placed in 5 ml_ glass tubes tightly capped with air-tight rubber stoppers. Anaerobic tubes were filled with anaerobic gas mixture (80% N ₂ , 10% H ₂ , and 10% C0 ₂ ) and aerobic tubes were filled with atmospheric air. The tubes were kept on ice for a week and a small aliquots of EREDs (5ul) were withdrawn by a syringe every day to measure residual activity in a reaction mixture containing 100 mM potassium phosphate buffer (pH 7.0), 0.5 mM NADH, indicated substrates (0.25 mM 2-hexenedioic acid for EREDBC and 0.75 mM cinnamic acid for EREDCA, and protein (1 μg) in a final volume of 200 μΙ_.

[187] After three days of storage in the absence of oxygen at 4°C, both EREDBC and EREDCA retained 35 and 19% of initial activity, respectively. In the presence of air (21 % oxygen), EREDBC showed significant oxygen tolerance (i.e. no oxygen inactivation after retaining 33% of initial activity after three days of storage) (Figure 13a). In contrast, EREDCA exhibited 30% residual activity after one day of storage and then, was completely inactivated by oxygen after two additional days of storage (Figure 13b). The oxygen tolerance of EREDBC and EREDCA may be associated with restricted access of oxygen to its [4Fe-4S]. [Jervis, A.J. et al. The 0 ₂ sensitivity of the transcription factor FNR is controlled by Ser24 modulating the kinetics of [4Fe-4S] to [2Fe-2S] conversion. Proceedings of the National Academy of Sciences of the United States of America 106, 4659-4664 (2009).].

Materials - Examples 6 and 7

[188] Adipaldehyde (≥ 95%) was purchased from Activate Scientific (UK), 6-hydroxyhexanoic acid was purchased from Alfa Aesar (Ward Hill, Massachusetts, USA), 4-hydroxybutyric acid was purchased from Arking Pharma (Guelph, ON, Canada), adipic acid (≥ 99.5%), butyraldehyde (≥ 99%), and aminocaproic acid (≥ 99%), 1 ,6-hexanediol (≥ 99%) were purchased from Sigma (St. Louis, MO, USA). Phusion® High-Fidelity DNA Polymerase and Dpnl were purchased from New England Biolabs (Whitby, Ontario, Canada). In-Fusion HD plus EcoDry for a ligation-independent cloning was obtained from Clontech (Mountain View, CA, USA). All other chemicals were purchased from Sigma.

[189] All results of in vitro experiments are means from at least three independent determinations. Control experiments were performed in parallel to correct substrate- independent oxidation of cofactors. Product analysis by HPLC and LC-MS - Examples 6 and 7

[190] 1.6-hexanediol, 1 ,4-butanediol, 6-hydroxyhexanoic and adipic acid standards and reaction samples were analyzed using a Varian ProStar HPLC system (Varian Medical Systems, Palo Alto, CA, USA) equipped with an Aminex HPX-87H column (300 x 7.8 mm) (Bio-Rad Laboratories Inc., Hercules, CA, USA). Samples were eluted with 5 mM H ₂ S0 ₄ at a flow rate of 0.6 ml/min, column temperature 50°C. The concentration of 1 ,6-hexanediol was determined by linear regression based on the peak areas at 210 nm UV or Rl.

[191] 6-aminocaproic acid standards and reaction samples were prepared derivatised with o- phtalaldehyde according to Interchim website protocol for pre-column procedure of amines derivatisation (http://www.interchim.fr/ft/0/02727A.pdf). After 2 min 30°C derivatisation, samples were analysed using a Varian ProStar HPLC system (Varian Medical Systems, Palo Alto, CA, USA) equipped with fluorescence detector (excitation -340 nm, emission - 450 nm) and a Pursuit 5 - C18 (150 x 4.0 mm) column. Samples were eluted with methanol/acetonitrile/water (45/45/10) (B) - 40 mM phosphate buffer pH 7. 6 (A) gradient. The solvent gradient was: 0 min, 0% B; 20 min, 60% B; 22 min, 60% B; 35 min, 0% B; followed by equilibration for 4 min with 0% B. The concentration of substrates and products was determined by linear regression based on the peak areas.

[192] The LC-MS platform consists of a Dionex Ultimate 3000 UHPLC system and a Q- Exactive mass spectrometer equipped with a HESI source (all from Thermo Scientific). Control of the system and data handling was performed using Thermo XCalibur 2.2 software and Chromeleon 7.2 software. Separation by liquid chromatography was conducted on a Hypersil Gold C18 column (50mm x 2.1 mm, 1.9μηι particle size, Thermo Scientific) equipped with a guard column. The pump was run at a flow rate of 200μΙ_/ηιίη. Solvent A is water containing 0.1 % formic acid; solvent B is acetonitrile. The gradient is Omin, 0% B; Detection of4min, 0% B; 15min, 100% B; 24min, 100% B; 25min, 0% B; 30min, 0% B; followed by equilibration for 5 min with 0% B. Autosampler temperature was maintained at 8°C and injection volume was ^0 ^L. Data collection was done in positive ionization mode with a scan range m/z 100-300, resolution 70000 at 1 Hz, AGC target of 3e6 and a maximum injection time of 200ms. Standard solutions of 1 ,6-hexanedioltime and m/z. (m/z 119.1062) and 6-hydroxycaproic acid (m/z 133.0864) were used for validation of retention time and m/z. Example 6

6.1 Gene cloning, expression, and purification of proteins

[193] Genes encoding the selected CARs, ARs, ATs, glutamate dehydrogenase YOR375C, alanine dehydrogenase BSU31930, polyphosphate kinases PA3455 and SMc02148 proteins were PCR-amplified from genomic DNA and cloned into a p15Tv-Lic plasmid with N-terminal 6His-tag via ligation-independent method as previously described [Bonsor D., Butz S. F., Solomons J., Grant S., Fairlamb I. J. S., Fogg M. J., Grogan G. Ligation independent cloning (LIC) as a rapid route to families of recombinant biocatalysts from sequenced prokaryotic genomes. Organic and Biomolecular Chemistry]. Previously it has been shown that post- translational phosphopantetheinylation of CARs is required for their activity [P. Venkitasubramanian et al. Reduction of Carboxylic Acids by Nocardia Aldehyde Oxidoreductase Requires a Phosphopantetheinylated Enzyme, January 5, 2007 The Journal of Biological Chemistry. 282, 478-485.]. Hence, genes encoding phosphopantetheinyl transferase BSU03570 and entD were amplified from Bacillus subtilis and E. coli K-12 genomic DNA and cloned to pCDFDuet plasmid without tag using standard ligation-dependent protocol [Sambrook J, Russell D. Molecular Cloning - A Laboratory Manual. Cold Spring Harbor Laboratory Pres. (4th ed.) (2012)]. Formate dehydrogenase gene P33160 was cloned in pET23b with C-terminal tag. Site directed mutagenesis was performed using standard protocol [Kunkel T.A. . Rapid and efficient site- specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U.S.A. 82, 488-492 (1985)].

[194] Recombinant plasmids were transformed into the E. coli BL21 (DE3) strain for the overexpression. Plasmids with phosphopantetheinyl transferase genes were co-transformed with CAR genes-containing plasmids. E. coli transformants were grown aerobically at 37°C in Terrific Broth (TB) medium (1 L) supplemented with 100 μg/mL ampicillin (p15Tv-Lic, pET23b) and/or 50 μg/mL streptomycin (pCDFDuet) until the culture optical density (OD 600 nm) reached 0.8-1. At this point, cultivation temperature was decreased to 16°C, and protein expression was induced with 0.4 mM IPTG. E. coli cells after overnight induction were harvested by centrifugation (4,500 g), and the cell pellets were stored at -20°C before protein purification. Cell pellets were resuspended in lysis buffer (400 mM NaCI, 50 mM HEPES, pH 7.5, 5 % glycerol, 5 mM imidazole) and sonicated on ice for 20 minutes in 5 secon pulses, followed by 5 seconds cooling. Insoluble cell material was removed (40,000 g) and the supernatant was incubated with a Ni-affinity resin (Qiagen, Valencia, CA, USA) at 4°C for 1 h. The resin was then washed with 100 ml_ of washing buffer (400 mM NaCI, 50 mM HEPES, pH 7.5, 5% glycerol, 20 mM imidazole) and eluted with elution buffer (400 mM NaCI, 50 mM HEPES, pH 7.5, 5% glycerol, 250 mM imidazole). Purified proteins were frozen in droplets in liquid N ₂ and stored at -80°C. Protein concentration was determined using Bradford assay and protein purity was evaluated using 13% SDS-PAGE gels.

6.2. Enzyme screening: CARs (1.2.1.30)

[195] It has been shown that the N. iowensis CAR has a broad substrate range, though its maximal activity was usually observed with aromatic substrates such as benzoic and cinnamic acids. CARs gene sequences homologues to the N. iowensis CAR (Uniprot number: Q6RKB1), were selected from GenBank database. Based on presence of adenylation (AMP-binding PF00501) and reduction (NAD-binding PF07993) domains accompanied with phosphopantetheinyl binding motif (PF00530) 13 CAR genes (mostly from Mycobacterium) were cloned and expressed in E. coli. (Table 4). As CAR activation enzymes, phosphopantetheinyl transferases (PPTs) from E. coli (P19925) and Bacillus subtilis (P39135), were used which were co-expressed with the selected CAR genes from a separate plasmid. Using 1-liter E. coli cultures with overnight induction by IPTG, 12 soluble CAR proteins were purified using affinity chromatography on a Ni-NTA resin. Based on a NADPH-oxidation assay, 8 proteins exhibited reductase activity towards the two common CAR substrates: benzoic acid and cinnamic acid (Figure 16-A). Screening of purified enzymes against aliphatic dicarboxylic acids revealed significant reductase activity towards longer chain (C6) dicarboxylic acids, whereas no detectable activity was found with the shorter chain diacids (malonic acid, succinic acid, and glutaric acid) (Figure 16). However, monocarboxylic C3-C4 monoacids with similar chain lengths (e.g. 4-hydroxybutyric acid, crotonic acid, butyric acid, and propionic acid) were found to be positive substrates for these enzymes (Figure 16 -B,D). The five CAR enzymes with the highest reductase activity towards adipic acid and 4-hydroxybutyric acid (MSMEI_5586, MAB_4714c, MSMEG_5739, MAP_1040c and MSMEG_2956) SEQ ID NOs: 35 - 39 were selected for the biochemical characterization and biotransformation reactions. Table 4. The 13 CARs cloned, purified and tested for reductase activity with 4-hydroxybutyric acid (5 mM) and adipic acid (5 mM) as substrates.

ND = no activity was detected. NS = no soluble protein was detected. 6.3 - Enzyme screening: ARs and ATs

[196] 28 aldehyde reductases from different bacteria were cloned and overexpressed in E. coli. Enzymes purified using affinity chromatography on Ni-NTA resin were screened for reductase activity with adipaldehyde and butyraldehyde in presence of both NADPH and NADH (Table 5). Butyraldehyde was used as a substrate substitute for 4-oxo-butanal, which is not commercially available. Reactions were followed spectrophotometncally, by cofactor oxidation at 340nm. The six AR enzymes (RHA1_ro05279 (SEQ I D NO:47), PA1 146 (SEQ I D NO:43), SCO0229 (SEQ I D NO:50), PP_3370 (SEQ I D NO:45), PSPTO_2097 (SEQ I D NO:46), and TM_01 1 1 (SEQ ID NO:52) demonstrated the highest reductase activity against these substrates, and they were selected for the biochemical characterization and biotransformations.

[197] Enzyme activity of purified ARs was measured spectrophotometncally in 96-well plates Reaction mixtures contained 100 mM HEPES buffer (pH 7.5), 0.4 mM NADH/NADPH, 10 mM adipaldehyde or butylaldehyde, and proteins (10 μg for adipaldehyde screen, 2 μg for butyraldehyde screen) in a final volume of 200 μΙ_ Reaction mixture for adipaldehyde screening contained 1 .8 % DMSO. Enzyme reactions were monitored by following the decrease in absorbance at 340 nm (ε340 nm = 6,220/M ^« cm) due to oxidation of NAD(P)H to NAD(P)+.

[198] 28 PLP-dependent aminotransferases (from the classes I , II and I I I) were cloned and overexpressed in E. coli (Table 6). Enzymes were purified using affinity chromatography on a Ni-NTA resin and were screened for reductase activity towards adipaldehyde using alanine and glutamate as amino-donors. Enzyme activity was measured spectrophotometncally using a coupled reaction with the NADPH/NADH-dependent alanine and glutamate dehydrogenases in the presence of excess of ammonium chloride. The five AT enzymes (GabT (SEQ I D NO:53), SM201 1_b20379 (SEQ I D NO:59), SAV2583 (SEQ I D NO:55), SM201 1_c04388 (SEQ I D NO:58), and SM201 1_b20423 (SEQ I D NO:60)) exhibited the highest activity with adipaldehyde/butyraldehyde, and they were used for biochemical characterization.

[199] Enzyme activity of ATs was measured spectrophotometncally in 96-well plates, coupled with NAD(P)H-dependent alanine and glutamate dehydrogenases (YOR375C (SEQ I D NO: 107) and BSU31930 (SEQ ID NO: 106)). Reaction was monitored by following the decrease in absorbance of NAD(P)H to NAD(P)+ at 340 nm (ε340 nm = 6,220/M ^« cm). Coupled enzymes can aminate pyruvate/ketoglutarate produced by ATs in excess of NH ₄ CI. Reaction mixtures contained 100 mM HEPES buffer (pH 7.5), 0.5 mM NADPH, 0.5 mM NADH, 1 mM alanine, 1 mM glutamate, 10 mM adipaldehyde, 5% ethanol, 37.5 mM NaCI, 50 mM ammonium chloride, 50 μΜ PLP, YOR375C and BSU31930 (2.5 μg each), and AT proteins (20 μg) in a final volume of 200 μΙ_.

Table 5. The 28 ARs cloned, purified and tested for the reduction of adipaldehyde (10mM) and butyraldehyde (10 mM).

44 Pseudomonas

1 Q9HZS9 PA2918 aeruginosa ND 0.137±0.03 3

45

1 Q88HI7 PP_3370 Pseudomonas putida 0.437±0.043 1.516±1.382 4

46

1 Q884J5 PSPTO_2097 Pseudomonas syringae 1.046±0.009 0.59±0.597 5

82

1 Q0S803 RHA1_ro04547 Rhodococcus jostii ND ND

6

83

1 Q0SFL7 RHA1_ro01858 Rhodococcus jostii ND ND

7

47

1 Q0S5X6 RHA1_ro05279 Rhodococcus jostii 0.721 ±0.026 0.905±0.834 8

48

1 Q0RYZ9 RHA1_ro08443 Rhodococcus jostii ND 0.188±0.142 9

84

2 Q0RYT2 RHA1_ro08510 Rhodococcus jostii ND ND

0

49

2 Q6NDT3 RPA0021 Rhodopseudomonas ND 0.1 16±0.031 1 palustris

85

2 Q82LP0 SAV_1970 Streptomyces ND ND

2 avermitilis

50

2 Q9S1 R2 SCO0229 Streptomyces coelicolor 0.362±0.05 0.892±0.847 3

86

2 Q93S07 SC06282 Streptomyces coelicolor ND ND

4

51

2 A0A0F6E SFyv_1886 Shigella flexneri ND 0.124±0.042 5 BS9

87

2 V1QPP4 SEEPB585 0967 Salmonella enterica ND ND

6 4

52

2 Q9WXW6 TM_011 1 Thermotoga maritima ND 1.055±0.43 7

88

2 Q8P5A9 XCC3431 Xanthomonas ND ND

8 campestris

*ND = no activity was detected. Table 6. The 28 ATs cloned, purified and tested for the amination of adipaldehyde (10 mM).

# Target Uniprot Uniprot gene ID SEQ ID Microorganism Adipaldehyd prot ID NO e 10 mM

U/mg

1 BAS0499 Q81YV0 BAS0499 89 Bacillus anthracis ND

2 BAS4776 Q81 K67 BASH2_00839 90 Bacillus anthracis ND

3 EC6020 P22256 gabT 53 Escherichia coli 0.337±0.008

4 MAR0012 A1 TWJ6 Maqu_0007 91 Marinobacter ND

hydrocarbonoclasticus

5 PA0221 Q9I6R7 PA0221 92 Pseudomonas aeruginosa ND

6 PA4805 Q9HV04 PA4805 93 Pseudomonas aeruginosa ND

7 PA5313 Q9HTP1 PA5313 94 Pseudomonas aeruginosa ND

8 PP2159 Q88KV9 PP2180 95 Pseudomonas putida ND

9 PP3681 Q88GK3 PP3718 96 Pseudomonas putida ND

10 PP4364 Q88EN3 PP4421 54 Pseudomonas putida 0.061 ±0.001

1 1 PP51 13 Q88CJ8 PP5182 97 Pseudomonas putida ND

12 RHA04845 Q0S806 RHA1_ro04544 98 Rhodococcus sp (strain ND

RHA1)

13 RHA07987 Q0S5M0 RHA1_ro05386 99 Rhodococcus sp (strain ND

RHA1)

14 SAV2585 Q82K21 SAV2583 55 Streptomyces avermitilis 0.136±0.01 1

15 SAV2614 Q82JZ2 SAV_2612 100 Streptomyces avermitilis ND

16 SC5440 086823 SC05676 56 Streptomyces coelicolor 0.084±0.015

17 SM2404 M4MUD8 SM201 1_c01534 57 Sinorhizobium meliloti 0.021 ±0.003

18 SM3293 M4MWT5 SM201 1_c04388 58 Sinorhizobium meliloti 0.152±0.001

19 SM4420 Q92Y66 SMa1855 101 Rhizobium meliloti ND

20 SM4966 M4MIX5 SM201 1_b20277 102 Sinorhizobium meliloti ND

21 SM5064 M4MML9 SM201 1_b20379 59 Sinorhizobium meliloti 0.106±0.008

22 SM5108 M4ML18 SM201 1_b20423 60 Sinorhizobium meliloti 0.162±0.002

23 SM5551 M4MKK7 SM201 1_b21 186 61 Sinorhizobium meliloti 0.051 ±0.014

24 mesta A3EYF7 - 103 Mesorhizobium sp. LUK ND

25 Spo3471 Q5LMU1 Spo3471 62 Ruegeria pomeroyi 0.021 ±0.001

26 MII7127 Q987B2 MII7127 63 Rhizobium loti 0.063±0.001

27 Syrb2 Q9RBY6 Syrb2 64 Pseudomonas syringae 0.040±0.001 28 Rsp3534 Q3IWE9 Rsp3534 65 Rhodobacter sphaeroides 0.034±0.005

ND = no activity was detected.

6.4 Regenerating enzymes: NADPH, ATP, glutamate and alanine.

[200] CARs adenylation domain uses 2 phosphates of ATP for substrate activation, forming acyl-AMP intermediate transferred to reducing domain, where one molecule of NADPH is oxidised for aldehyde release. Application of CARs together with ARs for full reduction of carboxylic group to alcohol needs 2 molecules of NADPH and 1 ATP. Full biotransformation of adipic acid to 1 ,6-hexanediol will cost in total 4 NADPH and 2 ATP molecules. In vitro application of cofactor dependent enzymes such as oxidoreductases or transferases needs enzymatic systems for regeneration of consumed cofactors to make the system cost-effective. There are four enzymes commonly employed in the regeneration of ATP: pyruvate kinase (uses phosphoenolpyruvate), acetate kinase (uses acetylphisphate), creatine kinase (uses creatine phosphate), and polyphosphate kinase (uses polyphosphate) [Donk W.A., Zhao H. Recent developments in pyridine nucleotide regeneration. Current Opinion in Biotechnology 14, 421-426 (2003)]. Majority of ATP-regenerating enzymes process only one step ADP phosphorylation. Taking into account price and stability of starting substrate for ATP regeneration, polyphosphate kinases was chosen. Polyphospate kinase family II comprises enzymes able to regenerate AMP to ATP in two steps. For ATP regeneration SMc02148 (SEQ ID NO: 105) from Sinorhizobium meliloti and PA3455 (SEQ ID NO: 104) from Pseudomonas aeruginosa, were applied (Table 7) [Nocek B., Kochinyan S., Proudfoot M., Brown G., Evdokimova E., Osipiuk J., Edwards A.M., Savchenko A., Joachimiak A., Yakunin A.F. Polyphosphate-dependent synthesis of ATP and ADP by the family-2 polyphosphate kinases in bacteria. Proc. Natl. Acad. Sci. U. S. A. 388, 17730-17735 (2008)]. Enzymes were cloned and overexpressed in E. coli. Enzymes purified by affinity chromatography using Ni-NTA resin were applied for CARs + ARs/ATs coupled reactions. Their activity for separate steps of ATP regeneration and full AMP to ATP regeneration in presence of polyphosphate (10-14 phosphates chain length) was confirmed by HPLC reverse-phase chromatography.

[201] Screened ATs enzymes consume alanine and/or glutamate as amino-group donors, that also need to be regenerated. Two enzymes were found suitable for this purposes - YOR375C (SEQ ID NO: 107), NADPH-dependent glutamate dehydrogenase from Saccharomyces cerevisiae, and BSU31930 (SEQ ID NO: 106), NADH-dependent alanine dehydrogenase from Bacillus subtilis (Table 7). Enzymes were cloned and expressed in E. coli. After purification with affinity chromatography on Ni-NTA resin, enzymes were tested for alanine (Figure 17 A) and glutamate regeneration (Figure 17 B). Both enzymes were applied for primary ATs screening and ATs biochemical characterization as coupled enzymes, enabling pyruvate and ketoglutarate detection in presence of reduced cofactors NADH and NADPH and NH ₄ CI excess.

[202] Formate dehydrogenase P33160 (D222Q/H224N) activity was measured spectrophotometncally in 96-well plates, monitored by increase in NAD+/NADP+ absorbance at 340 nm (ε340 nm = 6,220/M ^« cm). Reaction mixture contained 100 mM Tris-HCI buffer (pH 8.0), 50mM sodium formate, 1 μg of enzyme.

[203] Polyphosphate kinase activity was measured using reverse phase Pursuit5 - C18 column HPLC in linear gradient of Acetonitrile - 50 mM KH ₂ P0 ₄ with 8 mM TBAH . Detecting wavelength - 245 nm. Reaction mixture contains 100mM Tris-HCI buffer (pH 8.0), 10 mM MgCI ₂ , 0.25 mM polyphosphate, 3 mM ADP/AMP, 0.5 μg enzyme.

[204] CARs, ARs and amino-donor regenerating enzymes use pyridine nucleotides are as cofactors. Several enzymatic methods have been developed for the regeneration of NAD(P)H, such as reduction with formate dehydrogenase, glucose dehydrogenase, glucose-6-phosphate dehydrogenase, and alcohol dehydrogenase [Woodyer R. D., Johannes T., Zhao H. Cofactor Regeneration for Biocatalytic Applications. In Enzyme Technology, (A. Pandey, C. Webb, C. S. Soccol, and C. Larroche, Eds.) Chapter 5, Asiatech Publishers Inc., New Delhi, India, 83-101 (2004)]. Formate dehydrogenase are widely applied for regeneration of NADH and use cheap substrate - formate, releasing C0 ₂ , that can be easily removed from reaction mixture. NADPH - dependent formate dehydrogenases are far less common, than NADH-dependent enzymes. Based on Masaki lhara work [lhara M., Okabe A., Kawano Y., and Urano M. Light Driven C02 Fixation by using cyanobacterial photosystem I and NADPH-dependent formate dehydrogenase. Plos One. 8, e71581 (2013)] two mutations (D222Q and H224N) were introduced in adenine ribose binding loop of Pseudomonas aeruginosa formate dehydrogenase P33160, changing its specificity from NADH to NADPH (Figure 18). Though NAD binding was significantly diminished, enzyme was still able to regenerate, what made it applicable for both cofactors regeneration. Table 7. Cofactor regenerating enzymes, purified and tested for in vitro coupled reaction

Example 7

7.1. In vitro biotransformation

[207] In vitro enzymatic biotransformation was performed in 200ul reaction mixture 30°C, 800 rpm during 12 h.

[208] CARs + PP_3370 reaction mixture contained 100 mM HEPES (pH 7.5), 1 mM NADPH, 2 mM ATP, 10 mM MgCI ₂ , 10 mM adipic or 4-hydroxybutyric acid, 50mM sodium formate, 5mM polyphosphate, 80 ^g of CAR, 20 ^g of PP_3370, 10 ^g of P33160 (D222Q/H224N), 10 ^g of PA3455, and 10 ^g of SMc02148.

[209] MAB_4714c + ATs reaction mixture contained 100 mM HEPES (pH 7.5), 0.5 mM NADPH, 1 mM glutamate, 2 mM ATP, 10 mM MgCI ₂ , 20 mM adipic, 50 mM sodium formate, 60mM ammonium chloride, 5 mM polyphosphate, 80 μg of MAB_4714c, 20 μg of gabT or SAV2583, 10 [Jig of P33160 (D222Q/H224N), 5 [Jig YOR375C 10 [Jig of PA3455, and 10 ^g of SMc02148. [210] After 12 h reactions were centrifuged (16,000 g), supernatant was filtered with 10 kDa filters, product formation was analyzed using HPLC.

[21 1] Negative control experiment were performed with all enzymes, but not CARs. 7.2. Biochemical characterization of CARs

[212] Enzymes showing the highest activity from initial screening (Figure 16) were characterized in vitro for adipic, and hydroxybutyric acids saturation (Table 8). The lowest K _m for both substrates belongs to MAB_4714c (35.87±2.68 mM and 26.52±1.77 mM respectively) also as highest catalytic efficiency (89.55±3.07 M ^~1■ s ^~1 and 71 ±3 M ^~1 -s ^~1 ). The specific activity of majority of CARs towards benzoic acid is in the same range as CAR from Nocardia iowensis (2 U/mg) [Akhtsr K. M., Turner N.J., Jones R.P. Carboxylic acid reductase is a versatile enzyme for the conversion of fatty acids into fuels and chemical commodities. Proc Natl Acad Sci U S A. 1 10, 87-92 (2013)]. Taking into account sequential reduction of carboxylic groups of adipic acid and formation of 1 ,6-hexanoic acid as intermediate, CARs were also characterised for activity towards 6-hydroxyhexanoic acid.

Table 8. CARs kinetic parameters for ATP/NADPH dependent adipic and 4-hydroxybutyric acids reduction.

Enzymes adipic acid kcat , s ^"1 K _m , mM k _cat /K _m , M

MAB_4714c 3.21 ±0.1 1 35.87±2.68 89.55±3.07 MSMEG_5739 2.40±0.26 87.55±16.20 27.39±3.02 MSMEG 2956 2.73±0.20 108.2±12.83 25.2±1.83

Enzymes 4-hydroxybutyric acid kcat , s ¹ K _m , mM k _cai /K _m , M ¹ - s ¹ MAB_4714c 1.878±0.052 26.52±1.77 70.81 ±1.96 MSMEG_5739 0.51±0.017 37.84±2.39 13.48±0.45 MSMEG_2956 0.513±0.017 69.57±4.16 7.37±0.24 MSMEI 5586 0.152±0.013 19.63±4.88 7.74±0.66

Table 9. CARs kinetic parameters for ATP/NADPH dependent 6-hydroxyhexanoic acid reduction.

Enzymes 6-hydroxyhexanoic acid kcaf . S ¹ K _m , mM k _ca K _m , M ¹ - s ¹

MSMEG_2956 2.32±0.22 66.15±9.48 35.09±3.29

MSMEI_5586 1.20±0.07 16.2±2.1 1 74.18±4.05

MSMEG_5739 1.21 ±0.04 8.33±0.73 145.4±4.4

MAP_1040c 2.91 ±0.19 70.1 ±7.04 41.58±2.77

MAB_4714c 2.62±0.03 2.64±0.13 995.04±13.02

7.3 - Biochemical characterization of ARs/ATs

[213] ARs RHA1_ro05279, PA1 146, SCO0229, PP_3370 were characterised for saturation with adipaldehyde, PP_3370, PSPTO_2097, RHA1_ro05279, SCO0229, TM_01 11 , PA1146 were characterised for butyraldehyde saturation (Table 10). Regarding CARs cofactor preference towards NADPH rather that NADH, ARs more active with NADPH were chosen. For both substrates maximal k _cat /K _m with minimal K _m values was shown by AR PP_3370 from Pseudomonas putida. Observed catalytic efficiency was determined as (2.08±0.09) ^χ 10 ⁴ M ¹ s ¹ for adipaldehyde and (5.58±0.14) ^χ 10 ³ M ¹ s ¹ for butyraldehyde, K _m values were estimated as 0.29±0.02 and 1.53±0.11 mM respectively. [214] ATs GabT, SM2011_b20379, SAV2583, SM2011_c04388, SM2011_b20423, that revealed highest activity with adipaldehyde were used for biochemical characterisation (Table 11). Maximal catalytic efficiency (k _cat /K _m ) and lowest K _m value was determined as (9.22±0.27)x10 ² M ^~1 s ¹ and 0.67 mM for E. coli gabT aminotransferase.

Table 10. ARs kinetic parameters for adipaldehyde and butyraldehyde reduction.

Parameters Cofactor adipaldehyde*

RHA1_ro05279 PA1146 SCO0229 PP_3370

Km , mM NADPH ND ND 8.48±0.58 0.29±0.02

Km , mM NADH 6.89±1.38 9.05±1.99 ND 4.78±0.49 kcaf , S NADPH ND ND 3.79±0.10 6.03±0.25 kcaf , S NADH 3.67±0.31 5.45±0.56 ND 1.74±0.08

kcaf/K _m , NADPH ND ND (4.47±0.12)x10 ² (2.08±0.09)x10 ⁴

M ^~1 - s ¹

kcaf/K _m , NADH (5.33±0.45)x10 ² (6.02±0.06) ND (3.64±0.16)x10 ²

x10 ²

M ^~1 - s ¹

*reactions were supplemented with 1,8% DMSO to increase adipaldehyde solubility.

Parameters Cofactor butyraldehyde

PP_3370 PSPTO_20 RHA1_ro05 SCO0229 TM_0111 PA1146

97 279

K _m , mM NADPH 1.53±0.11 10.3±1.06 1.53±0.39 35.7±10.5 2.72±1.39 3.37±0.9

K _m , mM NADH 16.1±1.89 ND 14.28±0.88 6.56±2.54 1.37±0.31 15.6±5.94 kcaf S NADPH 8.54±0.22 12.2±0.63 1.28±0.09 21.9±4.69 0.30±0.06 0.84±0.08 kcaf S NADH 10.7±0.73 ND 25.77±0.88 0.90±0.05 0.90±0.05 9.01 ±1.9 kcaf/Km , NADPH (5.58±0.14 (1.18±0.06) (8.37±0.59) (6.15±1.31) (1.10±0.22) (2.49±0.24)x

)x10 ³ x10 ³ x10 ² x10 ² x10 ² 10 ²

M ¹ - s ¹ k _caf /K _m , NADH (6.64±0.45 ND (1 .80±0.06) (1 .07±0.18) (6.57±0.36) (5.76±1 .22)x _n/r i _? )x10 ² x10 ³ x10 ² x10 ² 10 ²

Table 11. ATs kinetic parameters for adipaldehyde

Parameters Amino- sdipaldehyde

donor

gabT SM2011_b SAV2583 SM2011_c SM2011_b

20379 04388 20423

K _m , mM Ala/Glu 0.67±0.07 0.32±0.10 1.35±0.19 8.58±3.34 2.64±0.35 kcat , S Ala/Glu 0.61±0.02 0.26±0.05 0.39±0.02 0.42±0.09 0.28±0.01 kcat/K _m , Ala/Glu (9.22±0.27 (8.08±1.52) (2.90±0.13) (4.86±1.07) (1.05±0.06)

)x10 ² x10 ² x10 ² x10 x10 ²

M ^"1 - s ^"1

7.4 - Coupling CARs with ARs for diol production in vitro and in vivo

[215] To investigate efficiency of adipic acid and 4-hydroxybutyric acid transformation to corresponding diols coupling CARs to ARs was tested. 10mM of substrate was used for 12 h conversion. MSMEG_5739, MAB_4714c, MAP_1040c, MSMEI_5586 and MSMEG_2956 active with adipic acid and 4-hydroxybutyric acid, were tested for coupled reaction with PP_3370 AR (Figure 19). ATP and NADPH-regenerating enzymes provided constant supply of reduced cofactors. Since PP_3370 substrate conversion yield is minimum 2 orders of magnitude higher than any CARs, its activity should not be a limiting step in coupled reaction. Product formation was analysed by HPLC, Rl-detector, Aminex-87H column. MAB_4714c exhibited maximal 32.9±2.2% transformation of 4-hydroxybutanoic acid to 1 ,4-butanediol, and 38.7±0.9% transformation of adipic acid to 1 ,6 hexanediol. MMAB_4714c converted 3,2±0.2% of adipic acid to 6-hydroxyhexanoic acid (Table 12).

[216] Next, a series of in vivo 4-hydroxybutyric and adipic acid biotransformation using E. coli cells expressing recombinant CARs were conducted. The same CARs, (coexpressed with BSU4205 PPTase) as used for in vitro transformation were chosen for whole cell biotransformation of 10 mM substrate. E. coli essentially possess several aldehyde reductases with different substrate preference. In the absence of additional ARs expression, second step of aldehyde reduction to alcohol was successfully fulfilled with endogenous E. coli ARs. Additional expression of PP_3370 for adipic acid biotransformation decreased transformation rates. Cells expressing MSMEG_5739 catalysed maximal conversion of 4-hydroxybutyric acid after 24h - 86.1±5.2% as well as adipic acid transformation to 1 ,6-hexandiol with 53.8±1.4% efficiency accompanied with minimal conversion to 6-hydroxyhexanoic acid - 9.1 %±0.7% (Figure 20 B). MAB_4714c, characterised with highest conversion efficiencies towards all substrates in vivo converted 63.4±23.8% of 4-hydroxybutyric acid and 5.3±0.3% of adipic acid to 1 ,6-hexanediol, though saving intermediate 6-hydroxyhexanoic acid - 53.8±1.4% (Table 13). Formation of 1 ,6-hexanediol, 1 ,4-butanediol and 6-hydroxyhexanoic acid was confirmed by LC- MS analysis.

[217] E. coli cells expressing recombinant CARs with BSU03570 phosphopantetheinyl transferase were grown on LB media with 100 μΜ ampicillin, 50 μΜ streptomycin, supplemented with 2 % glycerol aerobically on 37°C, until the culture optical density (OD 600 nm) reached 0.6-0.8. At this point protein expression was induced with 0.4 mM IPTG and substrate (adipic acid or 4-hydroxybutyric acid) for final 10 mM concentration was added. Samples were taken at 6h, 24h and 48h, centrifuged, supernatant was filtered through 10 kDa centrifugal filters. Products were analyzed with HPLC or LC-MS. Negative control experiments were performed using E. coli cells harboring empty plasmids. All results of in vivo experiments are means from at least two independent determinations.

Table 12. Conversion efficiencies of 10mM adipic aicd or 10mM 4-hydroxybutyric acid (12h) in vitro by CARs coupled with aldehyde reductase PP3370. Reaction was supplied with ATP and NADPH - regenerating enzymes, supplied with 50mM formate and 5mM polyphosphate.

Enzyme In vivo conversion efficiency (%) to:

In vivo conversion efficiency % to:

1 ,4-butanediol 1 ,6-hexanediol 6-hydroxyhexanoic acid MSMEI_5586 78.4 ±6.2 10.2±3.4 30.3±0.4

MAB_4713c 63.4 ±23.8 5.3±0.3 53.8±1.4

MSMEG_5739 86.1 ±5.2 57.2±0.6 9.1 ±0.7

MAP_1040c 81.6 ±18.3 15.4±1.7 5.8±0.2

MSMEG_2956 59.4 ±7.3 27.7±10.3 34.2±9.1

Table 13. Conversion of efficiencies of 10mM adipic acid or 10mM 4-hydroxybutyric acic in vivo by E. coli expressing CARs.

Enzyme In vivo conversion efficiency (%) to:

1 ,4-butanediol 1 ,6-hexanediol 6-hydroxyhexanoic acid

MSMEI_5586 78.4 ±6.2 10.2±3.4 30.3±0.4

MAB_4713c 63.4 ±23.8 5.3±0.3 53.8±1.4

MSMEG_5739 86.1 ±5.2 57.2±0.6 9.1 ±0.7

MAP_1040c 81.6 ±18.3 15.4±1.7 5.8±0.2

MSMEG_2956 59.4 ±7.3 27.7±10.3 34.2±9.1

7.5 - Coupling CARs with ATs for the in vitro adipic acid conversion to aminocaproic acid.

[218] Screened CARs exhibited no activity towards aminated substrates. MAB_4714c K _m value with adipic acid is 35.87±2.68 mM (Table 8). Under optimal conditions, the conversion yields for the characterized ATs with adipaldehyde are at least 10 times higher, than that with CARs's. In such case majority of monoaldehyde will be trapped by aminotransferases and excepted from catalytic transformation in form of 6-aminocaproic acid. MAB_4714c was coupled with GabT or SAV2583 ATs, glutamate was used as amino-donor. Reaction was supplied with ATP, NAD(P)H and glutamate regenerating enzymes and their substrates - 5 mM polyphosphate (10-14 phosphates in chain length), 40 mM formate, 50 mM NH ₄ CI. 20 mM of substrate was used for 12 h conversion. Product formation was analyzed by HPLC using C18 pre-column O-phtalaldehyde derivatization. Maximum transformation efficiency of adipic acid to 6-aminocaproic acid was estimated as 21.3±0.8% (Table 14).

Table 14. In vitro (12h) conversion efficiency of 20mM adipic acid to 6-aminocaproic acid by coupled reaction of CARs with ATs in presence of ATP, NAD(P)H and glutamate regenerating enzymes.

Enzyme In vitro conversion efficiency (%) to

MAB_4714c + ATs: 6-aminocaproic acid

GabT 21.3±0.8

SAV2583 19.5±0.4