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(12) Patent Application Publication (10) Pub. No.: US 2015/0307854 A1 B0tes Et Al

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(12) Patent Application Publication (10) Pub. No.: US 2015/0307854 A1 B0tes Et Al US 20150307854A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0307854 A1 B0tes et al. (43) Pub. Date: Oct. 29, 2015 (54) METHODS OF PRODUCING 6-CARBON Publication Classification CHEMICALS VA COA-DEPENDENT CARBON CHAIN ELONGATION (51) Int. Cl. ASSOCATED WITH CARBON STORAGE CI2N 9/02 (2006.01) CI2P 7/44 (2006.01) (71) Applicant: INVISTA North America S.ár.l., (52) U.S. Cl. Wilmington, DE (US) CPC ....... CI2N 9/0008 (2013.01); C12Y 102/02001 (2013.01); CI2P 7/44 (2013.01) (72) Inventors: Adriana Leonora Botes, Rosedale East (GB); Alex Van Eck Conradie, Eaglescliffe (GB) (57) ABSTRACT (21) Appl. No.: 14/666,055 This document describes biochemical pathways for produc ing adipic acid, caprolactam, 6-aminohexanoic acid, hexam (22) Filed: Mar. 23, 2015 ethylenediamine or 1.6-hexanediol by forming two terminal functional groups, comprised of carboxyl, amine or hydroxyl Related U.S. Application Data groups, in a C6 aliphatic backbone Substrate. These path ways, metabolic engineering and cultivation strategies (62) Division of application No. 13/715,981, filed on Dec. described herein rely on CoA-dependent elongation enzymes 14, 2012, now Pat. No. 9,102.958. or analogues enzymes associated with the carbon Storage (60) Provisional application No. 61/576,401, filed on Dec. pathways from polyhydroxyalkanoate accumulating bacte 16, 2011. 18. Patent Application Publication Oct. 29, 2015 Sheet 1 of 8 US 2015/0307854 A1 Patent Application Publication Oct. 29, 2015 Sheet 2 of 8 US 2015/0307854 A1 3. EC 38 Patent Application Publication Oct. 29, 2015 Sheet 3 of 8 US 2015/0307854 A1 Patent Application Publication Oct. 29, 2015 Sheet 4 of 8 US 2015/0307854 A1 r C th it. $$$$$$ Patent Application Publication Oct. 29, 2015 Sheet 5 of 8 US 2015/0307854 A1 gºInfö?? Patent Application Publication Oct. 29, 2015 Sheet 6 of 8 US 2015/0307854 A1 O Patent Application Publication Oct. 29, 2015 Sheet 7 of 8 US 2015/0307854 A1 Patent Application Publication Oct. 29, 2015 Sheet 8 of 8 US 2015/0307854 A1 US 2015/0307854 A1 Oct. 29, 2015 METHODS OF PRODUCING 6-CARBON 0009. However, no wild-type prokaryote or eukaryote CHEMICALS VA COA-DEPENDENT naturally overproduces or excretes C6 building blocks to the CARBON CHAIN ELONGATION extracellular environment. Nevertheless, the metabolism of ASSOCATED WITH CARBON STORAGE adipic acid and caprolactam has been reported (Ramsay et al., Appl. Environ. Microbiol., 1986, 52(1), 152-156; and CROSS-REFERENCE TO RELATED Kulkarni and Kanekar, Current Microbiology, 1998, 37, 191 APPLICATIONS 194). 0001. This application is a divisional application of U.S. 0010. The dicarboxylic acid, adipic acid, is converted effi application Ser. No. 13/715,981, filed Dec. 14, 2012, which ciently as a carbon Source by a number of bacteria and yeasts claims priority to U.S. Application Ser. No. 61/576,401, filed via B-oxidation into central metabolites. 3-oxidation of adi Dec. 16, 2011. The disclosures of these applications are incor pate to 3-oxoadipate faciliates further catabolism via, for porated by reference in their entirety. example, the ortho-cleavage pathway associated with aro matic Substrate degradation. The catabolism of 3-oxoadipyl TECHNICAL FIELD CoA to acetyl-CoA and succinyl-CoA by several bacteria and fungi has been characterised comprehensively (Harwood and 0002 This invention relates to methods for biosynthesiz Parales, Annual Review of Microbiology, 1996, 50,553-590). ing adipic acid, 6-aminohexanoic acid, hexamethylenedi Both adipate and 6-aminohexanoate are intermediates in the amine, caprolactam, and 1.6-hexanediol using one or more catabolism of caprolactam, finally degraded via 3-oxoadipyl isolated enzymes Such as B-ketothiolases, dehydrogenases, CoA to central metabolites. reductases, hydratases, monooxygenases, co-hydroxylases 0011 Potential metabolic pathways have been suggested and transaminases or using recombinant host cells expressing for producing adipic acid from biomass-Sugar: (1) biochemi one or more such enzymes. cally from glucose to cis,cis muconic acid via the ortho cleavage aromatic degradation pathway, followed by chemi BACKGROUND cal catalysis to adipic acid; (2) a reversible adipic acid 0003 Nylons are polyamides that are generally synthe degradation pathway via the condensation of Succinyl-CoA sized by the condensation polymerisation of a diamine with a and acetyl-CoA and (3) combining B-oxidation, a fatty acid dicarboxylic acid. Similarly, nylons may be produced by the synthase and ()-oxidation. However, no information using condensation polymerisation of lactams. A ubiquitous nylon these strategies has been reported (Jang et al., Biotechnology is nylon 6.6, which is produced by reaction of hexamethyl & Bioengineering, 2012, 109(10), 2437-2459). enediamine (HMD) and adipic acid. Nylon 6 is produced by 0012. The optimality principle states that microorganisms a ring opening polymerisation of caprolactam. Therefore, regulate their biochemical networks to Support maximum adipic acid, hexamethylenediamine and caprolactam are biomass growth. Beyond the need for expressing heterolo important intermediates in the production of nylons (Anton & gous pathways in a host organism, directing carbon flux Baird, Polyamides Fibers, Encyclopedia of Polymer Science towards C6 building blocks that serve as carbon sources and Technology, 2001). rather than as biomass growth constituents, contradicts the 0004 Industrially, adipic acid and caprolactam are pro optimality principle. For example, transferring the 1-butanol duced via air oxidation of cyclohexane. The air oxidation of pathway from Clostridium species into other production cyclohexane produces, in a series of steps, a mixture of cyclo strains has often fallen short by an order of magnitude com hexanone (K) and cyclohexanol (A), designated as KA oil. pared to the production performance of native producers Nitric acid oxidation of KA oil produces adipic acid (Musser, (Shen et al., Appl. Environ. Microbiol., 2011, 77(9), 2905 Adipic acid, Ullmann's Encyclopedia of Industrial Chemis 2915). try, 2000). Caprolactam is produced from cyclohexanone via 0013 The efficient synthesis of the six carbon aliphatic its oxime and Subsequent acid rearrangement (Fuchs, Kiec backbone precursor is a key consideration in synthesizing C6 Zka and Moran, Caprolactam, Ullmann's Encyclopedia of building blocks prior to forming terminal functional groups, Industrial Chemistry, 2000) Such as carboxyl, amine or hydroxyl groups, on the C6 ali 0005 Industrially, hexamethylenediamine (HMD) is pro phatic backbone. duced by hydrocyanation of C6 building block to adiponitrile, followed by hydrogenation to HMD (Herzog and Smiley, SUMMARY Hexamethylenediamine, Ullmann's Encyclopedia of Indus trial Chemistry, 2012). 0014. This document is based at least in part on the dis 0006 Given a reliance on petrochemical feedstocks; bio covery that it is possible to construct biochemical pathways technology offers an alternative approach via biocatalysis. for producing a six carbon chain aliphatic backbone precur Biocatalysis is the use of biological catalysts. Such as Sor, in which two functional groups, e.g., carboxyl, amine or enzymes, to perform biochemical transformations of organic hydroxyl, can be formed, leading to the synthesis of one or compounds. more of adipic acid, 6-aminohexanoic acid, hexamethylene 0007 Both bioderived feedstocks and petrochemical feed diamine, caprolactam, and 1.6-hexanediol (hereafter “C6 stocks are viable starting materials for the biocatalysis pro building blocks”). These pathways, metabolic engineering, CCSSCS. and cultivation strategies described herein rely on CoA-de 0008 Accordingly, against this background, it is clear that pendent elongation enzymes or homologs thereof associated there is a need for Sustainable methods for producing adipic with the carbon storage pathways from polyhydroxyal acid, caprolactam, 6-aminohexanoic acid, hexamethylenedi kanoate accumulating bacteria Such as Cupriavidus necator: amine and 1.6-hexanediol (hereafter “C6 building blocks”) 0015. In the face of the optimality principle, it surprisingly wherein the methods are biocatalyst based (Tang et al., Bio has been discovered that appropriate non-natural pathways, technology & Bioengineering, 2012, 109(10), 2437-2459). feedstocks, host microorganisms, attenuation strategies to the US 2015/0307854 A1 Oct. 29, 2015 host’s biochemical network, and cultivation strategies may be acetoacetyl-CoA can be formed by conversion of malonyl combined to efficiently produce C6 building blocks. CoA by an acetoacetyl-CoA synthase classified under EC 0016. In some embodiments, the C6 aliphatic backbone 2.3.1.194. The malonyl-CoA can be formed by conversion of for conversion to a C6 building block can be formed from acetyl-CoA by an acetyl-CoA carboxylase classified under acetyl-CoA via two cycles of CoA-dependent carbon chain EC 6.4.1.2. The trans-2-enoyl-CoA hydratase can be the gene elongation using either NADH or NADPH dependent product of pha. enzymes. See FIG. 1 and FIG. 2. 0023 The (R) 3-hydroxyhexanoyl-CoA can be formed by 0017. In some embodiments, the enzyme in the CoA-de conversion of 3-oxohexanoyl-CoA by a 3-oxoacyl-CoA pendent carbon chain elongation pathway generating the C6 reductase classified under EC 1.1.1.100 such as that encoded aliphatic backbone catalyzes irreversible enzymatic steps. by fabG. The crotonyl-CoA can be formed by conversion of 0018. In some embodiments, the terminal carboxyl groups (R) 3-hydroxybutanoyl-CoA by a trans-2-enoyl-CoA can be enzymatically formed using an acyl-CoA hydrolase, hydratase classified under EC 4.2.1.119. (R) 3-hydroxybu an aldehyde dehydrogenase, a 6-oxohexanoate dehydroge tanoyl-CoA can beformed by conversion of acetoacetyl-CoA nase or a cytochrome P450/co-hydroxylase. See FIG. 3 and by an acetoacyl-CoA reductase classified under EC 1.1.1.36 FIG. 4. such as that encoded by phaB. 0019. In some embodiments, the terminal amine groups 0024. In any of the methods described herein, the method can be enzymatically formed using an co-transaminase or a can include producing hexanoate by forming a first terminal diamine transaminase. See FIG. 5 and FIG. 6. carboxyl group in hexanoyl CoA using an acyl-CoA hydro 0020.
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