US20170152531A1 - Process for producing glutarate and glutaric acid methyl ester - Google Patents

Process for producing glutarate and glutaric acid methyl ester Download PDF

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US20170152531A1
US20170152531A1 US15/318,403 US201515318403A US2017152531A1 US 20170152531 A1 US20170152531 A1 US 20170152531A1 US 201515318403 A US201515318403 A US 201515318403A US 2017152531 A1 US2017152531 A1 US 2017152531A1
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Adriana Leonora Botes
Alex Van Eck Conradie
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Invista North America LLC
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Definitions

  • This invention relates to a method of increasing the activity of a polypeptide having carboxylate reductase activity on a dicarboxylic acid by enzymatically converting the dicarboxylic acid to a methyl ester using a polypeptide having malonyl-CoA methyltransferase activity.
  • This invention also relates to methods for biosynthesizing 2,4-pentadienoyl-CoA (e.g., as a precursor to the biosynthesis of 1,3-butadiene), and more particularly to synthesizing 2,4-pentadienoyl-CoA using one or more isolated enzymes such as one or more of a malonyl-CoA O-methyltransferase, methyl ester esterase, a carboxylate reductase, or a 5-hydroxyvaleryl-CoA dehydratase, or using recombinant host cells expressing one or more of such enzymes.
  • isolated enzymes such as one or more of a malonyl-CoA O-methyltransferase, methyl ester esterase, a carboxylate reductase, or a 5-hydroxyvaleryl-CoA dehydratase, or using recombinant host cells expressing one or more of such enzymes.
  • 1,3-butadiene (hereinafter butadiene) is an important monomer for the production of synthetic rubbers including styrene-butadiene-rubber (SBR), polybutadiene (PB), styrene-butadiene latex (SBL), acrylonitrile-butadiene-styrene resins (ABS), nitrile rubber, and adiponitrile, which is used in the manufacture of Nylon-66 (White, Chemico-Biological Interactions, 2007, 166, 10-14).
  • SBR styrene-butadiene-rubber
  • PB polybutadiene
  • SBL styrene-butadiene latex
  • ABS acrylonitrile-butadiene-styrene resins
  • nitrile rubber nitrile rubber
  • adiponitrile adiponitrile
  • Butadiene is typically produced as a co-product from the steam cracking process, distilled to a crude butadiene stream, and purified via extractive distillation (White, Chemico-Biological Interactions, 2007, 166, 10-14).
  • On-purpose butadiene has been prepared among other methods by dehydrogenation of n-butane and n-butene (Houdry process); and oxidative dehydrogenation of n-butene (Oxo-D or O-X-D process) (White, Chemico-Biological Interactions, 2007, 166, 10-14).
  • Biocatalysis is the use of biological catalysts, such as enzymes, to perform biochemical transformations of organic compounds.
  • This disclosure is based at least in part on the development of enzymatic systems and recombinant hosts for biosynthesizing 2,4-pentadienoyl-CoA or precursors thereof, which are useful for producing, for example, 1,3-butadiene and polymers or copolymers of 1,3-butadiene.
  • 2,4-pentadienoyl-CoA can be biosynthetically produced from renewable feedstocks without the need for any chemical catalysts such as metal oxides.
  • 2,4-pentadienoyl-CoA can be produced from malonyl-CoA or malonyl-[acp] via various methyl-ester shielded routes.
  • methyl-ester shielded routes include using a methyl ester esterase such as a pimelyl-[acp] methyl ester esterase or esterase to hydrolyze the methyl ester of glutaryl-[acp] methyl ester, glutaryl-CoA methyl ester, glutarate methyl ester, glutarate semialdehyde methyl ester, or 5-hydroxypentanoate methyl ester, and using a 5-hydroxyvaleryl-CoA dehydratase to introduce the first terminal vinyl group of 1,3-butadiene.
  • 1,3-butadiene can be produced from precursors stemming from 2,4-pentadienoyl-CoA as outlined in FIG. 7 .
  • the C5 aliphatic backbone for conversion to 1,3-butadiene can be formed from malonyl-[acp] or malonyl-CoA via conversion to glutaryl-[acp] methyl ester or glutaryl-CoA methyl ester, followed by (i) de-esterification of glutaryl-[acp] methyl ester or glutaryl-CoA methyl ester to glutaryl-[acp] or glutaryl-CoA respectively, or (ii) hydrolysis of glutaryl-[acp] methyl ester or glutaryl-CoA methyl ester to glutarate methyl ester. See FIG. 1-3 .
  • an enzyme in the pathway generating the C5 aliphatic backbone purposefully contains irreversible enzymatic steps.
  • the terminal carboxyl groups can be enzymatically formed using an esterase, a thioesterase, a reversible CoA-ligase, a CoA-transferase, an aldehyde dehydrogenase, a 7-oxoheptanoate dehydrogenase, a 6-oxohexanoate dehydrogenase or a 5-oxopentanoate dehydrogenase. See FIG. 4 .
  • the terminal hydroxyl group can be enzymatically formed using an alcohol dehydrogenase, a 4-hydroxybutyrate dehydrogenase, a 5-hydroxypentanoate dehydrogenase and a 6-hydroxyhexanoate dehydrogenase. See FIG. 5 .
  • the terminal vinyl group can be enzymatically formed using a 5-hydroxyvaleryl-CoA dehydratase. See FIG. 6 .
  • this document features a method of biosynthesizing glutarate methyl ester in a recombinant host.
  • the method includes enzymatically converting at least one of malonyl-[acp] and malonyl-CoA to glutarate methyl ester in the host using at least one polypeptide having malonyl-CoA O-methyltransferase activity and at least one polypeptide having thioesterase activity.
  • the malonyl-[acp] is enzymatically converted to malonyl-[acp] methyl ester using the at least one polypeptide having malonyl-CoA O-methyltransferase activity.
  • the the malonyl-[acp] methyl ester can be enzymatically converted to glutaryl-[acp] methyl ester using at least one polypeptide having an activity selected from the group consisting of synthase activity, dehydrogenase activity, dehydratase activity, and reductase activity.
  • the glutaryl-[acp] methyl ester can be enzymatically converted to glutarate methyl ester using the at least one polypeptide having thioesterase activity.
  • malonyl-CoA is enzymatically converted to malonyl-CoA methyl ester using the at least one polypeptide having malonyl-CoA O-methyltransferase activity.
  • the malonyl-CoA methyl ester can be enzymatically converted to glutaryl-CoA methyl ester using at least one polypeptide having an activity selected from the group consisting of synthase activity, ⁇ -ketothiolase activity, dehydrogenase activity, hydratase activity, and reductase activity.
  • the glutaryl-CoA methyl ester can be enzymatically converted to glutarate methyl ester using the at least one polypeptide having thioesterase activity.
  • the polypeptide having malonyl-CoA O-methyltransferase activity can have at least 70% sequence identity (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence set forth in SEQ ID NO:13.
  • the polypeptide having reductase activity can have at least 70% sequence identity (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence set forth in SEQ ID NO: 11 or 12.
  • the method further includes enzymatically converting glutarate methyl ester to glutarate semialdehyde methyl ester in the host using at least one polypeptide having carboxylate reductase activity.
  • the polypeptide having carboxylate reductase activity can be used in combination with a polypeptide having phosphopantetheine transferase enhancer activity.
  • the method further includes enzymatically converting glutarate methyl ester to 5-oxopentanoic acid using at least one polypeptide having an activity selected from the group consisting of carboxylate reductase activity and esterase activity.
  • the polypeptide having carboxylate reductase activity can be used in combination with a polypeptide having phosphopantetheine transferase enhancer activity.
  • the method further includes enzymatically converting glutarate semialdehyde methyl ester to 5-hydroxypentanoic acid using at least one polypeptide having esterase activity. In some embodiments, the method further includes using at least one polypeptide having dehydrogenase activity to enzymatically convert glutarate semialdehyde methyl ester to 5-hydroxypentanoic acid.
  • the polypeptide having esterase activity can have at least 70% sequence identity (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence set forth in SEQ ID NO:8.
  • the method further includes enzymatically converting glutarate methyl ester to glutaric acid using at least one polypeptide having esterase activity.
  • the method can further include enzymatically converting glutaric acid to 5-hydroxypentanoic acid using at least one polypeptide having carboxylate reductase activity and at least one polypeptide having dehydrogenase activity classified under EC 1.1.1.-.
  • the polypeptide having carboxylate reductase activity can be used in combination with a polypeptide having phosphopantetheine transferase enhancer activity.
  • the polypeptide having carboxylate reductase activity can have at least 70% sequence identity (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to any one of the amino acid sequences set forth in any one of SEQ ID NOs: 2-7.
  • the polypeptide having thioesterase activity can have at least 70% sequence identity (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to any one of the amino acid sequences set forth in SEQ ID NO: 9, 10, 14 or 15.
  • the method further includes enzymatically converting 5-hydroxypentanoic acid to 2,4-pentadienoyl-CoA using at least one polypeptide having an activity selected from the group consisting of CoA-transferase activity, a synthase activity, and dehydratase activity.
  • a polypeptide having a CoA-transferase activity or a synthase activity and a polypeptide having dehydratase activity can enzymatically convert 5-hydroxypentanoic acid to 2,4-pentadienoyl-CoA.
  • the method can further include enzymatically converting 2,4-pentadienoyl-CoA into 1,3 butadiene using at least one polypeptide having an activity selected from the group consisting of hydratase activity, thioesterase activity, decarboxylase activity, dehydrogenase activity, CoA-transferase activity, and dehydratase activity.
  • the polypeptide having thioesterase activity can have at least 70% sequence identity (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to any one of the amino acid sequences set forth in SEQ ID NOs: 14-15.
  • this document features a method of making glutarate.
  • the method includes (i) enzymatically converting glutaryl-[acp] methyl ester to glutaryl-[acp] or glutaryl-CoA methyl ester to glutaryl-CoA using a polypeptide having pimeloyl-[acp] methyl ester methylesterase activity, and (ii) enzymatically converting glutaryl-[acp] or glutaryl-CoA to glutarate using at least one polypeptide having thioesterase activity, reversible CoA-ligase activity, a CoA-transferase activity, an acylating dehydrogenase activity, an aldehyde dehydrogenase activity, a glutarate semialdehyde dehydrogenase activity, or a succinate-semialdehyde dehydrogenase activity.
  • the polypeptide having pimeloyl-[acp] methyl ester methylesterase activity can have at least 70% sequence identity (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence set forth in SEQ ID NO: 1.
  • glutaryl-[acp] or glutaryl-CoA is enzymatically converted to glutaric acid using a polypeptide having thioesterase activity. In some embodiments, glutaryl-[acp] or glutaryl-CoA is enzymatically converted to glutaric acid using a polypeptide having reversible CoA-ligase activity or a CoA-transferase activity.
  • glutaryl-[acp] or glutaryl-CoA is enzymatically converted to glutaric acid using a polypeptide having an acylating dehydrogenase activity, an aldehyde dehydrogenase activity, a glutarate semialdehyde dehydrogenase activity, or a succinate-semialdehyde dehydrogenase activity.
  • this document features a recombinant host cell.
  • the recombinant host cell includes at least one exogenous nucleic acid encoding a polyp eptide having malonyl-CoA O-methyltransferase activity and a polypeptide having thioesterase activity, the host producing glutarate methyl ester.
  • the host can further include an exogenous polypeptide having carboxylate reductase activity, the host further producing glutarate semialdehyde methyl ester.
  • the host furthers include one or more exogenous polypeptides having an activity selected from the group consisting of synthase activity, dehydrogenase activity, dehydratase activity, and reductase activity.
  • the host further includes one or more exogenous polypeptides having an activity selected from the group consisting of synthase activity, ⁇ -ketothiolase activity, dehydrogenase activity, hydratase activity, and reductase activity.
  • the polypeptide having malonyl-CoA O-methyltransferase activity can have at least 70% sequence identity (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence set forth in SEQ ID NO: 13.
  • the polypeptide having thioesterase activity can have at least 70% sequence identity (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to any one of the amino acid sequences set forth in any one of SEQ ID NOs: 14-15.
  • the polypeptide having reductase activity can have at least 70% sequence identity (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to any one of the amino acid sequences set forth in SEQ ID NOs: 11 or 12.
  • the host can further include an exogenous polypeptide having esterase activity, the host further producing glutaric acid or 5-oxopentanoic acid.
  • the host includes one or more exogenous polypeptides having an activity selected from the group consisting of esterase activity, 6-hydroxyhexanoate dehydrogenase activity, 4-hydroxybutyrate dehydrogenase activity, 5-hydroxypentanoate dehydrogenase activity, and alcohol dehydrogenase activity, the host producing 5-hydroxypentanoic acid.
  • the host can further include one or more exogenous polypeptides having an activity selected from the group consisting of CoA-transferase activity, a synthase activity, and dehydratase activity, the host producing 2,4-pentadienoyl-CoA from 5-hydroxypentanoic acid.
  • the host can further include one or more exogenous polypeptides having an activity selected from the group consisting of hydratase activity, thioesterase activity, decarboxylase activity, dehydrogenase activity, CoA-transferase activity, and dehydratase activity, the host producing 1,3-butadiene from 2,4-pentadienoyl-CoA.
  • the polypeptide having thioesterase activity can at least 70% sequence identity (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence set forth in SEQ ID NO: 14 or SEQ ID NO: 15
  • the polypeptide having carboxylate reductase activity can have at least 70% sequence identity (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to any one of the amino acid sequences set forth in any one of SEQ ID NOs: 2-7.
  • the host when the host includes an exogenous polypeptide having carboxylate reductase activity it is used in combination with an exogenous polypeptide having phosphopantetheine transferase enhancer activity.
  • this document features a recombinant host including at least one exogenous nucleic acid encoding a polypeptide having pimeloyl-[acp] methyl ester methylesterase activity, and at least one polypeptide having an activity selected from the group consisting of thioesterase activity, reversible CoA-ligase activity, a CoA-transferase activity, an acylating dehydrogenase activity, an aldehyde dehydrogenase activity, a glutarate semialdehyde dehydrogenase activity, and a succinate-semialdehyde dehydrogenase activity.
  • the polypeptide having pimeloyl-[acp] methyl ester methylesterase activity can have at least 70% sequence identity (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence set forth in SEQ ID NO: 1.
  • the host when the host includes an exogenous polypeptide having carboxylate reductase activity it is used in combination with an exogenous polypeptide having phosphopantetheine transferase enhancer activity.
  • this document features a bio-derived product, bio-based product or fermentation-derived product, wherein the product includes (i.) a composition including at least one bio-derived, bio-based or fermentation-derived compound as described herein, or any combination thereof; (ii.) a bio-derived, bio-based or fermentation-derived polymer including the bio-derived, bio-based or fermentation-derived composition or compound of (i.), or any combination thereof; (iii.) a bio-derived, bio-based or fermentation-derived resin including the bio-derived, bio-based or fermentation-derived compound or bio-derived, bio-based or fermentation-derived composition of (i.) or any combination thereof or the bio-derived, bio-based or fermentation-derived polymer of ii.
  • This document also features a method of increasing the activity of a polypeptide having carboxylate reductase activity on a substituted or unsubstituted C 4 -C 8 dicarboxylic acid such as glutaric acid or adipic acid.
  • the method includes enzymatically converting the C 4 -C 8 dicarboxylic acid to a HOC( ⁇ O)(C 2 -C 6 alkyl)—C( ⁇ O)OCH 3 ester using a polypeptide having malonyl-CoA methyltransferase activity before enzymatically converting the HOC( ⁇ O)(C 2 -C 6 alkyl)—C( ⁇ O)OCH 3 ester to a HC( ⁇ O)(C 2 -C 6 alkyl)-C( ⁇ O)OCH 3 using a polypeptide having carboxylate reductase activity.
  • the method further can include enzymatically converting the HC( ⁇ O)(C 2 -C 6 alkyl)—C( ⁇ O)OCH 3 to HOCH 2 (C 2 -C 6 alkyl)—C( ⁇ O)OCH 3 using a polypeptide having dehydrogenase activity.
  • the method further includes enzymatically converting the HOCH 2 (C 2 -C 6 alkyl)—C( ⁇ O)OCH 3 product to a HOCH 2 (C 2 -C 6 alkyl)—C( ⁇ O)OH product using a polypeptide having the activity of an esterase.
  • This document also features a recombinant host that includes at least one exogenous nucleic acid encoding a (i) malonyl-[acp] O-methyltransferase, (ii) a pimeloyl-[acp] methyl ester methylesterase and (iii) a thioesterase, and produce glutarate methyl ester, glutaryl-[acp] or glutaryl-CoA.
  • Such a recombinant host producing glutarate methyl ester further can include an esterase, and further produce glutaric acid.
  • Such a recombinant host producing glutaryl-[acp] further can include a thioesterase and produce glutaric acid.
  • Such a recombinant host producing glutaryl-CoA further can include one or more of (i) a thioesterase, (ii) a reversible CoA-ligase, (iii) a CoA-transferase, or (iv) an acylating dehydrogenase, and (v) an aldehyde dehydrogenase such as such as 7-oxoheptanoate dehydrogenase, 6-oxohexanoate dehydrogenase or 5-oxopentanoate dehydrogenase and further produce glutaric acid or 5-oxopentanoate.
  • a recombinant host producing 5-oxopentanoate or glutaric acid further can include one or more of (i) an alcohol dehydrogenase or (ii) a carboxylate reductase and further produce 5-hydroxypentanoate.
  • a recombinant host producing glutarate methyl ester further can include one or more of (i) an alcohol dehydrogenase, (ii) an esterase or (iii) a carboxylate reductase and further produce 5-hydroxypentanoate.
  • this document features a method for producing a bioderived four or five carbon compound.
  • the method includes culturing or growing a host as described herein under conditions and for a sufficient period of time to produce the bioderived four or five carbon compound, wherein, optionally, the bioderived four or five carbon compound can be selected from the group consisting of 2,4-pentadienoyl-CoA, glutaryl-[acp] methyl ester, 5-hydroxypentanoic acid, 3-buten-2-one, 3-buten-2-ol, 1,3-butadiene and combinations thereof.
  • this document features a composition including a bioderived for or five carbon compound and a compound other than the bioderived four or five carbon compound, wherein the bioderived four or five carbon compound is selected from the group consisting of 2,4-pentadienoyl-CoA, glutaryl-[acp] methyl ester, 5-hydroxypentanoic acid, 3-buten-2-one, 3-buten-2-ol, 1,3-butadiene and combinations thereof.
  • the bioderived 4-carbon compound can be a cellular portion of a host cell or an organism.
  • biobased polymer including the bioderived four or five carbon compound including 2,4-pentadienoyl-CoA, glutaryl-[acp] methyl ester, 5-hydroxypentanoic acid, 3-buten-2-one, 3-buten-2-ol, 1,3-butadiene and combinations thereof.
  • biobased resin including the bioderived four or five carbon compound including 2,4-pentadienoyl-CoA, glutaryl-[acp] methyl ester, 5-hydroxypentanoic acid, 3-buten-2-one, 3-buten-2-ol, 1,3-butadiene and combinations thereof, as well as a molded product obtained by molding a biobased resin.
  • this document also features a process for producing a biobased polymer including chemically reacting the bioderived four or five carbon compound with itself or another compound in a polymer-producing reaction.
  • this document features a process for producing a biobased resin as described herein including chemically reacting the bioderived four or five carbon compound with itself or another compound in a resin producing reaction.
  • This document also features a biochemical network including a malonyl-CoA O-methyltransferase, wherein the malonyl-CoA O-methyltransferase enzymatically converts malonyl-[acp] to malonyl-[acp] methyl ester.
  • the biochemical network can further include a synthase, a dehydrogenase, a dehydratase, a reductase, and a thioesterase, wherein the synthase, the dehydrogenase, the dehydratase, the reductase, and the thioesterase, enzymatically convert the malonyl-[acp] methyl ester to glutarate methyl ester.
  • the biochemical network further includes a carboxylate reductase, wherein the carboxylate reductase enzymatically converts glutarate methyl ester to glutarate semialdehyde methyl ester.
  • the biochemical network can further include an esterase and a dehydrogenase, wherein the esterase and dehydrogenase enzymatically convert glutarate semialdehyde methyl ester to 5-hydroxypentanoic acid.
  • the biochemical network can further include a CoA-transferase and dehydratase, wherein the CoA-transferase and dehydratase enzymatically convert 5-hydroxypentanoic acid to 2,4-pentadienoyl-CoA.
  • the biochemical network can further include a hydratase, a thioesterase, a decarboxylase, a dehydrogenase, a CoA-transferase, and a dehydratase, wherein the hydratase, the thioesterase, the decarboxylase, the dehydrogenase, the CoA-transferase, and the dehydratase enzymatically convert the 2,4-pentadienoyl-CoA to 1,3-butadiene.
  • This document also features a biochemical network including a malonyl-CoA O-methyltransferase, wherein the malonyl-CoA O-methyltransferase enzymatically converts malonyl-CoA to malonyl-CoA methyl ester.
  • the biochemical network can further include a synthase, a ⁇ -ketothiolase, a dehydrogenase, a hydratase, a reductase, and a thioesterase, wherein the synthase, the ⁇ -ketothiolase, the dehydrogenase, the hydratase, the reductase, and the thioesterase, enzymatically convert the malonyl-CoA methyl ester to glutarate methyl ester.
  • the biochemical network further includes a carboxylate reductase, wherein the carboxylate reductase enzymatically converts glutarate methyl ester to glutarate semialdehyde methyl ester.
  • the biochemical network can further include an esterase and a dehydrogenase, wherein the esterase and dehydrogenase enzymatically convert glutarate semialdehyde methyl ester to 5-hydroxypentanoic acid.
  • the biochemical network can further include a CoA-transferase and dehydratase, wherein the CoA-transferase and dehydratase enzymatically convert 5-hydroxypentanoic acid to 2,4-pentadienoyl-CoA.
  • the biochemical network can further include a hydratase, a thioesterase, a decarboxylase, a dehydrogenase, a CoA-transferase, and a dehydratase, wherein the hydratase, the thioesterase, the decarboxylase, the dehydrogenase, the CoA-transferase, and the dehydratase enzymatically convert the 2,4-pentadienoyl-CoA to 1,3-butadiene.
  • This document also features a method of increasing the activity of a polypeptide having carboxylate reductase activity on a substituted or unsubstituted C 4 -C 8 dicarboxylic acid such as glutaric acid or adipic acid.
  • the method includes enzymatically converting the C 4 -C 8 dicarboxylic acid to a HOC( ⁇ O)(C 2 -C 6 alkyl)—C( ⁇ O)OCH 3 ester using a polypeptide having malonyl-CoA methyltransferase activity before enzymatically converting the HOC( ⁇ O)(C 2 -C 6 alkyl)—C( ⁇ O)OCH 3 ester to a HC( ⁇ O)(C 2 -C 6 alkyl)-C( ⁇ O)OCH 3 using a polypeptide having carboxylate reductase activity.
  • the method further can include enzymatically converting the HC( ⁇ O)(C 2 -C 6 alkyl)—C( ⁇ O)OCH 3 to HOCH 2 (C 2 -C 6 alkyl)—C( ⁇ O)OCH 3 using a polypeptide having dehydrogenase activity.
  • the method further includes enzymatically converting the HOCH 2 (C 2 -C 6 alkyl)—C( ⁇ O)OCH 3 product to a HOCH 2 (C 2 -C 6 alkyl)—C( ⁇ O)OH product using a polypeptide having the activity of an esterase.
  • Any of the methods can be performed in a recombinant host by fermentation.
  • the host can be subjected to a cultivation strategy under aerobic, anaerobic, or micro-aerobic cultivation conditions.
  • the host can be cultured under conditions of nutrient limitation such as phosphate, oxygen or nitrogen limitation.
  • the host can be retained using a ceramic membrane to maintain a high cell density during fermentation.
  • the host is subjected to a cultivation strategy under aerobic or micro-aerobic cultivation conditions.
  • a biological feedstock can be used as the principal carbon source for the fermentation.
  • the biological feedstock can be, or can derive from monosaccharides, disaccharides, lignocellulose, hemicellulose, cellulose, lignin, levulinic acid and formic acid, triglycerides, glycerol, fatty acids, agricultural waste, condensed distillers' solubles, or municipal waste.
  • a non-biological feedstock can be used as the principal carbon source for the fermentation.
  • the non-biological feedstock can be, or can be derived from, natural gas, syngas, CO 2 /H 2 , methanol, ethanol, benzoate, non-volatile residue (NVR) or a caustic wash waste stream from cyclohexane oxidation processes, or terephthalic acid/isophthalic acid mixture waste streams.
  • the host can be a prokaryote.
  • the prokaryote can be selected from the group consisting of Escherichia; Clostridia; Corynebacteria; Cupriavidus; Pseudomonas; Delftia; Bacilluss; Lactobacillus; Lactococcus ; and Rhodococcus .
  • the prokaryote can be selected from the group consisting of Escherichia coli, Clostridium ljungdahlii, Clostridium autoethanogenum, Clostridium kluyveri, Corynebacterium glutamicum, Cupriavidus necator, Cupriavidus metallidurans.
  • Pseudomonas fluorescens Pseudomonas putida
  • Pseudomonas oleavorans Delftia acidovorans
  • Bacillus subtillis Lactobacillus delbrueckii
  • Lactococcus lactis Lactococcus lactis
  • Rhodococcus equi Rhodococcus equi.
  • the host can be a eukaryote.
  • the eukaryote can selected from the group consisting of Aspergillus, Saccharomyces, Pichia, Yarrowia, Issatchenkia, Debaryomyces, Arxula , and Kluyveromyces .
  • the eukaryote can be selected from the group consisting of Aspergillus niger, Saccharomyces cerevisiae, Pichia pastoris, Yarrowia lipolytica, Issathenkia orientalis, Debaryomyces hansenii, Arxula adenoinivorans , and Kluyveromyces lactis.
  • the host exhibits tolerance to high concentrations of a C5 building block, and wherein the tolerance to high concentrations of a C5 building block is improved through continuous cultivation in a selective environment.
  • the host's endogenous biochemical network is attenuated or augmented to (1) ensure the intracellular availability of acetyl-CoA, (2) create a cofactor, i.e. NADH or NADPH, imbalance that may be balanced via the formation of glutarate methyl ester, 2,4-pentadienoyl-CoA, or 1,3-butadiene, (3) prevent degradation of central metabolites, central precursors leading to and including glutarate methyl ester, 2,4-pentadienoyl-CoA, or 1,3-butadiene and (4) ensure efficient efflux from the cell.
  • a cofactor i.e. NADH or NADPH
  • the host includes one or more of the following: the intracellular concentration of oxaloacetate for biosynthesis of a C5 building block is increased in the host by overexpressing recombinant genes forming oxaloacetate; wherein an imbalance in NADPH is generated that can be balanced via the formation of a C5 building block; wherein an exogenous lysine biosynthesis pathway synthesizing lysine from 2-oxoglutarate via 2-oxoadipate is introduced in a host using the meso 2,6 diaminopimelate pathway for lysine synthesis; wherein an exogenous lysine biosynthesis pathway synthesizing lysine from oxaloacetate to meso 2,6 diaminopimelate is introduced in a host using the 2-oxoadipate pathway for lysine synthesis; wherein endogenous degradation pathways of central metabolites and central precursors leading to and including C5 building blocks are attenuated in the host; or wherein the efflux
  • any of the recombinant hosts described herein further can include one or more of the following attenuated polypeptides having attenuated activity of a: polyhydroxyalkanoate synthase, an acetyl-CoA thioesterase, an acetyl-CoA specific ⁇ -ketothiolase, an acetoacetyl-CoA reductase, a phosphotransacetylase forming acetate, an acetate kinase, a lactate dehydrogenase, a menaquinol-fumarate oxidoreductase, a 2-oxoacid decarboxylase producing isobutanol, an alcohol dehydrogenase forming ethanol, a triose phosphate isomerase, a pyruvate decarboxylase, a glucose-6-phosphate isomerase, a transhydrogenase dissipating the cofactor imbalance, aglutamate dehydrogen
  • any of the recombinant hosts described herein further can overexpress one or more genes encoding a polypeptide having: an acetyl-CoA synthetase, a 6-phosphogluconate dehydrogenase; a transketolase; a feedback resistant threonine deaminase; a puridine nucleotide transhydrogenase; aformate dehydrogenase; a glyceraldehyde-3P-dehydrogenase; a malic enzyme; a glucose-6-phosphate dehydrogenase; a fructose 1,6 diphosphatase; a propionyl-CoA synthetase; a L-alanine dehydrogenase; a L-glutamate dehydrogenase; a L-glutamine synthetase; a lysine transporter; a dicarboxylate transporter; and/or a multidrug transporter activity
  • the reactions of the pathways described herein can be performed in one or more cell (e.g., host cell) strains (a) naturally expressing one or more relevant enzymes, (b) genetically engineered to express one or more relevant enzymes, or (c) naturally expressing one or more relevant enzymes and genetically engineered to express one or more relevant enzymes.
  • relevant enzymes can be extracted from of the above types of host cells and used in a purified or semi-purified form. Extracted enzymes can optionally be immobilized to the floors and/or walls of appropriate reaction vessels.
  • extracts include lysates (e.g. cell lysates) that can be used as sources of relevant enzymes.
  • all the steps can be performed in cells (e.g., host cells), all the steps can be performed using extracted enzymes, or some of the steps can be performed in cells and others can be performed using extracted enzymes.
  • carboxylic acid groups including, but not limited to, organic monoacids, hydroxyacids, aminoacids, and dicarboxylic acids
  • carboxylic acid groups include, but are not limited to, organic monoacids, hydroxyacids, aminoacids, and dicarboxylic acids
  • a metal ion e.g., an alkali metal ion, an alkaline earth ion, or an aluminum ion
  • Acceptable organic bases include, but are not limited to, ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine, and the like.
  • Acceptable inorganic bases include, but are not limited to, aluminum hydroxide, calcium hydroxide, potassium hydroxide, sodium carbonate, sodium hydroxide, and the like.
  • a salt of the present invention is isolated as a salt or converted to the free acid by reducing the pH to below the pKa, through addition of acid or treatment with an acidic ion exchange resin.
  • amine groups including, but not limited to, organic amines, aminoacids, and diamines
  • ionic salt form for example, by addition of an acidic proton to the amine to form the ammonium salt, formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like; or formed with organic acids including, but not limited to, acetic acid, propionic acid, hexanoic acid, cyclopentanepropionic acid, glycolic acid, pyruvic acid, lactic acid, malonic acid, succinic acid, malic acid, maleic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, 3-(4-hydroxybenzoyl)benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, 1,2-ethaned
  • Acceptable inorganic bases include, but are not limited to, aluminum hydroxide, calcium hydroxide, potassium hydroxide, sodium carbonate, sodium hydroxide, and the like.
  • a salt of the present invention is isolated as a salt or converted to the free amine by raising the pH to above the pKb through addition of base or treatment with a basic ion exchange resin.
  • Acceptable inorganic bases include, but are not limited to, aluminum hydroxide, calcium hydroxide, potassium hydroxide, sodium carbonate, sodium hydroxide, and the like, or 2) when an acidic proton present in the parent compound either is replaced by a metal ion, e.g., an alkali metal ion, an alkaline earth ion, or an aluminum ion; or coordinates with an organic base.
  • Acceptable organic bases include, but are not limited to, ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine, and the like.
  • Acceptable inorganic bases include, but are not limited to, aluminum hydroxide, calcium hydroxide, potassium hydroxide, sodium carbonate, sodium hydroxide, and the like.
  • a salt can of the present invention is isolated as a salt or converted to the free acid by reducing the pH to below the pKa through addition of acid or treatment with an acidic ion exchange resin.
  • FIG. 1 is a schematic of exemplary biochemical pathways leading to glutarate methyl ester or glutaryl-[acp] from malonyl-[acp].
  • FIG. 2 is a schematic of exemplary biochemical pathways leading to glutarate methyl ester or glutaryl-CoA from malonyl-CoA using NADPH as reducing equivalent.
  • FIG. 3 is a schematic of exemplary biochemical pathways leading to glutarate methyl ester or glutaryl-CoA from malonyl-CoA using NADH as reducing equivalent.
  • FIG. 4 is a schematic of exemplary biochemical pathways leading to glutarate using glutarate methyl ester, glutaryl-[acp] or glutaryl-CoA as central precursor.
  • FIG. 5 is a schematic of an exemplary biochemical pathway leading to 5-hydroxypentanoate using glutarate methyl ester or glutarate as a central precursor.
  • FIG. 6 is a schematic of an exemplary biochemical pathway leading to 2,4-pentadienoyl-CoA using 5-hydroxypentanoate as a central precursor.
  • FIG. 7 is a schematic of an exemplary biochemical pathway leading to 1,3-butadiene using 2,4-pentadienoyl-CoA as central precursor.
  • FIG. 8 contains the amino acid sequences of an Escherichia coli pimeloyl-[acp] methyl ester methylesterase (see Genbank Accession No. AAC76437.1, SEQ ID NO: 1), a Mycobacterium marinum carboxylate reductase (see Genbank Accession No. ACC40567.1, SEQ ID NO: 2), a Mycobacterium smegmatis carboxylate reductase (see Genbank Accession No. ABK71854.1, SEQ ID NO: 3), a Segniliparus rugosus carboxylate reductase (see Genbank Accession No.
  • EFV11917.1, SEQ ID NO: 4 a Mycobacterium smegmatis carboxylate reductase (see Genbank Accession No. ABK75684.1, SEQ ID NO: 5), a Mycobacterium massiliense carboxylate reductase (see Genbank Accession No. EIV11143.1, SEQ ID NO: 6), a Segniliparus rotundus carboxylate reductase (see Genbank Accession No. ADG98140.1, SEQ ID NO: 7), an Pseudomonas fluorescens esterase (see Genbank Accession No.
  • Genbank Accession No. 11 an Euglena gracilis enoyl-CoA reductase (see, e.g., Genbank Accession No. AAW66853.1, SEQ ID NO: 12), a Bacillus cereus malonyl-[acp] O-methyltransferase (see, e.g., Genbank Accession No. AAP11034.1, SEQ ID NO: 13), an Escherichia coli thioesterase (see, e.g., Genbank Accession No. AAB59067.1, SEQ ID NO: 14), and an Escherichia coli thioesterase (see, e.g., Genbank Accession No.
  • FIG. 9 is a bar graph summarizing the change in absorbance at 340 nm after 20 minutes, which is a measure of the consumption of NADPH and activity of five carboxylate reductase preparations in enzyme only controls (no substrate).
  • FIG. 10 is a bar graph of the change in absorbance at 340 nm after 20 minutes, which is a measure of the consumption of NADPH and activity of a carboxylate reductase preparation for converting glutarate methyl ester to glutarate semialdehyde methyl ester relative to the empty vector control.
  • FIG. 11 is a table of conversion after 1 hour of glutaryl-CoA methyl ester to glutaryl-CoA by pimeloyl-[acp] methyl ester methylesterase.
  • This document provides enzymes, non-natural pathways, cultivation strategies, feedstocks, host microorganisms and attenuations to the host's biochemical network, which can be used to synthesize 2,4-pentadienoyl-CoA and, optionally, 1,3-butadiene (also known as buta-1,3 -diene, biethylene, or vinylethylene) from central precursors or central metabolites.
  • 1,3-butadiene also known as buta-1,3 -diene, biethylene, or vinylethylene
  • Production of butadiene thus can proceed through a common intermediate, 2,4-pentadienoyl-CoA, even though there are a number of different feedstocks and different pathways that can be used to produce 2,4-pentadienoyl-CoA.
  • malonyl-CoA or malonyl-[acp] can be used to produce 2,4-pentadienoyl-CoA via different methyl-ester shielded routes.
  • central precursor is used to denote any metabolite in any metabolic pathway shown herein leading to the synthesis of 5-hydroxypentanoate, 2,4-pentadienoyl-CoA or butadiene.
  • central metabolite is used herein to denote a metabolite that is produced in all microorganisms to support growth.
  • host microorganisms described herein can include endogenous pathways that can be manipulated such that 2,4-pentadienoyl-CoA can be produced.
  • an endogenous pathway the host microorganism naturally expresses all of the enzymes catalyzing the reactions within the pathway.
  • a host microorganism containing an engineered pathway does not naturally express all of the enzymes catalyzing the reactions within the pathway but has been engineered such that all of the enzymes within the pathway are expressed in the host.
  • exogenous refers to a nucleic acid that does not occur in (and cannot be obtained from) a cell of that particular type as it is found in nature or a protein encoded by such a nucleic acid.
  • a non-naturally-occurring nucleic acid is considered to be exogenous to a host once in the host. It is important to note that non-naturally-occurring nucleic acids can contain nucleic acid subsequences or fragments of nucleic acid sequences that are found in nature provided the nucleic acid as a whole does not exist in nature.
  • a nucleic acid molecule containing a genomic DNA sequence within an expression vector is non-naturally-occurring nucleic acid, and thus is exogenous to a host cell once introduced into the host, since that nucleic acid molecule as a whole (genomic DNA plus vector DNA) does not exist in nature.
  • any vector, autonomously replicating plasmid, or virus e.g., retrovirus, adenovirus, or herpes virus
  • genomic DNA fragments produced by PCR or restriction endonuclease treatment as well as cDNAs are considered to be non-naturally-occurring nucleic acid since they exist as separate molecules not found in nature. It also follows that any nucleic acid containing a promoter sequence and polypeptide-encoding sequence (e.g., cDNA or genomic DNA) in an arrangement not found in nature is non-naturally-occurring nucleic acid.
  • a nucleic acid that is naturally-occurring can be exogenous to a particular host microorganism. For example, an entire chromosome isolated from a cell of yeast x is an exogenous nucleic acid with respect to a cell of yeast y once that chromosome is introduced into a cell of yeast y.
  • the term “endogenous” as used herein with reference to a nucleic acid (e.g., a gene) (or a protein) and a host refers to a nucleic acid (or protein) that does occur in (and can be obtained from) that particular host as it is found in nature.
  • a cell “endogenously expressing” a nucleic acid (or protein) expresses that nucleic acid (or protein) as does a host of the same particular type as it is found in nature.
  • a host “endogenously producing” or that “endogenously produces” a nucleic acid, protein, or other compound produces that nucleic acid, protein, or compound as does a host of the same particular type as it is found in nature.
  • one or more of the following enzymes may be expressed in the host including a malonyl-[acp] O-methyltransferase, a pimeloyl-[acp] methyl ester methylesterase, an esterase, a reversible CoA-ligase, CoA-transferase, a 4-hydroxybutyrate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, a 6-hydroxyhexanoate dehydrogenase, an alcohol dehydrogenase, a 5-oxopentanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, a 7-oxoheptanoate dehydrogenase, an aldehyde dehydrogenase, or a carboxylate reductase.
  • a carboxylate reductase a malonyl-[acp] O-methyltransferase, a pi
  • This document also features a recombinant host that includes at least one exogenous nucleic acid encoding (i) a polypeptide having malonyl-[acp] O-methyltransferase activity, (ii) a polypeptide having pimeloyl-[acp] methyl ester methylesterase activity and (iii) a polypeptide having thioesterase activity, and produce glutarate methyl ester, glutaryl-[acp] or glutaryl-CoA.
  • Such a recombinant host producing glutarate methyl ester further can include a polypeptide having esterase activity, and further produce glutaric acid.
  • Such a recombinant host producing glutaryl-[acp] further can include a polypeptide having thioesterase activity and produce glutaric acid.
  • Such a recombinant host producing glutaryl-CoA further can include one or more of (i) a polypeptide having thioesterase activity, (ii) a polypeptide having reversible CoA-ligase activity, (iii) a polypeptide having CoA-transferase activity, or (iv) a polypeptide having acylating dehydrogenase activity, and (v) a polypeptide having aldehyde dehydrogenase activity such as a 7-oxoheptanoate dehydrogenase, 6-oxohexanoate dehydrogenase or 5-oxopentanoate dehydrogenase activity and further produce glutaric acid or 5-oxopentanoate.
  • a recombinant host producing 5-oxopentanoate or glutaric acid further can include one or more of (i) a polypeptide having alcohol dehydrogenase activity or (ii) a polypeptide having carboxylate reductase activity and further produce 5-hydroxypentanoate.
  • a recombinant host producing glutarate methyl ester further can include one or more of (i) a polypeptide having alcohol dehydrogenase activity, (ii) a polypeptide having esterase activity or (iii) a polypeptide having carboxylate reductase activity and further produce 5-hydroxypentanoate.
  • the enzymes can be from a single source, i.e., from one species or genus, or can be from multiple sources, i.e., different species or genera.
  • Nucleic acids encoding the enzymes described herein have been identified from various organisms and are readily available in publicly available databases such as GenBank or EMBL.
  • any of the enzymes described herein that can be used for production of one or more C5 building blocks can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of the corresponding wild-type enzyme.
  • sequence identity can be determined on the basis of the mature enzyme (e.g., with any signal sequence removed) or on the basis of the immature enzyme (e.g., with any signal sequence included).
  • the initial methionine residue may or may not be present on any of the enzyme sequences described herein.
  • a polypeptide having pimeloyl-[acp] methyl ester methylesterase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of an Escherichia coli (see Genbank Accession Nos. AAC76437.1, SEQ ID NO: 1)pimeloyl-[acp] methyl ester methylesterase. See FIG. 1-3 .
  • a polypeptide having carboxylate reductase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Mycobacterium marinum (see Genbank Accession No. ACC40567.1, SEQ ID NO: 2), a Mycobacterium smegmatis (see Genbank Accession No. ABK71854.1, SEQ ID NO: 3), a Segniliparus rugosus (see Genbank Accession No.
  • EFV11917.1, SEQ ID NO: 4 a Mycobacterium smegmatis (see Genbank Accession No. ABK75684.1, SEQ ID NO: 5), a Mycobacterium massiliense (see Genbank Accession No. EIV11143.1, SEQ ID NO: 6), or a Segniliparus rotundus (see Genbank Accession No. ADG98140.1, SEQ ID NO: 7) carboxylate reductase. See, FIG. 5 .
  • a polypeptide having phosphopantetheinyl transferase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Bacillus subtilis phosphopantetheinyl transferase (see Genbank Accession No. CAA44858.1, SEQ ID NO: 16) or a Nocardia sp. NRRL 5646 phosphopantetheinyl transferase (see Genbank Accession No. ABI83656.1, SEQ ID NO: 17). See FIG. 5 .
  • a polypeptide having esterase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Pseudomonas fluorescens esterase (see Genbank Accession Nos. AAC60471.2, SEQ ID NO: 8). See FIG. 4, 5 .
  • a polypeptide having thioesterase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Lactobacillus brevis acyl-[acp] thioesterase (see Genbank Accession Nos. ABJ63754.1, SEQ ID NO: 9), a Lactobacillus plantarum acyl-[acp] thioesterase (see Genbank Accession Nos. CCC78182.1, SEQ ID NO: 10), or a Escherichia coli thioesterase (see Genbank Accession Nos. AAB59067.1 or AAA24665.1, SEQ ID NO: 14 or 15). See FIG. 4 .
  • a polypeptide having malonyl-[acp] O-methyltransferase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Bacillus cereus (see Genbank Accession Nos. AAP11034.1, SEQ ID NO: 13) malonyl-[acp] O-methyltransferase. See FIG. 1-3 .
  • a polypeptide having enoyl-CoA reductase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Treponema denticola (see Genbank Accession Nos. AAS11092.1, SEQ ID NO:11), or a Euglena gracilis (see Genbank Accession Nos. AAW66853.1, SEQ ID NO:12) enoyl-CoA reductase. See FIGS. 1-3 .
  • sequence identity e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%
  • the percent identity (homology) between two amino acid sequences can be determined as follows. First, the amino acid sequences are aligned using the BLAST 2 Sequences (B12seq) program from the stand-alone version of BLASTZ containing BLASTP version 2.0.14. This stand-alone version of BLASTZ can be obtained from Fish & Richardson's web site (e.g., www.fr.com/blast/) or the U.S. government's National Center for Biotechnology Information web site (www.ncbi.nlm.nih.gov). Instructions explaining how to use the B12seq program can be found in the readme file accompanying BLASTZ. B12seq performs a comparison between two amino acid sequences using the BLASTP algorithm.
  • B12seq performs a comparison between two amino acid sequences using the BLASTP algorithm.
  • B12seq are set as follows: -i is set to a file containing the first amino acid sequence to be compared (e.g., C: ⁇ seq1.txt); -j is set to a file containing the second amino acid sequence to be compared (e.g., C: ⁇ seq2.txt); -p is set to blastp; -o is set to any desired file name (e.g., C: ⁇ output.txt); and all other options are left at their default setting.
  • -i is set to a file containing the first amino acid sequence to be compared (e.g., C: ⁇ seq1.txt)
  • -j is set to a file containing the second amino acid sequence to be compared (e.g., C: ⁇ seq2.txt)
  • -p is set to blastp
  • -o is set to any desired file name (e.g., C: ⁇ output.txt); and all other options are left at their
  • the following command can be used to generate an output file containing a comparison between two amino acid sequences: C: ⁇ B12seq -i c: ⁇ seq1.txt -j c: ⁇ seq2.txt -p blastp -o c: ⁇ output.txt. If the two compared sequences share homology (identity), then the designated output file will present those regions of homology as aligned sequences. If the two compared sequences do not share homology (identity), then the designated output file will not present aligned sequences. Similar procedures can be following for nucleic acid sequences except that blastn is used.
  • the number of matches is determined by counting the number of positions where an identical amino acid residue is presented in both sequences.
  • the percent identity (homology) is determined by dividing the number of matches by the length of the full-length polypeptide amino acid sequence followed by multiplying the resulting value by 100. It is noted that the percent identity (homology) value is rounded to the nearest tenth. For example, 78.11, 78.12, 78.13, and 78.14 is rounded down to 78.1, while 78.15, 78.16, 78.17, 78.18, and 78.19 is rounded up to 78.2. It also is noted that the length value will always be an integer.
  • nucleic acids can encode a polypeptide having a particular amino acid sequence.
  • the degeneracy of the genetic code is well known to the art; i.e., for many amino acids, there is more than one nucleotide triplet that serves as the codon for the amino acid.
  • codons in the coding sequence for a given enzyme can be modified such that optimal expression in a particular species (e.g., bacteria or fungus) is obtained, using appropriate codon bias tables for that species.
  • Functional fragments of any of the enzymes described herein can also be used in the methods of the document.
  • the term “functional fragment” as used herein refers to a peptide fragment of a protein that has at least 25% (e.g., at least: 30%; 40%; 50%; 60%; 70%; 75%; 80%; 85%; 90%; 95%; 98%; 99%; 100%; or even greater than 100%) of the activity of the corresponding mature, full-length, wild-type protein.
  • the functional fragment can generally, but not always, be comprised of a continuous region of the protein, wherein the region has functional activity.
  • This document also provides (i) functional variants of the enzymes used in the methods of the document and (ii) functional variants of the functional fragments described above.
  • Functional variants of the enzymes and functional fragments can contain additions, deletions, or substitutions relative to the corresponding wild-type sequences.
  • Enzymes with substitutions will generally have not more than 50 (e.g., not more than one, two, three, four, five, six, seven, eight, nine, ten, 12, 15, 20, 25, 30, 35, 40, or 50) amino acid substitutions (e.g., conservative substitutions). This applies to any of the enzymes described herein and functional fragments.
  • a conservative substitution is a substitution of one amino acid for another with similar characteristics.
  • Conservative substitutions include substitutions within the following groups: valine, alanine and glycine; leucine, valine, and isoleucine; aspartic acid and glutamic acid; asparagine and glutamine; serine, cysteine, and threonine; lysine and arginine; and phenylalanine and tyrosine.
  • the nonpolar hydrophobic amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine.
  • the polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine and glutamine.
  • the positively charged (basic) amino acids include arginine, lysine and histidine.
  • the negatively charged (acidic) amino acids include aspartic acid and glutamic acid. Any substitution of one member of the above-mentioned polar, basic or acidic groups by another member of the same group can be deemed a conservative substitution. By contrast, a nonconservative substitution is a substitution of one amino acid for another with dissimilar characteristics.
  • Deletion variants can lack one, two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid segments (of two or more amino acids) or non-contiguous single amino acids.
  • Additions include fusion proteins containing: (a) any of the enzymes described herein or a fragment thereof; and (b) internal or terminal (C or N) irrelevant or heterologous amino acid sequences.
  • heterologous amino acid sequences refers to an amino acid sequence other than (a).
  • a heterologous sequence can be, for example a sequence used for purification of the recombinant protein (e.g., FLAG, polyhistidine (e.g., hexahistidine), hemagglutinin (HA), glutathione-S-transferase (GST), or maltosebinding protein (MBP)).
  • Heterologous sequences also can be proteins useful as detectable markers, for example, luciferase, green fluorescent protein (GFP), or chloramphenicol acetyl transferase (CAT).
  • the fusion protein contains a signal sequence from another protein.
  • the fusion protein can contain a carrier (e.g., KLH) useful, e.g., in eliciting an immune response for antibody generation) or ER or Golgi apparatus retention signals.
  • a carrier e.g., KLH
  • Heterologous sequences can be of varying length and in some cases can be a longer sequences than the full-length target proteins to which the heterologous sequences are attached.
  • Engineered hosts can naturally express none or some (e.g., one or more, two or more, three or more, four or more, five or more, or six or more) of the enzymes of the pathways described herein.
  • a pathway within an engineered host can include all exogenous enzymes, or can include both endogenous and exogenous enzymes.
  • Endogenous genes of the engineered hosts also can be disrupted to prevent the formation of undesirable metabolites or prevent the loss of intermediates in the pathway through other enzymes acting on such intermediates.
  • Engineered hosts can be referred to as recombinant hosts or recombinant host cells.
  • recombinant hosts can include nucleic acids encoding one or more polypeptide having the activity of a reductase, deacetylase, N-acetyltransferase, malonyl-[acp] O-methyltransferase, esterase, thioesterase, hydratase, dehydrogenase, CoA-ligase, and/or CoA-transferase as described herein.
  • the production of one or more C5 building blocks can be performed in vitro using the isolated enzymes described herein, using a lysate (e.g., a cell lysate) from a host microorganism as a source of the enzymes, or using a plurality of lysates from different host microorganisms as the source of the enzymes.
  • a lysate e.g., a cell lysate
  • a terminal carboxyl group can be enzymatically formed using (i) a polypeptide having thioesterase activity, (ii) a polypeptide having reversible CoA-ligase activity, (iii) a polypeptide having CoA-transferase activity, (iv) a polypeptide having acylating dehydrogenase activity, or (v) a polypeptide having aldehyde dehydrogenase activity such as a 7-oxoheptanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, or a 5-oxopentanoate dehydrogenase activity, or (vi) a polypeptide having esterase activity.
  • a terminal carboxyl group leading to the synthesis of glutarate is enzymatically formed by a thioesterase classified under EC 3.1.2.—, such as the gene product of YciA (SEQ ID NO: 14), tesB (Genbank Accession No. AAA24665.1, SEQ ID NO: 15) or Acot13 (see, for example, Cantu et al., Protein Science, 2010, 19, 1281-1295; Zhuang et al., Biochemistry, 2008, 47(9), 2789-2796; or Naggert et al., J. Biol. Chem., 1991, 266(17), 11044-11050).
  • a thioesterase classified under EC 3.1.2.— such as the gene product of YciA (SEQ ID NO: 14), tesB (Genbank Accession No. AAA24665.1, SEQ ID NO: 15) or Acot13 (see, for example, Cantu et al., Protein Science, 2010, 19, 1281-1295;
  • the second terminal carboxyl group leading to the synthesis of glutaric acid is enzymatically formed by a CoA-transferase such as a glutaconate CoA-transferase classified, for example, under EC 2.8.3.12 such as from Acidaminococcus fermentans . See, for example, Buckel et al., 1981, Eur. J. Biochem., 118:315-321. FIG. 4 .
  • the second terminal carboxyl group leading to the synthesis of glutaric acid is enzymatically formed by a reversible CoA-ligase such as a succinate-CoA ligase classified, for example, under EC 6.2.1.5 such as from Thermococcus kodakaraensis . See, for example, Shikata et al., 2007, J. Biol. Chem., 282(37):26963-26970.
  • the second terminal carboxyl group leading to the synthesis of glutaric acid is enzymatically formed by an acyl-[acp] thioesterase classified under EC 3.1.2.—, such as the acyl-[acp] thioesterase from Lactobacillus brevis (GenBank Accession No. ABJ63754.1, SEQ ID NO: 9) or from Lactobacillus plantarum (GenBank Accession No. CCC78182.1, SEQ ID NO: 10).
  • Such acyl-[acp] thioesterases have C6-C8 chain length specificity (see, for example, Jing et al., 2011, BMC Biochemistry, 12(44)). See, e.g., FIG. 4 .
  • the second terminal carboxyl group leading to the synthesis of glutaric acid is enzymatically formed by an aldehyde dehydrogenase classified, for example, under EC 1.2.1.3 (see, Guerrillot & Vandecasteele, Eur. J. Biochem., 1977, 81, 185-192). See, FIG. 4 .
  • the second terminal carboxyl group leading to the synthesis of glutaric acid is enzymatically formed by an aldehyde dehydrogenase classified under EC 1.2.1.—such as a glutarate semialdehyde dehydrogenase classified, for example, under EC 1.2.1.20, a succinate-semialdehyde dehydrogenase classified, for example, under EC 1.2.1.16 or EC 1.2.1.79, or an aldehyde dehydrogenase classified under EC 1.2.1.3.
  • an aldehyde dehydrogenase classified under EC 1.2.1. such as a glutarate semialdehyde dehydrogenase classified, for example, under EC 1.2.1.20, a succinate-semialdehyde dehydrogenase classified, for example, under EC 1.2.1.16 or EC 1.2.1.79, or an aldehyde dehydrogenase classified under EC 1.2.1.3.
  • a 5-oxopentanoate dehydrogenase such as the gene product of CpnE
  • a 6-oxohexanoate dehydrogenase e.g., the gene product of ChnE from Acinetobacter s
  • a 6-oxohexanoate dehydrogenase can be classified under EC 1.2.1.63 such as the gene product of ChnE.
  • a 7-oxoheptanoate dehydrogenase can be classified under EC 1.2.1.-.
  • the second terminal carboxyl group leading to the synthesis of glutaric acid is enzymatically formed by a polypeptide having esterase activity such as an esterase classified under EC 3.1.1.—such as EC 3.1.1.1 or EC 3.1.1.6.
  • a terminal hydroxyl group can be enzymatically formed using an alcohol dehydrogenase such as a 6-hydroxyhexanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, or a 4-hydroxybutyrate dehydrogenase.
  • an alcohol dehydrogenase such as a 6-hydroxyhexanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, or a 4-hydroxybutyrate dehydrogenase.
  • a terminal hydroxyl group leading to the synthesis of 5-hydroxypentanoate can be enzymatically formed by a dehydrogenase classified, for example, under EC 1.1.1.—such as a 6-hydroxyhexanoate dehydrogenase classified, for example, under EC 1.1.1.258 (e.g., the gene from of ChnD), a 5-hydroxypentanoate dehydrogenase classified, for example, under EC 1.1.1.—such as the gene product of CpnD (see, for example, Iwaki et al., 2002, Appl. Environ.
  • a terminal vinyl group can be enzymatically formed using a dehydratase such as 5-hydroxypentanoyl-CoA dehydratase from Clostridium viride (Eikmanns and Buckel, 1991, Eur. J. Biochem., 197, 661-668).
  • a dehydratase such as 5-hydroxypentanoyl-CoA dehydratase from Clostridium viride (Eikmanns and Buckel, 1991, Eur. J. Biochem., 197, 661-668).
  • glutarate methyl ester can be synthesized from malonyl-[acp] by conversion of malonyl-[acp] to malonyl-[acp] methyl ester by a malonyl-CoA O-methyltransferase classified, for example, under EC 2.1.1.197 such as the gene product of bioC; followed by conversion to 3-oxoglutaryl-[acp] methyl ester by condensation with malonyl-[acp] and a ⁇ -ketoacyl-[acp] synthase classified, for example, under EC 2.3.1.—such as EC 2.3.1.41, EC 2.3.1.179 or EC 2.3.1.180 (e.g., the gene product of fabB, fabF or fabH); followed by conversion to 3-hydroxy-glutaryl-[acp] methyl ester by a 3-hydroxyacyl-CoA dehydrogenase classified, for example, under EC 1.1.1.
  • EC 2.3.1.
  • AAO77182 or a Lactobacillus plantarum acyl-CoA thioesterase (GenBank Accession No. CCC78182.1) or (ii) conversion to glutaryl-[acp] by a pimeloyl-[acp] methyl ester methylesterase classified, for example, under EC 3.1.1.85 such as bioH(SEQ ID NO: 1).
  • glutarate methyl ester can be synthesized from malonyl-CoA by conversion of malonyl-CoA to malonyl-CoA methyl ester by a malonyl-CoA O-methyltransferase classified, for example, under EC 2.1.1.197 such as the gene product of bioC; followed by conversion to 3-oxoglutaryl-CoA methyl ester by condensation with acetyl-CoA by a ⁇ -ketothiolase classified, for example, under EC 2.3.1.16 such as the gene product of bktB or by condensation with malonyl-CoA by a ⁇ -ketoacyl-[acp] synthase classified, for example, under EC 2.3.1.180 such as the gene product of fabH; followed by conversion to 3-hydroxy-glutaryl-CoA methyl ester by a 3-hydroxyacyl-CoA dehydrogenase classified, for example, under EC 1.1.1.—such as EC
  • AAO77182 or a Lactobacillus plantarum acyl-ACP thioesterase (GenBank Accession No. CCC78182.1) or (ii) conversion to glutaryl-CoA by a pimeloyl-[acp] methyl ester methylesterase classified, for example, under EC 3.1.1.85 such as bioH (SEQ ID NO: 1).
  • glutarate methyl ester can be synthesized from malonyl-CoA by conversion of malonyl-CoA to malonyl-CoA methyl ester by a malonyl-CoA O-methyltransferase classified, for example, under EC 2.1.1.197 such as the gene product of bioC; followed by conversion to 3-oxoglutaryl-CoA methyl ester by condensation with acetyl-CoA by a ⁇ -ketothiolase classified, for example, under EC 2.3.1.16 such as the gene product of bktB or by condensation with malonyl-CoA by a ⁇ -ketoacyl-[acp] synthase classified, for example, under EC 2.3.1.180 such as the gene product of fabH; followed by conversion to 3-hydroxy-glutaryl-CoA methyl ester by a 3-hydroxyacyl-CoA dehydrogenase classified, for example, under EC 1.1.1.—such as EC
  • AAO77182 or a Lactobacillus plantarum acyl-CoA thioesterase (GenBank Accession No. CCC78182.1) or (ii) conversion to glutaryl-CoA by a pimeloyl-[acp] methyl ester methylesterase classified, for example, under EC 3.1.1.85 such as bioH (SEQ ID NO: 1).
  • glutarate methyl ester can be converted to glutarate by an esterase classified, for example, EC 3.1.1.—, such as EC 3.1.1.1 or EC 3.1.1.6 such as estC (SEQ ID NO: 8).
  • esterase classified, for example, EC 3.1.1.—, such as EC 3.1.1.1 or EC 3.1.1.6 such as estC (SEQ ID NO: 8).
  • glutaryl-CoA can be converted to glutarate by a (i) a thioesterase classified, for example, EC 3.1.2.—, such as the tesB (SEQ ID NO:15), YciA (SEQ ID NO:14) or Acot13, a Bacteroides thetaiotaomicron acyl-ACP thioesterase (GenBank Accession No. AAO77182) or a Lactobacillus plantarum acyl-CoA thioesterase (GenBank Accession No.
  • a 5-oxovalerate dehydrogenase such as the gene product of CpnE
  • a 6-oxohexanoate dehydrogenase such as the gene product of ChnE
  • a 7-oxoheptanoate dehydrogenase e.g., the gene product of ThnG from Sphingomonas macrogolitabida
  • a 5-oxovalerate dehydrogenase such as the gene product of CpnE
  • a 6-oxohexanoate dehydrogenase such as the gene product of ChnE
  • a 7-oxoheptanoate dehydrogenase e.g., the gene product of ThnG from Sphingomonas macrogolitabida
  • glutaryl-[acp] can be converted to glutarate by a thioesterase classified, for example, EC 3.1.2.-, such as the tesB (SEQ ID NO:15), YciA (SEQ ID NO:14) or Acot13, a Bacteroides thetaiotaomicron acyl-ACP thioesterase (GenBank Accession No. AAO77182) or a Lactobacillus plantarum acyl-CoA thioesterase (GenBank Accession No. CCC78182.1).
  • a thioesterase classified, for example, EC 3.1.2.-, such as the tesB (SEQ ID NO:15), YciA (SEQ ID NO:14) or Acot13, a Bacteroides thetaiotaomicron acyl-ACP thioesterase (GenBank Accession No. AAO77182) or a Lactobacillus plantarum acyl-CoA thio
  • 5 -hydroxypentanoate can be synthesized from the central precursor glutarate methyl ester by conversion of glutarate methyl ester to glutaric acid by an esterase classified under EC 3.1.1.—(e.g., the gene product of estC) such as a carboxyl esterase classified under EC 3.1.1.1 or an acetylesterase classified under EC 3.1.1.6; followed by conversion of glutaric acid to glutarate semialdehyde by a carboxylate reductase classified, for example, under EC 1.2.99.6 such as the gene product of car in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp (Genbank Accession No.
  • 5 -hydroxypentanoate can be synthesized from the central precursor glutarate methyl ester by conversion of glutarate methyl ester to glutarate semialdehyde methyl ester by a carboxylate reductase classified, for example, under EC 1.2.99.6 such as from a Mycobacterium marinum (see Genbank Accession No. ACC40567.1, SEQ ID NO: 2), a Mycobacterium smegmatis (see Genbank Accession No. ABK71854.1, SEQ ID NO: 3), a Mycobacterium massiliense (see Genbank Accession No.
  • EIV11143.1, SEQ ID NO: 6), or a Segniliparus rotundus see Genbank Accession No. ADG98140.1, SEQ ID NO: 7
  • a phosphopantetheine transferase enhancer e.g., encoded by a sfp (Genbank Accession No. CAA44858.1, SEQ ID NO:16) gene from Bacillus subtilis or npt (Genbank Accession No. ABI83656.1, SEQ ID NO:17) gene from Nocardia
  • GriC & GriD the gene product of GriC & GriD
  • 5 -hydroxypentanoate can be synthesized from the central precursor glutarate methyl ester by conversion of glutarate methyl ester to glutarate semialdehyde methyl ester by a carboxylate reductase classified, for example, under EC 1.2.99.6 such as from a Mycobacterium marinum (see Genbank Accession No. ACC40567.1, SEQ ID NO: 2), a Mycobacterium smegmatis (see Genbank Accession No. ABK71854.1, SEQ ID NO: 3), a Mycobacterium massiliense (see Genbank Accession No.
  • EIV11143.1, SEQ ID NO: 6), or a Segniliparus rotundus see Genbank Accession No. ADG98140.1, SEQ ID NO: 7
  • a phosphopantetheine transferase enhancer e.g., encoded by a sfp (Genbank Accession No. CAA44858.1, SEQ ID NO:16) gene from Bacillus subtilis or npt (Genbank Accession No. ABI83656.1, SEQ ID NO:17) gene from Nocardia
  • GriC & GriD the gene product of GriC & GriD
  • 2,4 -pentadienoyl-CoA can be synthesized from 5-hydroxypentanoate by conversion of 5-hydroxypentanoate to 5-hydroxypentanoyl-CoA by a 5-hydroxypentanoate CoA-transferase or 4-hydroxybutryrate CoA-transferase classified, for example, under EC 2.8.3.—such as EC 2.8.3.14 or EC 2.8.3.9 or by a synthase classified, for example, under EC 6.2.1.—such as a 3-hydroxypropionyl-CoA synthase classified under EC 6.2.1.36; followed by conversion to 2,4-pentadienoyl-CoA by a dehydratase such as 5-hydroxypentanoy-CoA dehydratase classified, for example, under EC 4.2.1.—obtained from Clostridium viride.
  • the cultivation strategy entails achieving an aerobic, anaerobic, micro-aerobic, or mixed oxygen/denitrification cultivation condition.
  • Enzymes characterized in vitro as being oxygen sensitive require a micro-aerobic cultivation strategy maintaining a very low dissolved oxygen concentration (See, for example, Chayabatra & Lu-Kwang, AppL Environ. Microbiol., 2000, 66(2), 493 0 498; Wilson and Bouwer, 1997, Journal of Industrial Microbiology and Biotechnology, 18(2-3), 116-130).
  • a cyclical cultivation strategy entails alternating between achieving an anaerobic cultivation condition and achieving an aerobic cultivation condition.
  • the cultivation strategy entails nutrient limitation such as nitrogen, phosphate or oxygen limitation.
  • a final electron acceptor other than oxygen such as nitrates can be utilized.
  • a cell retention strategy using, for example, ceramic membranes can be employed to achieve and maintain a high cell density during either fed-batch or continuous fermentation.
  • the principal carbon source fed to the fermentation in the synthesis of one or more C5 building blocks can derive from biological or non-biological feedstocks.
  • the biological feedstock can be or can derive from, monosaccharides, disaccharides, lignocellulose, hemicellulose, cellulose, lignin, levulinic acid and formic acid, triglycerides, glycerol, fatty acids, agricultural waste, condensed distillers' solubles, or municipal waste.
  • fermentable sugars such as monosaccharides and disaccharides derived from cellulosic, hemicellulosic, cane and beet molasses, cassava, corn and other agricultural sources has been demonstrated for several microorganism such as Escherichia coli, Corynebacterium glutamicum and Lactobacillus delbrueckii and Lactococcus lactis (see, e.g., Hermann et al, J. Biotechnol., 2003, 104:155-172; Wee et al., Food Technol. Biotechnol., 2006, 44(2):163-172; Ohashi et al., J. Bioscience and Bioengineering, 1999, 87(5):647-654).
  • microorganism such as Escherichia coli, Corynebacterium glutamicum and Lactobacillus delbrueckii and Lactococcus lactis
  • the non-biological feedstock can be or can derive from natural gas, syngas, CO 2 /H 2 , methanol, ethanol, benzoate, non-volatile residue (NVR) or a caustic wash waste stream from cyclohexane oxidation processes, or terephthalic acid/isophthalic acid mixture waste streams.
  • the present document provides methods involving less than all the steps described for all the above pathways. Such methods can involve, for example, one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve or more of such steps. Where less than all the steps are included in such a method, the first, and in some embodiments the only, step can be any one of the steps listed.
  • recombinant hosts described herein can include any combination of the above enzymes such that one or more of the steps, e.g., one, two, three, four, five, six, seven, eight, nine, ten, or more of such steps, can be performed within a recombinant host.
  • This document provides host cells of any of the genera and species listed and genetically engineered to express one or more (e.g., two, three, four, five, six, seven, eight, nine, 10, 11, 12 or more) recombinant forms of any of the enzymes recited in the document.
  • the host cells can contain exogenous nucleic acids encoding enzymes catalyzing one or more of the steps of any of the pathways described herein.
  • the enzymes in the pathways outlined herein are the result of enzyme engineering via non-direct or rational enzyme design approaches with aims of improving activity, improving specificity, reducing feedback inhibition, reducing repression, improving enzyme solubility, changing stereo-specificity, or changing co-factor specificity.
  • the enzymes in the pathways outlined here can be gene dosed, i.e., overexpressed, into the resulting genetically modified organism via episomal or chromosomal integration approaches.
  • genome-scale system biology techniques such as Flux Balance Analysis can be utilized to devise genome scale attenuation or knockout strategies for directing carbon flux to a 2,4-pentadienoyl-CoA.
  • Attenuation strategies include, but are not limited to; the use of transposons, homologous recombination (double cross-over approach), mutagenesis, enzyme inhibitors and RNAi interference.
  • fluxomic, metabolomic and transcriptomal data can be utilized to inform or support genome-scale system biology techniques, thereby devising genome scale attenuation or knockout strategies in directing carbon flux to 2,4-pentadienoyl-CoA.
  • the host microorganism's tolerance to high concentrations of 2,4-pentadienoyl-CoA can be improved through continuous cultivation in a selective environment.
  • the host microorganism's endogenous biochemical network can be attenuated or augmented to (1) ensure the intracellular availability of acetyl-CoA, (2) create a NADH or NADPH imbalance that may be balanced via the formation of 2,4-pentadienoyl-CoA, and/or (3) prevent degradation of central metabolites, central precursors leading to and including 2,4-pentadienoyl-CoA.
  • endogenous enzymes catalyzing the hydrolysis of acetyl-CoA such as short-chain length thioesterases can be attenuated in the host organism.
  • one or more endogenous ⁇ -ketothiolases catalyzing the condensation of only acetyl-CoA to acetoacetyl-CoA such as the endogenous gene products of AtoB or phaA can be attenuated.
  • an endogenous phosphotransacetylase generating acetate such as pta can be attenuated (Shen et al., Appl. Environ. Microbiol., 2011, 77(9):2905-2915).
  • an endogenous gene in an acetate synthesis pathway encoding an acetate kinase, such as ack can be attenuated.
  • an endogenous gene encoding an enzyme that catalyzes the degradation of pyruvate to lactate such as a lactate dehydrogenase encoded by ldhA can be attenuated (Shen et al., 2011, supra).
  • endogenous genes encoding enzymes such as menaquinol-fumarate oxidoreductase, that catalyze the degradation of phophoenolpyruvate to succinate such as frdBC can be attenuated (see, e.g., Shen et al., 2011, supra).
  • an endogenous gene encoding an enzyme that catalyzes the degradation of acetyl-CoA to ethanol such as the alcohol dehydrogenase encoded by adhE can be attenuated (Shen et al., 2011, supra).
  • a recombinant formate dehydrogenase gene can be overexpressed in the host organism (Shen et al., 2011, supra).
  • acetyl-CoA carboxylase can be overexpressed in the host organisms.
  • one or more of 3-phosphoglycerate dehydrogenase, 3-phosphoserine aminotransferase and phosphoserine phosphatase can be overexpressed in the host to generate serine as a methyl donor for the S-Adenosyl-L-methionine cycle.
  • a methanol dehydrogenase or a formaldehyde dehydrogenase can be overexpressed in the host to allow methanol catabolism via formate.
  • a transhydrogenase dissipating the cofactor imbalance can be attenuated.
  • an endogenous gene encoding an enzyme that catalyzes the degradation of pyruvate to ethanol such as pyruvate decarboxylase can be attenuated.
  • an endogenous gene encoding an enzyme that catalyzes the generation of isobutanol such as a 2-oxoacid decarboxylase can be attenuated.
  • a recombinant acetyl-CoA synthetase such as the gene product of acs can be overexpressed in the microorganism (Satoh et al., J. Bioscience and Bioengineering, 2003, 95(4):335-341).
  • carbon flux can be directed into the pentose phosphate cycle to increase the supply of NADPH by attenuating an endogenous glucose-6-phosphate isomerase (EC 5.3.1.9).
  • carbon flux can be redirected into the pentose phosphate cycle to increase the supply of NADPH by overexpression a 6-phosphogluconate dehydrogenase and/or a transketolase (Lee et al., 2003, Biotechnology Progress, 19(5), 1444-1449).
  • a gene such as UdhA encoding apuridine nucleotide transhydrogenase can be overexpressed in the host organisms (Brigham et al., Advanced Biofuels and Bioproducts, 2012, Chapter 39, 1065-1090).
  • a recombinant glyceraldehyde-3-phosphate-dehydrogenase gene such as GapN can be overexpressed in the host organisms (Brigham et al., 2012, supra).
  • a recombinant malic enzyme gene such as maeA or maeB can be overexpressed in the host organisms (Brigham et al., 2012, supra).
  • a recombinant glucose-6-phosphate dehydrogenase gene such as zwf can be overexpressed in the host organisms (Lim et al., J. Bioscience and Bioengineering, 2002, 93(6), 543-549).
  • a recombinant fructose 1,6 diphosphatase gene such as fbp can be overexpressed in the host organisms (Becker et al., J. Biotechnol., 2007, 132:99-109).
  • endogenous triose phosphate isomerase (EC 5.3.1.1) can be attenuated.
  • a recombinant glucose dehydrogenase such as the gene product of gdh can be overexpressed in the host organism (Satoh et al., J. Bioscience and Bioengineering, 2003, 95(4):335-341).
  • endogenous enzymes facilitating the conversion of NADPH to NADH can be attenuated, such as the NADH generation cycle that may be generated via inter-conversion of glutamate dehydrogenases classified under EC 1.4.1.2 (NADH-specific) and EC 1.4.1.4 (NADPH-specific).
  • an endogenous glutamate dehydrogenase (EC 1.4.1.3) that utilizes both NADH and NADPH as co-factors can be attenuated.
  • a membrane-bound enoyl-CoA reductase can be solubilized via expression as a fusion protein to a small soluble protein such as a maltose binding protein (Gloerich et al., FEBS Letters, 2006, 580, 2092-2096).
  • the endogenous polyhydroxyalkanoate synthase enzymes can be attenuated in the host strain.
  • the genes encoding enzymes involved with lipid body synthesis are attenuated.
  • a L-glutamate dehydrogenase, a L-glutamine synthetase, or a glutamate synthase can be overexpressed in the host to regenerate L-glutamate from 2-oxoglutarate as an amino donor for ⁇ -transaminase reactions.
  • enzymes such as pimeloyl-CoA dehydrogenase classified under, EC 1.3.1.62; an acyl-CoA dehydrogenase classified, for example, under EC 1.3.8.7 or EC 1.3.8.1; and/or a glutaryl-CoA dehydrogenase classified, for example, under EC 1.3.8.6 that degrade central metabolites and central precursors leading to and including C5 building blocks can be attenuated.
  • endogenous enzymes activating C5 building blocks via Coenzyme A esterification such as CoA-ligases (e.g., a glutaryl-CoA synthetase) classified under, for example, EC 6.2.1.6 can be attenuated.
  • CoA-ligases e.g., a glutaryl-CoA synthetase classified under, for example, EC 6.2.1.6
  • 2,4-pentadienoyl-CoA can be produced by providing a host microorganism and culturing the provided microorganism with a culture medium containing a suitable carbon source as described above.
  • the culture media and/or culture conditions can be such that the microorganisms grow to an adequate density and produce 2,4-pentadienoyl-CoA efficiently.
  • any method can be used such as those described elsewhere (Manual of Industrial Microbiology and Biotechnology, 2 nd Edition, Editors: A. L. Demain and J. E. Davies, ASM Press; and Principles of Fermentation Technology, P. F. Stanbury and A. Whitaker, Pergamon).
  • a large tank e.g., a 100 gallon, 200 gallon, 500 gallon, or more tank
  • an appropriate culture medium is inoculated with a particular microorganism.
  • the microorganism is incubated to allow biomass to be produced.
  • the broth containing the microorganisms can be transferred to a second tank.
  • This second tank can be any size.
  • the second tank can be larger, smaller, or the same size as the first tank.
  • the second tank is larger than the first such that additional culture medium can be added to the broth from the first tank.
  • the culture medium within this second tank can be the same as, or different from, that used in the first tank.
  • the microorganisms can be incubated to allow for the production of 2,4-pentadienoyl-CoA.
  • any method can be used to produce 1,3-butadiene from 2,4-pentadienoyl-CoA such as depicted in FIG. 7 .
  • the invention is further described in the following examples, which do not limit the scope of the invention described in the claims.
  • a nucleotide sequence encoding a His-tag was added to the genes from Mycobacterium marinum, Mycobacterium smegmatis, Segniliparus rugosus, Mycobacterium massiliense , and Segniliparus rotundus that encode the carboxylate reductases of SEQ ID NOs: 2-4, 6 and 7, respectively (GenBank Accession Nos. ACC40567.1, ABK71854.1, EFV11917.1, EIV11143.1, and ADG98140.1, respectively) (see FIG. 8 ) such that N-terminal HIS tagged carboxylate reductases could be produced.
  • Each of the modified genes was cloned into a pET Duet expression vector alongside a sfp gene encoding a His-tagged phosphopantetheine transferase from Bacillus subtilis , both under control of the T7 promoter.
  • Each expression vector was transformed into a BL21[DE3] E. coli host along with the expression vectors from Example 2.
  • Each resulting recombinant E. coli strain was cultivated at 37° C. in a 250mL shake flask culture containing 50 mL LB media and antibiotic selection pressure, with shaking at 230 rpm. Each culture was induced overnight at 37° C. using an auto-induction media.
  • the enzyme activity assay reaction was initiated by adding purified carboxylate reductase and phosphopantetheine transferase or the empty vector control to the assay buffer containing the glutarate methyl ester and then incubated at room temperature for 20 min.
  • the consumption of NADPH was monitored by absorbance at 340 nm.
  • the enzyme only control without glutarate methyl ester demonstrated low base line consumption of NADPH. See FIG. 9 .
  • a sequence encoding an C-terminal His-tag was added to the gene from Escherichia coli encoding the pimeloyl-[acp] methyl ester methylesterase of SEQ ID NO: 1 (see FIG. 8 ) such that C-terminal HIS tagged pimeloyl-[acp] methyl ester methylesterase could be produced.
  • the resulting modified gene was cloned into a pET28b+ expression vector under control of the T7 promoter and the expression vector was transformed into a BL21[DE3] E. coli host.
  • the resulting recombinant E. coli strain was cultivated at 37° C. in a 500mL shake flask culture containing 100 mL LB media and antibiotic selection pressure, with shaking at 230 rpm. Each culture was induced overnight at 18° C. using 0.3 mM IPTG.
  • the enzyme activity assay reaction was initiated by adding pimeloyl-[acp] methyl ester methylesterase to a final concentration of 10 [ ⁇ M] to the assay buffer containing the glutaryl-CoA methyl ester and incubated at 30° C. for 1 h, with shaking at 250 rpm.
  • the formation of glutaryl-CoA was quantified via LC-MS.
  • the substrate only control without enzyme showed no trace quantities of the substrate glutaryl-CoA. See FIG. 11 .
  • the pimeloyl-[acp] methyl ester methylesterase of SEQ ID NO. 1 accepted glutaryl-CoA methyl ester as substrate and synthesized glutaryl-CoA as reaction product as confirmed via LC-MS. See FIG. 11 .

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