Source: http://www.freepatentsonline.com/y2014/0107377.html
Timestamp: 2019-03-21 01:26:50
Document Index: 202087230

Matched Legal Cases: ['Application No. 2011', 'art 2', 'art 2', 'art 2', 'art 2', 'art 2']

Microorganisms And Methods For Producing Acrylate And Other Products From Propionyl-CoA - THE PROCTER & GAMBLE COMPANY
United States Patent Application 20140107377
This invention relates to microorganisms that convert a carbon source to acrylate or other desirable products using propionyl-CoA as an intermediate. The invention provides genetically engineered microorganisms that carry out the conversion, as well as methods for producing acrylate by culturing the microorganisms. Also provided are microorganisms and methods for converting propionyl-CoA and propionate to 3-hydroxypropionyl-CoA, 3-hydroxypropionate (3-HP) and poly-3-hydroxypropionate.
Xu, Jun (Mason, OH, US)
Saunders, Charles Winston (Fairfield, OH, US)
Velasquez, Juan Estaban (Cincinnati, OH, US)
13/652226
435/136, 435/252.3, 435/252.33, 435/254.11, 435/254.2, 435/257.2
C12P7/40; C07C57/04; C12N1/13; C12N1/15; C12N1/19; C12N1/21
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Daegelen et al., Tracing ancestors and relatives of Escherichia coli B, and the derivation of B strains REL606 and BL21(DE3), J. Mol. Biol., 2009, 394, 634-43.
1. A cultured recombinant microorganism, said microorganism comprising a gene encoding an acyl-CoA oxidase that converts propionyl-CoA in said microorganism to acryloyl-CoA, wherein the gene is over expressed.
2. The microorganism of claim 1 wherein the oxidase is the Arabidopsis thaliana acyl-CoA oxidase (SEQ ID NO: 1).
3. The microorganism of claim 1 that further converts acryloyl-CoA to acrylic acid, wherein the at least one gene selected from the group consisting of CoA thioesterase, CoA transferase, a combination of a phosphate transferase and kinase is expressed.
4. The microorganism of claim 1 that further converts acryloyl-CoA to 3-hydroxypropionyl-CoA, wherein an acryloyl-CoA dehydratase gene is expressed.
5. The microorganism of claim 4 expressing a poly-3-hydroxyalkanoate synthase to produce a poly-3-hydroxypropionate containing poly-3-hydroxyalkanoate.
6. The microorganism of claim 4 that further converts acryloyl-CoA to 3-hydroxypropionic acid, wherein at least one gene selected from the group consisting of a thioesterase and an acyl-CoA transferase is expressed.
7. An acrylic acid producing recombinant microorganism that overproduces propionyl-CoA and which expresses an acyl-CoA oxidase gene.
8. A method for producing acrylic acid wherein propionyl-CoA is converted to acrylic acid comprising the steps of: a) converting propionyl-CoA to acryloyl-CoA; and b) converting acryloyl-CoA to acrylic acid, wherein at least one step is catalyzed by an isolated enzyme.
10. The method of claim 8 in which propionyl-CoA is produced from propionic acid
11. The method of claim 8 wherein threonine is converted to propionyl-CoA comprising the steps of: a) converting threonine to 2-ketobutyrate; and b) converting 2-ketobutyrate to propionyl-CoA;
12. The method of claim 8 in which succinic acid is converted to propionyl-CoA comprising the steps of: a) converting succinic acid to succinyl-CoA; b) converting succinyl-CoA to methymalonyl-CoA; and c) converting methylmalonyl-CoA to propionyl-CoA.
13. The method of claim 8 in which pyruvate is converted to propionyl-CoA comprising the steps of: a) converting pyruvate to citramalate; b) converting citramalate to citraconate; c) converting citraconate to β-methyl-D-malate; d) converting β-methyl-D-malate to 2-ketobutyrate; and e) converting 2-ketobutyrate to propionyl-CoA;
14. The acrylic acid produced by the microorganism of claim 3.
15. The acrylic acid produced by the method of claim 8.
This invention relates to microorganisms that convert a carbon source to acrylate or other desirable products using propionyl-CoA as an intermediate and which can be produced from glucose using a threonine and a 2-keto-butyrate intermediate, from glucose using a citramalate and a 2-keto-butyrate intermediate, or from glucose using succinyl-CoA and methylmalonyl-CoA intermediates. The invention provides genetically engineered microorganisms that carry out the conversion, as well as methods for producing acrylate by culturing the microorganisms or by using isolated enzymes. Also provided are microorganisms and methods for converting the propionyl-CoA to 3-hydroxypropionyl-CoA, 3-hydroxypropionate (3-HP) and poly-3-hydroxypropionate.
One organic chemical used to make super absorbent polymers (used in diapers), plastics, coatings, paints, adhesives, and binders (used in leather, paper and textile products) is acrylic acid. Acrylic acid (IUPAC: prop-2-enoic acid) is the simplest unsaturated carboxylic acid. Traditionally, acrylic acid is made from propene. Propene itself is a byproduct of oil refining from petroleum (i.e., crude oil) and of natural gas production. Disadvantages associated with traditional acrylic acid production are that petroleum is a nonrenewable starting material and that the oil refining process pollutes the environment. Synthesis methods for acrylic acid utilizing other starting materials have not been adopted for widespread use due to expense or environmental concerns. These starting materials included, for example, acetylene, ethenone and ethylene cyanohydrins.
To avoid petroleum-based production, researchers have proposed other methods for producing acrylic acid involving the fermentation of sugars by engineered microorganisms. Straathof et al., Appl Microbiol Biotechnol, 67: 727-734 (2005) discusses conceptual metabolic pathways for acrylic acid production from sugars. The pathways proposed in the article proceed via a lactoyl-CoA, β-alanyl-CoA, 3-hydroxypropionyl-CoA or propanoyl-CoA intermediate in the microorganism. The described dehydratase, ammonia lyase and dehydrogenase reactions required to convert these to the acryloyl-CoA intermediate are all thermodynamically unfavorable in vivo (Jiang et. al, Appl Microbiol Biotechnol, 82: 995-1003 (2009). Another process described in Lynch, U.S. Patent Publication No. 2011/0125118 relates to using synthesis gas components as a carbon source in a microbial system to produce 3-hydroxypropionic acid, with subsequent conversion of the 3-hydroxyproprionic acid to acrylic acid.
Methods to manufacture other organic chemicals in genetically engineered microorganisms have been proposed. See, for example, U.S. Patent Publication No. 2011/0014669 published Jan. 20, 2011 relating to microorganisms for converting L-glutamate to 1,4-butanediol.
Since at least four million metric tons of acrylic acid are produced annually, there remains a need in the art for cost-effective, environmentally-friendly methods for its production from renewable carbon sources.
Propionic acid and its CoA thioester are naturally made from glucose in the bacterium E. coli and many other organisms. Propionic acid can also be directly activated to its CoA thioester.
Most microorganisms do not naturally make acrylate and the other products, but microorganisms (such as bacteria, yeast, fungi or algae) are genetically modified according to the invention to carry out the conversions in the pathways. The present invention utilizes propionyl-CoA as an intermediate to make acrylate (the chemical form of acrylic acid at neutral pH) and other products of interest. FIGS. 1-4 set out the contemplated metabolic pathways for making acrylate, 3-hydroxypropionate and poly-3-hydroxypropionate from glucose via propionyl-CoA. FIG. 5 describes a strategy for converting propionic acid to acrylic acid in a cell free enzymatic system. Surprisingly, use of a short chain acyl-CoA oxidase overcomes the equilibrium issues observed in other pathways and enables production of acrylic acid in microorganisms. Microorganisms include, but are not limited to, an E. coli bacterium.
Producing Acrylate
In a first aspect, the invention provides a first type of microorganism, one that converts propionyl-CoA to acrylate, wherein the microorganism expresses recombinant genes encoding an acyl-CoA oxidase and a thioesterase, phosphate acyltransferase/kinase or acyl-CoA transferase.
The oxidase catalyzes a reaction to convert propionyl-CoA to acryloyl-CoA. In some embodiments, the oxidase is a short chain oxidase. Oxidases include, but are not limited to the Arabidopsis thaliana short chain acyl-CoA oxidase. The amino acid sequence of the A. thaliana short chain acyl-CoA oxidase known in the art is set out in SEQ ID NO: 1. Exemplary DNA sequence encoding the Arabidopsis thaliana short chain acyl-CoA oxidase is respectively set out in SEQ ID NO: 2.
The thioesterase, the phosphate acyltransferase/kinase or the acyl-CoA transferase catalyzes a reaction to convert acryloyl-CoA to acrylate. In some embodiments, the thioesterase is an acryloyl-CoA thioesterase. Acryloyl-CoA thioesterases include, but are not limited to E. coli TesB set out in amino acid SEQ ID NO: 7, the Clostridium propionicum-derived thioesterase including an E324D substitution set out in SEQ ID NO: 9 and the Megasphaera elsdenii-derived thioesterase including an E325D substitution set out in SEQ ID NO: 11. Exemplary DNA sequences encoding these acryloyl-CoA thioesterases are respectively set out in SEQ ID NOs: 8, 10 and 12. The amino acid sequence of a phosphate acyltransferase known in the art is set out in SEQ ID NO: 13. An exemplary DNA sequence encoding the phosphate acyltransferase is SEQ ID NO: 14. The amino acid sequence of a kinase known in the art is set out in SEQ ID NO: 15. An exemplary DNA sequence encoding the kinase is set out in SEQ ID NO: 16. The amino acid sequence of an acyl-CoA transferase known in the art is set out in SEQ ID NO: 17. An exemplary DNA sequence encoding the acyl-CoA transferase is set out in SEQ ID NO: 18.
In a second aspect, the invention provides a first type of method, one for producing acrylate in which the first type of microorganism is cultured to produce acrylate. The first type of method for producing acrylate converts propionyl-CoA to acryloyl-CoA and then acryloyl-CoA to acrylate.
In a third aspect, the invention provides a second type of microorganism, one that converts threonine to acrylate, wherein the microorganism expresses recombinant genes encoding: a dehydratase or deaminase, a dehydrogenase or lyase, an oxidase and a thioesterase, phosphate acyltransferase/kinase or acyl-CoA transferase.
The dehydratase or deaminase catalyzes a reaction to convert threonine to 2-keto-butyrate. In some embodiments, the dehydratase is an L-amino acid dehydratase. Dehydratases include, but are not limited to, Klebsiella pneumoniae or Escherichia coli threonine dehydratase tdcB. The amino acid sequences of K. pneumonia and E. coli threonine dehydratase TdcB is known in the art and is set out in SEQ ID NOs: 19 and 56. Exemplary DNA sequences encoding K. pneumonia and E. coli threonine dehydratase tdcB are set out in SEQ ID NOs: 20 and 55. In some embodiments, the deaminase is an L-amino acid deaminase. Deaminases include, but are not limited to, E. coli threonine deaminase ilvA. The Amino acid sequence of an E. coli threonine deaminase IlvA is known in the art and is set out in SEQ ID NO: 21. An exemplary DNA sequence encoding E. coli threonine deaminase ilvA is set out in SEQ ID NO: 22.
The dehydrogenase or combination of 2-keto acid decarboxylase and Coenzyme-A acylating propionaldehyde dehydrogenase, or lyase catalyzes a reaction to convert 2-keto-butyrate to propionyl-CoA. In some embodiments, the dehydrogenase is a 2-keto acid dehydrogenase. The 2-keto acid dehydrogenases include, but are not limited to, pyruvate dehydrogenase PDH and branched chain keto acid dehydrogenase BKD. The pyruvate dehydrogenase is an enzyme complex containing 3 kinds of peptides set out in SEQ ID NOs: 91, 93 and 95. Exemplary DNA sequences encoding pyruvate dehydrogenase are set out in SEQ ID NOs: 92, 94 and 96. The branched chain keto acid dehydrogenase BKD set out in SEQ ID NOs: 97, 99, 101 and 103. Exemplary DNA sequences encoding branched chain keto acid dehydrogenase BKD are set out in SEQ ID NOs: 98, 100, 102 and 104. The 2-keto acid decarboxylase KdcA is set out in SEQ ID NO: 23 and its derivatives. An exemplary DNA sequence encoding kdcA is set out in SEQ ID NO: 24. A Coenzyme-A acylating propionaldehyde dehydrogenase PduP is set out in SEQ ID NO: 89. An exemplary DNA sequence encoding pduP is set out in SEQ ID NO: 90 (codon optimized for E. coli). In some embodiments, the lyase is a 2-keto acid lyase. The 2-keto acid lyases include, but are not limited to, the 2-ketobutyrate formate lyase is set out in SEQ ID NO: 25 and its derivatives. An exemplary DNA sequence encoding 2-ketobutyrate formate lyase is set out in SEQ ID NO: 26.
The oxidase catalyzes a reaction to convert propionyl-CoA to acryloyl-CoA. In some embodiments, the oxidase is a short chain oxidase. Oxidases include, but are not limited to the short chain acyl-CoA oxidase. The amino acid sequence of an oxidase known in the art is set out in SEQ ID NO: 1. Exemplary DNA sequence encoding the oxidase is respectively set out in SEQ ID NO: 2.
The thioesterase, the phosphate acyltransferase/kinase or the acyl-CoA transferase catalyzes a reaction to convert acryloyl-CoA to acrylate. In some embodiments, the thioesterase is an acryloyl-CoA thioesterase. Acryloyl-CoA thioesterases include, but are not limited to E. coli TesB set out in amino acid SEQ ID NO: 7, the C. propionicum-derived thioesterase including an E324D substitution set out in SEQ ID NO: 9 and the M. elsdenii-derived thioesterase including an E325D substitution set out in SEQ ID NO: 11. Exemplary DNA sequences encoding these acryloyl-CoA thioesterases are respectively set out in SEQ ID NOs: 8, and 12. The amino acid sequence of a phosphate acyltransferase known in the art is set out in SEQ ID NO: 13. An exemplary DNA sequence encoding the phosphate acyltransferase is set out in SEQ ID NO: 14. The amino acid sequence of a kinase known in the art is set out in SEQ ID NO: 15. An exemplary DNA sequence encoding the kinase is set out in SEQ ID NO: 16. The amino acid sequence of an acyl-CoA transferase known in the art is set out in SEQ ID NO: 17. An exemplary DNA sequence encoding the acyl-CoA transferase is set out in SEQ ID NO: 18.
In a fourth aspect, the invention provides a second type of method, one for producing acrylate in which the second type of microorganism is cultured to produce acrylate. The second type of method for producing acrylate converts threonine to 2-ketobutyrate, 2-ketobutyrate to propionyl-CoA, propionyl-CoA to acryloyl-CoA and then acryloyl-CoA to acrylate.
In a fifth aspect, the invention provides a third type of microorganism, one that converts succinyl-CoA to acrylate, wherein the microorganism expresses recombinant genes encoding: an acyl-CoA mutase, an acyl-CoA decarboxylase, an oxidase and a thioesterase, phosphate acyltransferase/kinase or acyl-CoA transferase.
The mutase catalyzes a reaction to convert succinyl-CoA to methylmalonyl-CoA. In some embodiments, the mutase is a methylmalonyl-CoA mutase. Mutases include, but are not limited to, methylmalonyl-CoA mutase. Amino acid sequences of the methylmalonyl-CoA mutase subunits A and B from Janibacter sp. HTCC2649 known in the art is set out in SEQ ID NOs: 27 and 29. Exemplary DNA sequences encoding the methylmalonyl-CoA mutase subunits A and B from Janibacter sp. HTCC2649 is respectively set out in SEQ ID NOs: 28 and 30.
The acyl-CoA decarboxylase catalyzes a reaction to convert methylmalonyl-CoA to propionyl-CoA. In some embodiments, the acyl-CoA decarboxylase is a methylmalonyl-CoA decarboxylase. The acyl-CoA decarboxylases include, but are not limited to, the E. coli methylmalonyl-CoA decarboxylase YgfG set out in SEQ ID NO: 31 and its derivatives. An exemplary DNA sequence encoding the E. coli methylmalonyl-CoA decarboxylase ygfG is set out in SEQ ID NO: 32.
The thioesterase, the phosphate acyltransferase/kinase or the acyl-CoA transferase catalyzes a reaction to convert acryloyl-CoA to acrylate. In some embodiments, the thioesterase is an acryloyl-CoA thioesterase. Acryloyl-CoA thioesterases include, but are not limited to E. coli TesB set out in amino acid SEQ ID NO: 7, the C. propionicum-derived thioesterase including an E324D substitution set out in SEQ ID NO: 9 and the M. elsdenii-derived thioesterase including an E325D substitution set out in SEQ ID NO: 11. Exemplary DNA sequences encoding these acryloyl-CoA thioesterases are respectively set out in SEQ ID NOs: 8, and 12. The amino acid sequence of a phosphate acyltransferase known in the art is set out in SEQ ID NO: 13. An exemplary DNA sequence encoding the phosphate acyltransferase is SEQ ID NO: 14. The amino acid sequence of a kinase known in the art is set out in SEQ ID NO: 15. An exemplary DNA sequence encoding the kinase is set out in SEQ ID NO: 16. The amino acid sequence of an acyl-CoA transferase known in the art is set out in SEQ ID NO: 17. An exemplary DNA sequence encoding the acyl-CoA transferase is set out in SEQ ID NO: 18.
In a sixth aspect, the invention provides a third type of method, one for producing acrylate in which the third type of microorganism is cultured to produce acrylate. The seventh type of method for producing acrylate converts succinyl-CoA to methylmalonyl-CoA, methylmalonyl-CoA to propionyl-CoA, propionyl-CoA to acryloyl-CoA and then acryloyl-CoA to acrylate.
In a seventh aspect, the invention provides a fourth type of microorganism, one that converts pyruvate to acrylate, wherein the microorganism expresses recombinant genes encoding: a synthase, a hydrolase, a dehydratase or isomerase, a dehydrogenase and a ketoacid dehydrogenase or lyase, an acyl-CoA oxidase and a thioesterase, phosphate acyltransferase/kinase or acyl-CoA transferase.
The synthase catalyzes a reaction to convert pyruvate to citramalate. In some embodiments, the synthase is a citramalate synthase. Synthases include, but are not limited to, citramalate synthase cimA from Methanobrevibacter ruminantium and Leptospira interrogans. Amino acid sequences of some synthases known in the art are set out in SEQ ID NOs: 33 and 35. Exemplary DNA sequences encoding those synthases are respectively set out in SEQ ID NOs: 34 and 36.
The hydrolase catalyzes a reaction to convert citramalate to citraconate. In some embodiments, the hydrolase is an isopropylmalate isomerase. Isomerases include, but are not limited to, isopropylmalate isomerase leuC (large subunit) from Salmonella typhimurium. Amino acid sequences of an isopropylmalate isomerase LeuC from S. typhimurium known in the art is set out in SEQ ID NO: 37. An exemplary DNA sequence encoding isopropylmalate isomerase (large subunit) leuC from S. typhimurium is respectively set out in SEQ ID NO: 38
The dehydratase, or isomerase, catalyzes a reaction to convert citraconate to β-methyl-D-malate. In some embodiments, the isomerase is an isopropylmalate isomerase. Amino acid sequences of an isopropylmalate isomerase (small subunit) LeuD from S. typhimurium known in the art is set out in SEQ ID NO: 39. An exemplary DNA sequence encoding isopropylmalate isomerase leuD from S. typhimurium is respectively set out in SEQ ID NO: 40.
The dehydrogenase catalyzes a reaction to convert β-methyl-D-malate to 2-ketobutyrate. In some embodiments, dehydrogenase is a methylmalate dehydrogenase. In other embodiments, the dehydrogenase is a β-isopropylmalate dehydrogenase. Dehydrogenases include, but are not limited to, methylmalate dehydrogenase or Shigella boydii leuB β-isopropylmalate dehydrogenase. The amino acid sequence of a leuB β-isopropylmalate dehydrogenase is known in the art and set out in SEQ ID NO:41. An exemplary DNA sequence encoding this leuB β-isopropylmalate dehydrogenase is set out in SEQ ID NO: 42.
The dehydrogenase or lyase catalyzes a reaction to convert 2-ketobutyrate (2-keto-butyrate) to propionyl-CoA. In some embodiments, the dehydrogenase is a 2-keto acid dehydrogenase. The 2-keto acid dehydrogenases include, but are not limited to, the 2-keto acid decarboxylase KdcA set out in SEQ ID NO: 23 and its derivatives. An exemplary DNA sequence encoding kdcA is set out in SEQ ID NO: 24. In some embodiments, the lyase is a 2-keto acid lyase. The 2-keto acid lyases include, but are not limited to, the 2-ketobutyrate formate lyase set out in SEQ ID NO: 25 and its derivatives. An exemplary DNA sequence encoding 2-ketobutyrate formate lyase is set out in SEQ ID NO: 26.
In an eighth aspect, the invention provides a fourth type of method, one for producing acrylate in which the fourth type of microorganism is cultured to produce acrylate. The fourth type of method for producing acrylate converts pyruvate to citramalate, citramalate to citraconate, citraconate to β-methyl-D-malate, β-methyl-D-malate to 2-ketobutyrate, 2-ketobutyrate to propionyl-CoA, propionyl-CoA to acryloyl-CoA and then acryloyl-CoA to acrylate.
Production of poly-3-hydroxypropionic acid
In a ninth aspect, the invention provides a fifth type of organism that converts acryloyl-CoA to poly-3-hydroxypropionic acid, wherein the microorganism expresses recombinant genes encoding a dehydratase and a polyhydroxyalknanoate synthase.
The dehydratase catalyzes a reaction to convert acryloyl-CoA to 3-hydroxypropionyl-CoA. In some embodiments, the dehydratase is a 3HP-dehydratase. The amino acid sequence of a 3HP-dehydratase known in the art is set out in SEQ ID NO: 49. An exemplary DNA sequence encoding the 3HP-dehydratase is set out in SEQ ID NO: 50.
The PHA synthase catalyzes a reaction to convert 3-hydroxypropionyl-CoA to poly-3-hydroxypropionate. The polymer may have a molecule of Coenzyme A (CoA) at the carboxy end. The amino acid sequence of a PHA synthase known in the art is set out in SEQ ID NO: 51. An exemplary DNA sequence encoding the PHA synthase is set out in SEQ ID NO: 52.
In a tenth aspect, the invention provides a fifth type of method, one for producing poly-3-hydroxypropionate in which the fifth type of microorganism is cultured to produce poly-3-hydroxypropionate. The fifth type of method for producing poly-3-hydroxypropionate converts acryloyl-CoA to 3-hydroxypropionyl-CoA, then 3-hydroxypropionyl-CoA to poly-3-hydroxypropionate.
In a eleventh aspect, the invention provides a sixth type of microorganism, one that converts threonine to poly-3-hydroxypropionic acid, wherein the microorganism expresses recombinant genes encoding: a dehydratase or deaminase, a dehydrogenase or lyase, an oxidase, a dehydratase and a polyhyroxyalknanoate synthase.
The dehydratase or deaminase catalyzes a reaction to convert threonine to 2-keto-butyrate. In some embodiments, the dehydratase is an L-amino acid dehydratase. Dehydratases include, but are not limited to, K. pneumonia or E. coli threonine dehydratase TdcB. The amino acid sequences of K. pneumonia and E. coli threonine dehydratase TdcB are known in the art and are set out in SEQ ID NOs: 19 and 56. Exemplary DNA sequences encoding K. pneumonia and E. coli threonine dehydratase tdcB are set out in SEQ ID NOs: 20 and 55. In some embodiments, the deaminase is an L-amino acid deaminase. Deaminases include, but are not limited to, E. coli threonine deaminase IlvA. The amino acid sequence of an E. coli threonine deaminase IlvA is known in the art and is set out in SEQ ID NO: 21. An exemplary DNA sequence encoding E. coli threonine deaminase ilvA is set out in SEQ ID NO: 22.
The dehydrogenase or combination of 2-keto acid decarboxylase and Coenzyme-A acylating propionaldehyde dehydrogenase, or lyase catalyzes a reaction to convert 2-keto-butyrate to propionyl-CoA. In some embodiments, the dehydrogenase is a 2-keto acid dehydrogenase. The 2-keto acid dehydrogenases include, but are not limited to, pyruvate dehydrogenase PDH and branched chain keto acid dehydrogenase BKD. The pyruvate dehydrogenase is an enzyme complex containing 3 kinds of peptides set out in SEQ ID NOs: 91, 93 and 95. Exemplary DNA sequences encoding pyruvate dehydrogenase are set out in SEQ ID NOs: 92, 94 and 96. The branched chain keto acid dehydrogenase BKD is set out in SEQ ID NOs: 97, 99, 101 and 103. Exemplary DNA sequences encoding branched chain keto acid dehydrogenase BKD are set out in SEQ ID NOs: 98, 100, 102 and 104. The 2-keto acid decarboxylase KdcA is set out in SEQ ID NO: 23 and its derivatives. An exemplary DNA sequence encoding kdcA is set out in SEQ ID NO: 24. A Coenzyme-A acylating propionaldehyde dehydrogenase PduP is set out in SEQ ID NO: 89. An exemplary DNA sequence encoding pduP is set out in SEQ ID NO: 90 (codon optimized for E. coli). In some embodiments, the lyase is a 2-keto acid lyase. The 2-keto acid lyases include, but are not limited to, the 2-ketobutyrate formate lyase set out in SEQ ID NO: 25 and its derivatives. An exemplary DNA sequence encoding 2-ketobutyrate formate lyase is set out in SEQ ID NO: 26.
In a twelfth aspect, the invention provides a sixth type of method, one for producing poly-3-hydroxypropionic acid in which the second type of microorganism is cultured to produce poly-3-hydroxypropionic acid. The sixth type of method for producing poly-3-hydroxypropionic acid converts threonine to 2-ketobutyrate, 2-ketobutyrate to propionyl-CoA, propionyl-CoA to acryloyl-CoA, acryloyl-CoA to 3-hydroxypropionyl-CoA, then 3-hydroxypropionyl-CoA to poly-3-hydroxypropionic acid.
In a thirteenth aspect, the invention provides a seventh type of microorganism, one that converts succinyl-CoA to poly-3-hydroxypropionic acid, wherein the microorganism expresses recombinant genes encoding: an acyl-CoA mutase, an acyl-CoA decarboxylase, an oxidase, a dehydratase and a polyhyroxyalknanoate synthase.
The mutase catalyzes a reaction to convert succinyl-CoA to methylmalonyl-CoA. In some embodiments, the mutase is a methylmalonyl-CoA mutase. Mutases include, but are not limited to, methylmalonyl-CoA mutase. Amino acid sequences of the methylmalonyl-CoA mutase subunits A and B from Janibacter sp. HTCC2649 known in the art is set out in SEQ ID NOs: 27 and 29. Exemplary DNA sequences encoding the methylmalonyl-CoA mutase subunits A and B from Janibacter sp. HTCC2649 are respectively set out in SEQ ID NOs: 28 and 30.
The PHA synthase catalyzes a reaction to convert 3-hydroxypropionyl-CoA to poly-3-hydroxypropionate. The polymer may have a molecule of Coenzyme A (CoA) at the carboxy end. The amino acid sequence of a PHA synthase known in the art is set out in SEQ ID NO: 51. An exemplary DNA sequence encoding the PHA synthase is set out in SEQ ID NO: 52
In a fourteenth aspect, the invention provides a seventh type of method, one for producing poly-3-hydroxypropionic acid in which the seventh type of microorganism is cultured to produce poly-3-hydroxypropionic acid. The seventh type of method for producing poly-3-hydroxypropionic acid converts succinyl-CoA to methylmalonyl-CoA, methylmalonyl-CoA to propionyl-CoA, propionyl-CoA to acryloyl-CoA, acryloyl-CoA to 3-hydroxypropionyl-CoA, then 3-hydroxypropionyl-CoA to poly-3-hydroxypropionic acid.
In a fifteenth aspect, the invention provides an eighth type of microorganism, one that converts pyruvate to poly-3-hydroxypropionic acid, wherein the microorganism expresses recombinant genes encoding: a synthase, a hydrolase, a dehydratase or isomerase, a dehydrogenase, a ketoacid dehydrogenase, an acyl-CoA oxidase or dehydrogenase, a dehydratase and a polyhydroxyalkananoate synthase.
The hydrolase catalyzes a reaction to convert citramalate to citraconate. In some embodiments, the hydrolase is an isopropylmalate isomerase. Isomerases include, but are not limited to, isopropylmalate isomerase LeuC (large subunit) from S. typhimurium. The amino acid sequence of an isopropylmalate isomerase LeuC from S. typhimurium known in the art is set out in SEQ ID NO: 37. An exemplary DNA sequence encoding isopropylmalate isomerase (large subunit) leuC from S. typhimurium is respectively set out in SEQ ID NO: 38
The dehydrogenase catalyzes a reaction to convert β-methyl-D-malate to 2-ketobutyrate. In some embodiments, the dehydrogenase is a methylmalate dehydrogenase. In other embodiments, the dehydrogenase is a β-isopropylmalate dehydrogenase. Dehydrogenases include, but are not limited to, methylmalate dehydrogenase or Shigella boydii LeuB β-isopropylmalate dehydrogenase. The amino acid sequence of a LeuB β-isopropylmalate dehydrogenase is known in the art and set out in SEQ ID NO: 41. An exemplary DNA sequence encoding this leuB β-isopropylmalate dehydrogenase is set out in SEQ ID NO: 42.
The oxidase catalyzes a reaction to convert propionyl-CoA to acryloyl-CoA. In some embodiments, the oxidase is a short chain oxidase. Oxidases include, but are not limited to the short chain acyl-CoA oxidase. The amino acid sequence of an oxidase known in the art is set out in SEQ ID NO: 1. An exemplary DNA sequence encoding the oxidase is respectively set out in SEQ ID NO: 2.
In a sixteenth aspect, the invention provides an eighth type of method, one for producing poly-3-hydroxypropionic acid in which the eighth type of microorganism is cultured to produce poly-3-hydroxypropionic acid. The eighth type of method for producing poly-3-hydroxypropionic acid converts pyruvate to citramalate, citramalate to citraconate, citraconate to β-methyl-D-malate, β-methyl-D-malate to 2-ketobutyrate, 2-ketobutyrate to propionyl-CoA, propionyl-CoA to acryloyl-CoA, acryloyl-CoA to 3-hydroxypropionyl-CoA, then 3-hydroxypropionyl-CoA to poly-3-hydroxypropionic acid.
In a seventeenth aspect, the invention provides a ninth type of organism that converts acryloyl-CoA to 3-hydroxypropionic acid, wherein the microorganism expresses recombinant genes encoding a dehydratase and a thioesterase or acyl-CoA transferase.
The thioesterase or the acyl-CoA transferase catalyzes a reaction to convert 3-hydroxypropionyl-CoA to 3-hydroxypropionic acid. In some embodiments, the thioesterase is a 3-hydroxypropionyl-CoA thioesterase. Thioesterases include, but are not limited to E. coli TesB set out in amino acid SEQ ID NO: 7, the C. propionicum-derived thioesterase including an E324D substitution set out in SEQ ID NO: 9 and the M. elsdenii-derived thioesterase including an E325D substitution set out in SEQ ID NO: 11. Exemplary DNA sequences encoding these thioesterase s are respectively set out in SEQ ID NOs: 8, 10 and 12. The amino acid sequence of an acyl-CoA transferase known in the art is set out in SEQ ID NO: 17. An exemplary DNA sequence encoding the acyl-CoA transferase is set out in SEQ ID NO: 18.
In an eighteenth aspect, the invention provides a ninth type of method, one for producing 3-hydroxypropionate in which the ninth type of microorganism is cultured to produce 3-hydroxypropionate. The ninth type of method for producing 3-hydroxypropionate converts acryloyl-CoA to 3-hydroxypropionyl-CoA, then 3-hydroxypropionyl-CoA to 3-hydroxypropionate.
In a nineteenth aspect, the invention provides a tenth type of microorganism, one that converts threonine to 3-hydroxypropionic acid, wherein the microorganism expresses recombinant genes encoding: a dehydratase or deaminase, a dehydrogenase or lyase, an oxidase, a dehydratase and a thioesterase or acyl-CoA transferase.
The dehydrogenase or combination of 2-keto acid decarboxylase and Coenzyme-A acylating propionaldehyde dehydrogenase, or lyase catalyzes a reaction to convert 2-keto-butyrate to propionyl-CoA. In some embodiments, the dehydrogenase is a 2-keto acid dehydrogenase. The 2-keto acid dehydrogenases include, but are not limited to, pyruvate dehydrogenase PDH and branched chain keto acid dehydrogenase BKD. The pyruvate dehydrogenase is an enzyme complex containing 3 kinds of peptides set out in SEQ ID NOs: 91, 93 and 95. Exemplary DNA sequences encoding pyruvate dehydrogenase are set out in SEQ ID NOs: 92, 94 and 96. The branched chain keto acid dehydrogenase BKD set out in SEQ ID NOs: 97, 99, 101 and 103. Exemplary DNA sequences encoding branched chain keto acid dehydrogenase BKD are set out in SEQ ID NOs: 98, 100, 102 and 104. The 2-keto acid decarboxylase KdcA is set out in SEQ ID NO: 23 and its derivatives. An exemplary DNA sequence encoding kdcA is set out in SEQ ID NO: 24. A Coenzyme-A acylating propionaldehyde dehydrogenase PduP is set out in SEQ ID NO: 89. An exemplary DNA sequence encoding pduP is set out in SEQ ID NO: 90 (codon optimized for E. coli). In some embodiments, the lyase is a 2-keto acid lyase. The 2-keto acid lyases include, but are not limited to, the 2-ketobutyrate formate lyase set out in SEQ ID NO: 25 and its derivatives. An exemplary DNA sequence encoding 2-ketobutyrate formate lyase is set out in SEQ ID NO: 26.
The thioesterase or the acyl-CoA transferase catalyzes a reaction to convert 3-hydroxypropionyl-CoA to 3-hydroxypropionic acid. In some embodiments, the thioesterase is a 3-hydroxypropionyl-CoA thioesterase. Thioesterases include, but are not limited to E. coli TesB set out in amino acid SEQ ID NO: 7, the C. propionicum-derived thioesterase including an E324D substitution set out in SEQ ID NO: 9 and the M. elsdenii-derived thioesterase including an E325D substitution set out in SEQ ID NO: 11. Exemplary DNA sequences encoding these thioesterases are respectively set out in SEQ ID NOs: 8, 10 and 12. The amino acid sequence of an acyl-CoA transferase known in the art is set out in SEQ ID NO: 17. An exemplary DNA sequence encoding the acyl-CoA transferase is set out in SEQ ID NO: 18.
In a twentieth aspect, the invention provides a tenth type of method, one for producing 3-hydroxypropionic acid in which the tenth type of microorganism is cultured to produce 3-hydroxypropionic acid. The tenth type of method for producing 3-hydroxypropionic acid converts threonine to 2-ketobutyrate, 2-ketobutyrate to propionyl-CoA, propionyl-CoA to acryloyl-CoA, acryloyl-CoA to 3-hydroxypropionyl-CoA, then 3-hydroxypropionyl-CoA to 3-hydroxypropionic acid.
In a twenty-first aspect, the invention provides an eleventh type of microorganism, one that converts succinyl-CoA to 3-hydroxypropionic acid, wherein the microorganism expresses recombinant genes encoding: an acyl-CoA mutase, an acyl-CoA decarboxylase, an oxidase or dehydrogenase, a dehydratase and a thioesterase or acyl-CoA transferase.
The mutase catalyzes a reaction to convert succinyl-CoA to methylmalonyl-CoA. In some embodiments, the mutase is a methylmalonyl-CoA mutase. Mutases include, but are not limited to, methylmalonyl-CoA mutase. Amino acid sequences of the methylmalonyl-CoA mutase subunits A and B from Janibacter sp. HTCC2649 known in the art are set out in SEQ ID NOs: 27 and 29. Exemplary DNA sequences encoding the methylmalonyl-CoA mutase subunits A and B from Janibacter sp. HTCC2649 are respectively set out in SEQ ID NOs: 28 and 30.
In a twenty-second aspect, the invention provides a eleventh type of method, one for producing 3-hydroxypropionic acid in which the eleventh type of microorganism is cultured to produce 3-hydroxypropionic acid. The eleventh type of method for producing 3-hydroxypropionic acid converts succinyl-CoA to methylmalonyl-CoA, methylmalonyl-CoA to propionyl-CoA, propionyl-CoA to acryloyl-CoA, acryloyl-CoA to 3-hydroxypropionyl-CoA, then 3-hydroxypropionyl-CoA to 3-hydroxypropionic acid.
In a twentythird aspect, the invention provides an twelfth type of microorganism, one that converts pyruvate to 3-hydroxypropionic acid, wherein the microorganism expresses recombinant genes encoding: a synthase, a hydrolase, a dehydratase or isomerase, a dehydrogenase, a ketoacid dehydrogenase, an acyl-CoA oxidase or dehydrogenase, a dehydratase and a thioesterase or acyl-CoA transferase
The synthase catalyzes a reaction to convert pyruvate to citramalate. In some embodiments, the synthase is a citramalate synthase. Synthases include, but are not limited to, citramalate synthase cimA from M. ruminantium and L. interrogans. Amino acid sequences of some synthases known in the art are set out in SEQ ID NOs: 33 and 35. Exemplary DNA sequences encoding those synthases are respectively set out in SEQ ID NOs: 34 and 36.
The hydrolase catalyzes a reaction to convert citramalate to citraconate. In some embodiments, the hydrolase is an isopropylmalate isomerase. Isomerases include, but are not limited to, isopropylmalate isomerase LeuC (large subunit) from S. typhimurium. Amino acid sequences of an isopropylmalate isomerase LeuC from S. typhimurium known in the art is set out in SEQ ID NO: 37. An exemplary DNA sequence encoding isopropylmalate isomerase (large subunit) leuC from S. typhimurium is respectively set out in SEQ ID NO: 38
The dehydrogenase catalyzes a reaction to convert β-methyl-D-malate to 2-ketobutyrate. In some embodiments, dehydrogenase is a methylmalate dehydrogenase. In other embodiments, the dehydrogenase is a β-isopropylmalate dehydrogenase. Dehydrogenases include, but are not limited to, methylmalate dehydrogenase or S. boydii LeuB β-isopropylmalate dehydrogenase. The amino acid sequence of a LeuB β-isopropylmalate dehydrogenase is known in the art and set out in SEQ ID NO: 41. An exemplary DNA sequence encoding this leuB β-isopropylmalate dehydrogenase is set out in SEQ ID NO: 42.
The dehydrogenase or lyase catalyzes a reaction to convert 2-ketobutyrate to propionyl-CoA. In some embodiments, the dehydrogenase is a 2-keto acid dehydrogenase. The 2-keto acid dehydrogenases include, but are not limited to, the 2-keto acid decarboxylase KdcA set out in SEQ ID NO: 23 and its derivatives. An exemplary DNA sequence encoding KdcA is set out in SEQ ID NO: 24. In some embodiments, the lyase is a 2-keto acid lyase. The 2-keto acid lyases include, but are not limited to, the 2-ketobutyrate formate lyase set out in SEQ ID NO: 25 and its derivatives. An exemplary DNA sequence encoding 2-ketobutyrate formate lyase is set out in SEQ ID NO: 26.
In a twenty-fourth aspect, the invention provides an twelfth type of method, one for producing 3-hydroxypropionic acid in which the twelfth type of microorganism is cultured to produce 3-hydroxypropionic acid. The twelfth type of method for producing 3-hydroxypropionic acid converts pyruvate to citramalate, citramalate to citraconate, citraconate to β-methyl-D-malate, β-methyl-D-malate to 2-ketobutyrate, 2-ketobutyrate to propionyl-CoA, propionyl-CoA to acryloyl-CoA, acryloyl-CoA to 3-hydroxypropionyl-CoA, then 3-hydroxypropionyl-CoA to 3-hydroxypropionic acid.
In an twenty-fifth aspect, the invention provides for a thirteenth method using isolated purified enzymes or from a cell lysate, one that converts propionyl-CoA to acrylate, wherein the enzymes are selected from the group consisting of an acyl-CoA oxidase or dehydrogenase, a thioesterase, phosphate acyltransferase/kinase or acyl-CoA transferase, and a peroxidase.
The oxidase or dehydrogenase catalyzes a reaction to convert propionyl-CoA to acryloyl-CoA. In some embodiments, the oxidase is a short chain oxidase. Oxidases include, but are not limited to the short chain acyl-CoA oxidase. The amino acid sequence of an oxidase known in the art is set out in SEQ ID NO: 1. An exemplary DNA sequence encoding the oxidase is respectively set out in SEQ ID NO: 2. In some embodiments, the dehydrogenase is a short chain acyl-CoA dehydrogenase. Dehydrogenases include, but are not limited to acyl-CoA dehydrogenase. Amino acid sequences of some dehydrogenases known in the art are set out in SEQ ID NOs: 3 and 5. Exemplary DNA sequences encoding those dehydrogenases are respectively set out in SEQ ID NOs: 4 and 6.
The thioesterase, the phosphate acyltransferase/kinase or the acyl-CoA a reaction to convert acryloyl-CoA to acrylate. In some embodiments, the thioesterase is an acryloyl-CoA thioesterase. Acryloyl-CoA thioesterases include, but are not limited to E. coli TesB set out in amino acid SEQ ID NO: 7, the C. propionicum-derived thioesterase including an E324D substitution set out in SEQ ID NO: 9 and the M. elsdenii-derived thioesterase including an E325D substitution set out in SEQ ID NO: 11. Exemplary DNA sequences encoding these acryloyl-CoA thioesterases are respectively set out in SEQ ID NOs: 8, 10 and 12. The amino acid sequence of a phosphate acyltransferase known in the art is set out in SEQ ID NO: 13. An exemplary DNA sequence encoding the phosphate acyltransferase is SEQ ID NO: 14. The amino acid sequence of a kinase known in the art is set out in SEQ ID NO: 15. An exemplary DNA sequence encoding the kinase is set out in SEQ ID NO: 16. The amino acid sequence of an acyl-CoA transferase known in the art is set out in SEQ ID NO: 17. An exemplary DNA sequence encoding the acyl-CoA transferase is set out in SEQ ID NO: 18.
The peroxidase catalyzes a reaction to convert hydrogen peroxide to water and oxygen. In some embodiments, the peroxidase is a catalase. The amino acid sequence of a Bos taurus catalase is known in the art and set out in SEQ ID NO: 53. An exemplary DNA sequence encoding the catalase is SEQ ID NO: 54.
In an twenty-sixth aspect, the invention provides for a fourteenth method using isolated purified enzymes or from a cell lysate, one that converts propionic acid to acrylate, wherein the enzymes are selected from the group consisting of an acyl-CoA synthetase, acyl-CoA oxidase or dehydrogenase a thioesterase, phosphate acyltransferase/kinase or acyl-CoA transferase, and a peroxidase.
The acyl-CoA synthetase catalyzes a reaction to convert propionic acid to propionyl-CoA. In some embodiments, the acyl-CoA synthetase is a short chain synthetase. The amino acid sequence of acyl-CoA synthetases are known in the art and set out in SEQ ID NOs: 85 and 87. Exemplary DNA sequences encoding the acyl-CoA synthetase are SEQ ID NO: 86 and 88.
The thioesterase, the phosphate acyltransferase/kinase or the acyl-CoA transferase catalyzes a reaction to convert acryloyl-CoA to acrylate. In some embodiments, the thioesterase is an acryloyl-CoA thioesterase. Acryloyl-CoA thioesterases include, but are not limited to E. coli TesB set out in amino acid SEQ ID NO: 7, the C. propionicum-derived thioesterase including an E324D substitution set out in SEQ ID NO: 9, and the M. elsdenii-derived thioesterase including an E325D substitution set out in SEQ ID NO: 11. Exemplary DNA sequences encoding these acryloyl-CoA thioesterases are respectively set out in SEQ ID NOs: 8, and 12. The amino acid sequence of a phosphate acyltransferase known in the art is set out in SEQ ID NO: 13. An exemplary DNA sequence encoding the phosphate acyltransferase is SEQ ID NO: 14. The amino acid sequence of a kinase known in the art is set out in SEQ ID NO: 15. An exemplary DNA sequence encoding the kinase is set out in SEQ ID NO: 16. The amino acid sequence of an acyl-CoA transferase known in the art is set out in SEQ ID NO: 17. An exemplary DNA sequence encoding the acyl-CoA transferase is set out in SEQ ID NO: 18.
The peroxidase catalyzes a reaction to convert hydrogen peroxide to water and oxygen. In some embodiments, the peroxidase is a catalase. The amino acid sequence of a B. taurus catalase is known in the art and set out in SEQ ID NO: 53. An exemplary DNA sequence encoding the catalase is SEQ ID NO: 54.
In an twenty-seventh aspect, the invention provides for a fifteenth method using isolated purified enzymes or from a cell lysate, one that converts threonine to acrylate, wherein the enzymes are selected from the group consisting of a dehydratase, a dehydrogenase or lyase, an oxidase or dehydrogenase, a thioesterase, phosphate acyltransferase/kinase or acyl-CoA transferase, and a peroxidase.
The thioesterase, the phosphate acyltransferase/kinase or the acyl-CoA transferase catalyzes a reaction to convert acryloyl-CoA to acrylate. In some embodiments, the thioesterase is an acryloyl-CoA thioesterase. Acryloyl-CoA thioesterases include, but are not limited to E. coli TesB set out in amino acid SEQ ID NO: 7, the C. propionicum-derived thioesterase including an E324D substitution set out in SEQ ID NO: 9 and the M. elsdenii derived thioesterase including an E325D substitution set out in SEQ ID NO: 11. Exemplary DNA sequences encoding these acryloyl-CoA thioesterases are respectively set out in SEQ ID NOs: 8, and 12. The amino acid sequence of a phosphate acyltransferase known in the art is set out in SEQ ID NO: 13. An exemplary DNA sequence encoding the phosphate acyltransferase is SEQ ID NO: 14. The amino acid sequence of a kinase known in the art is set out in SEQ ID NO: 15. An exemplary DNA sequence encoding the kinase is set out in SEQ ID NO: 16. The amino acid sequence of an acyl-CoA transferase known in the art is set out in SEQ ID NO: 17. An exemplary DNA sequence encoding the acyl-CoA transferase is set out in SEQ ID NO: 18.
In an twenty-eighth aspect, the invention provides for a sixteenth method using isolated purified enzymes or from a cell lysate, one that converts succinate to acrylate, wherein the enzymes are selected from the group consisting of an acyl-CoA mutase, an acyl-CoA decarboxylase, an oxidase or dehydrogenase, a thioesterase, phosphate acyltransferase/kinase or acyl-CoA transferase, and a peroxidase.
The thioesterase, the phosphate acyltransferase/kinase or the acyl-CoA transferase catalyzes a reaction to convert acryloyl-CoA to acrylate. In some embodiments, the thioesterase is an acryloyl-CoA thioesterase. Acryloyl-CoA thioesterases include, but are not limited to E. coli TesB set out in amino acid SEQ ID NO: 7, the C. propionicum-derived thioesterase including an E324D substitution set out in SEQ ID NO: 9 and the M. elsdenii-derived thioesterase including an E325D substitution set out in SEQ ID NO: 11. Exemplary DNA sequences encoding these acryloyl-CoA thioesterases are respectively set out in SEQ ID NOs: 8, 10 and 12. The amino acid sequence of a phosphate acyltransferase known in the art is set out in SEQ ID NO: 13. An exemplary DNA sequence encoding the phosphate acyltransferase is SEQ ID NO: 14. The amino acid sequence of a kinase known in the art is set out in SEQ ID NO: 15. An exemplary DNA sequence encoding the kinase is set out in SEQ ID NO: 16. The amino acid sequence of an acyl-CoA transferase known in the art is set out in SEQ ID NO: 17. An exemplary DNA sequence encoding the acyl-CoA transferase is set out in SEQ ID NO: 18.
In an twenty-ninth aspect, the invention provides for a seventeenth method using isolated purified enzymes or from a cell lysate, one that converts pyruvate, citramalate, citraconate, β-methyl-D-malate or 2-ketobutyrate to acrylate, wherein the enzymes comprise a synthase, a hydrolase, a dehydratase or isomerase, a dehydrogenase and a ketoacid dehydrogenase, an oxidase or dehydrogenase, thioesterase, phosphate acyltransferase/kinase or acyl-CoA transferase, a peroxidase.
Increasing the Carbon Flow to Propionyl-CoA
In a thirtieth aspect, the invention provides microorganisms that include further genetic modifications in order to increase the carbon flow to propionyl-CoA which, in turn, increases the production of acrylate or other products of the invention. The microorganisms exhibit one or more of the following characteristics.
In some embodiments, the microorganism exhibits increased carbon flow to oxaloacetate in comparison to a corresponding wild-type microorganism. The microorganism expresses a recombinant gene encoding, for example, phosphoenolpyruvate carboxylase or pyruvate carboxylase (or both). The phosphoenolpyruvate carboxylases include, but are not limited to, the phosphoenolpyruvate carboxylase set out in SEQ ID NO: 63. An exemplary DNA sequence encoding the phosphoenolpyruvate carboxylase is set out in SEQ ID NO: 64. The pyruvate carboxylases include, but are not limited to, the pyruvate carboxylases set out in SEQ ID NOs: 65 and 67. Exemplary DNA sequences encoding the pyruvate carboxylases are set out in SEQ ID NOS: 66 and 68.
In some embodiments, the microorganism exhibits reduced aspartate kinase feedback inhibition in comparison to a corresponding wild-type microorganism. The microorganism expresses one or more of the genes encoding the polypeptides including, but not limited to, S345F ThrA (SEQ ID NO: 69), T352I LysC (SEQ ID NO: 71) and MetL (SEQ ID NO: 73). Exemplary coding sequences encoding the polypeptides are respectively set out in SEQ ID NO: 70, SEQ ID NO: 72 and SEQ ID NO: 75.
In some embodiments, the microorganism exhibits reduced lysA gene expression or diaminopimelate decarboxylase activity in comparison to a corresponding wild-type microorganism. In some embodiments, the microorganism exhibits reduced dapA expression or dihydropicolinate synthase activity in comparison to a corresponding wild type organism. An exemplary DNA sequence of a lysA coding sequence known in the art is set out in SEQ ID NO: 76. It encodes the amino acid sequence set out in SEQ ID NO: 75. An exemplary DNA sequence of a dapA coding sequence known in the art is set out in SEQ ID NO: 78. It encodes the amino acid sequence set out in SEQ ID NO: 77.
In some embodiments, the microorganism exhibits reduced metA gene expression or homoserine succinyltransferase activity in comparison to a corresponding wild-type microorganism. An exemplary DNA sequence of a metA coding sequence known in the art is set out in SEQ ID NO: 80. It encodes the amino acid sequence set out in SEQ ID NO: 79.
In some embodiments, the microorganism exhibits increased thrB gene expression or homoserine kinase activity in comparison to a corresponding wild-type microorganism. An exemplary DNA sequence of a thrB coding sequence known in the art is set out in SEQ ID NO: 82. It encodes the amino acid sequence set out in SEQ ID NO: 81.
In some embodiments, the microorganism exhibits increased thrC gene expression or threonine synthase activity in comparison to a corresponding wild-type microorganism. An exemplary DNA sequence of a thrC coding sequence known in the art is set out in SEQ ID NO: 84. It encodes the amino acid sequence set out in SEQ ID NO: 83.
In a thirty-first aspect, the invention provides a method of culturing the further modified microorganisms to produce products of the invention.
FIG. 1 shows steps in the conversion of glucose to propionyl-CoA via the threonine pathway.
FIG. 2 shows steps in the conversion of glucose to propionyl-CoA via the succinyl-CoA pathway.
FIG. 3 shows steps in the conversion of glucose to propionyl-CoA via the citramalate pathway.
FIG. 4 shows steps in methods of the invention for producing acrylic acid, 3-hydroxypropionate and poly-3-hydroxypropionate from propionyl-CoA.
FIG. 5 shows steps in a method of the invention for producing acrylate from propionic acid using isolated enzymes.
FIG. 6 shows steps in a method of the invention for producing acrylate from propionic acid using isolated enzymes.
FIG. 7 shows LC-MS analysis of samples of propionyl-CoA after incubation of 2-ketobutyric acid with pyruvate dehydrogenase or 2-ketoglutarate dehydrogenase and the proper cofactors.
FIG. 8 shows the propionyl-CoA oxidase assay results, an LC-MS analysis of samples of propionyl-CoA after incubation with or without propionyl-CoA oxidase.
FIG. 9 shows the visible spectra of samples of propionyl-CoA and ADHP after incubation with or without propionyl-CoA oxidase and HRP. Reaction time: 2 min.
FIG. 10 is a High Pressure Liquid Chromatography analysis of a propionic acid and acrylic acid.
The invention provides the products acrylic acid and acrylate. As is understood in the art, acrylate is the carboxylate anion (i.e., conjugate base) of acrylic acid. The pH of the product solution determines the relative amount of acrylate versus acrylic in a preparation according to the Henderson-Hasselbalch equation {pH=pKa+log([A−]/[HA]}, where pKa is −log(Ka). Ka is the acid dissociation constant of acrylic acid. The pKa of acrylic acid in water is about 4.35. Thus, at or near neutral pH, acrylic acid will exist primarily as the carboxylate anion. As used herein, “acrylic acid” and “acrylate” are both meant to encompass the other.
As used herein, “amplify,” “amplified,” or “amplification” refers to any process or protocol for copying a polynucleotide sequence into a larger number of polynucleotide molecules, e.g., by reverse transcription, polymerase chain reaction, and ligase chain reaction.
As used herein, an “antisense sequence” refers to a sequence that specifically hybridizes with a second polynucleotide sequence. For instance, an antisense sequence is a DNA sequence that is inverted relative to its normal orientation for transcription. Antisense sequences can express an RNA transcript that is complementary to a target mRNA molecule expressed within the host cell (e.g., it can hybridize to target mRNA molecule through Watson-Crick base pairing).
As used herein, “cDNA” refers to a DNA that is complementary or identical to an mRNA, in either single stranded or double stranded form.
As used herein, “complementary” refers to a polynucleotide that base pairs with a second polynucleotide. Put another way, “complementary” describes the relationship between two single-stranded nucleic acid sequences that anneal by base-pairing. For example, a polynucleotide having the sequence 5′-GTCCGA-3′ is complementary to a polynucleotide with the sequence 5′-TCGGAC-3′.
As used herein, a “conservative substitution” refers to the substitution in a polypeptide of an amino acid with a functionally similar amino acid. Put another way, a conservative substitution involves replacement of an amino acid residue with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined within the art, and include amino acids with basic side chains (e.g., lysine, arginine, and histidine), acidic side chains (e.g., aspartic acid and glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, and cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, and tryptophan), beta-branched side chains (e.g., threonine, valine, and isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, and histidine).
As used herein, a “corresponding wild-type microorganism” is the naturally-occurring microorganism that would be the same as the microorganism of the invention except that the naturally-occurring microorganism has not been genetically engineered to express any recombinant genes.
As used herein, “encoding” refers to the inherent property of nucleotides to serve as templates for synthesis of other polymers and macromolecules. Unless otherwise specified, a “nucleotide sequence encoding an amino acid sequence” includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence.
As used herein, “endogenous” refers to polynucleotides, polypeptides, or other compounds that are expressed naturally or originate within an organism or cell. That is, endogenous polynucleotides, polypeptides, or other compounds are not exogenous. For instance, an “endogenous” polynucleotide or peptide is present in the cell when the cell was originally isolated from nature.
As used herein, “expression vector” refers to a vector comprising a recombinant polynucleotide comprising expression control sequences operatively linked to a nucleotide sequence to be expressed. For example, suitable expression vectors can be an autonomously replicating plasmid or integrated into the chromosome.
As used herein, “exogenous” refers to any polynucleotide or polypeptide that is not naturally found or expressed in the particular cell or organism where expression is desired. Exogenous polynucleotides, polypeptides, or other compounds are not endogenous.
As used herein “threonine” includes enantiomers such as L-threonine ine and D-threonine.
As used herein, “hybridization” includes any process by which a strand of a nucleic acid joins with a complementary nucleic acid strand through base-pairing. Thus, the term refers to the ability of the complement of the target sequence to bind to a test (i.e., target) sequence, or vice-versa.
As used herein, “hybridization conditions” are typically classified by degree of “stringency” of the conditions under which hybridization is measured. The degree of stringency can be based, for example, on the melting temperature (Tm) of the nucleic acid binding complex or probe. For example, “maximum stringency” typically occurs at about Tm −5° C. (5° below the Tm of the probe); “high stringency” at about 5-10° below the Tm; “intermediate stringency” at about 10-20° below the Tm of the probe; and “low stringency” at about 20-25° below the Tm. Alternatively, or in addition, hybridization conditions can be based upon the salt or ionic strength conditions of hybridization and/or one or more stringency washes. For example, 6×SSC=very low stringency; 3×SSC=low to medium stringency; 1×SSC=medium stringency; and 0.5×SSC=high stringency. Functionally, maximum stringency conditions may be used to identify nucleic acid sequences having strict (i.e., about 100%) identity or near-strict identity with the hybridization probe; while high stringency conditions are used to identify nucleic acid sequences having about 80% or more sequence identity with the probe.
As used herein, “identical” or percent “identity,” in the context of two or more polynucleotide or polypeptide sequences, refers to two or more sequences that are the same or have a specified percentage of nucleotides or amino acid residues that are the same, when compared and aligned for maximum correspondence, as measured using sequence comparison algorithms or by visual inspection.
As used herein, “isolated enzyme” refers to enzymes free of a living organism. Isolated enzymes of the invention may be suspended in solution following lysing of the cell they were expressed in, partially or highly purified, soluble or bound to an insoluble matrix.
“Microorganisms” of the invention expressing recombinant genes are not naturally-occurring. In other words, the microorganisms are man-made and have been genetically engineered to express recombinant genes. The microorganisms of the invention have been genetically engineered to express the recombinant genes encoding the enzymes necessary to carry out the conversion of homoserine to the desired product. Microorganisms of the invention are bacteria, yeast, fungi or algae. Bacteria include, but not limited to, E. coli strains K, B or C. Microorganisms that are more resistant to acrylate are preferred. Plant cells that are not naturally-occurring (are man-made) and have been genetically engineered to express recombinant genes carrying out the conversions detailed herein are contemplated by the invention to be alternative cells to microorganisms, for example in the production of poly-3-hydroxypropionate.
As used herein, “naturally-occurring” refers to an object that can be found in nature. For example, a polypeptide or polynucleotide sequence that is present in an organism (including viruses) that can be isolated from a source in nature and which has not been intentionally modified by man in the laboratory is naturally-occurring. As used herein, “naturally-occurring” and “wild-type” are synonyms.
As used herein, “operably linked,” when describing the relationship between two DNA regions or two polypeptide regions, means that the regions are functionally related to each other. For example, a promoter is operably linked to a coding sequence if it controls the transcription of the sequence; a ribosome binding site is operably linked to a coding sequence if it is positioned so as to permit translation; and a sequence is operably linked to a peptide if it functions as a signal sequence, such as by participating in the secretion of the mature form of the protein.
As used herein, a recombinant gene that is “over-expressed” produces more RNA and/or protein than a corresponding naturally-occurring gene in the microorganism. Methods of measuring amounts of RNA and protein are known in the art. Over-expression can also be determined by measuring protein activity such as enzyme activity. Depending on the embodiment of the invention, “over-expression” is an amount at least 3%, at least 5%, at least 10%, at least 20%, at least 25%, or at least 50% more. An over-expressed polynucleotide is generally a polynucleotide native to the host cell, the product of which is generated in a greater amount than that normally found in the host cell. Over-expression is achieved by, for instance and without limitation, operably linking the polynucleotide to a different promoter than the polynucleotide's native promoter or introducing additional copies of the polynucleotide into the host cell.
As used herein, “polynucleotide” refers to a polymer composed of nucleotides. The polynucleotide may be in the form of a separate fragment or as a component of a larger nucleotide sequence construct, which has been derived from a nucleotide sequence isolated at least once in a quantity or concentration enabling identification, manipulation, and recovery of the sequence and its component nucleotide sequences by standard molecular biology methods, for example, using a cloning vector. When a nucleotide sequence is represented by a DNA sequence (i.e., A, T, G, C), this also includes an RNA sequence (i.e., A, U, G, C) in which “U” replaces “T.” Put another way, “polynucleotide” refers to a polymer of nucleotides removed from other nucleotides (a separate fragment or entity) or can be a component or element of a larger nucleotide construct, such as an expression vector or a polycistronic sequence. Polynucleotides include DNA, RNA and cDNA sequences.
As used herein, “polypeptide” refers to a polymer composed of amino acid residues which may or may not contain modifications such as phosphates and formyl groups.
As used herein, “primer” refers to a polynucleotide that is capable of specifically hybridizing to a designated polynucleotide template and providing a point of initiation for synthesis of a complementary polynucleotide when the polynucleotide primer is placed under conditions in which synthesis is induced.
As used herein, “recombinant polynucleotide” refers to a polynucleotide having sequences that are not joined together in nature. A recombinant polynucleotide may be included in a suitable vector, and the vector can be used to transform a suitable host cell. A host cell that comprises the recombinant polynucleotide is referred to as a “recombinant host cell.” The polynucleotide is then expressed in the recombinant host cell to produce, e.g., a “recombinant polypeptide.”
As used herein, “recombinant expression vector” refers to a DNA construct used to express a polynucleotide that, e.g., encodes a desired polypeptide. A recombinant expression vector can include, for example, a transcriptional subunit comprising (i) an assembly of genetic elements having a regulatory role in gene expression, for example, promoters and enhancers, (ii) a structural or coding sequence which is transcribed into mRNA and translated into protein, and (iii) appropriate transcription and translation initiation and termination sequences. Recombinant expression vectors are constructed in any suitable manner. The nature of the vector is not critical, and any vector may be used, including plasmid, virus, bacteriophage, and transposon. Possible vectors for use in the invention include, but are not limited to, chromosomal, nonchromosomal and synthetic DNA sequences, e.g., bacterial plasmids; phage DNA; yeast plasmids; and vectors derived from combinations of plasmids and phage DNA, DNA from viruses such as vaccinia, adenovirus, fowl pox, baculovirus, SV40, and pseudorabies.
As used herein, a “recombinant gene” is not a naturally-occurring gene. A recombinant gene is man-made. A recombinant gene includes a protein coding sequence operably linked to expression control sequences. Embodiments include, but are not limited to, an exogenous gene introduced into a microorganism, an endogenous protein coding sequence operably linked to a heterologous promoter (i.e., a promoter not naturally linked to the protein coding sequence) and a gene with a modified protein coding sequence (e.g., a protein coding sequence encoding an amino acid change or a protein coding sequence optimized for expression in the microorganism). The recombinant gene is maintained in the genome of the microorganism, on a plasmid in the microorganism or on a phage in the microorganism.
As used herein, “reduced” expression is expression of less RNA or protein than the corresponding natural level of expression. Methods of measuring amounts of RNA and protein are known in the art. Reduced expression can also be determined by measuring protein activity such as enzyme activity. Depending on the embodiment of the invention, “reduced” is an amount at least 3%, at least 5%, at least 10%, at least 20%, at least 25%, or at least 50% less.
As used herein, “specific hybridization” refers to the binding, duplexing, or hybridizing of a polynucleotide preferentially to a particular nucleotide sequence under stringent conditions.
As used herein, “stringent conditions” refers to conditions under which a probe will hybridize preferentially to its target subsequence, and to a lesser extent to, or not at all to, other sequences.
As used herein, “substantially homologous” or “substantially identical” in the context of two nucleic acids or polypeptides, generally refers to two or more sequences or subsequences that have at least 40%, 60%, 80%, 90%, 95%, 96%, 97%, 98% or 99% nucleotide or amino acid residue identity, when compared and aligned for maximum correspondence, as measured using sequence comparison algorithms or by visual inspection. The substantial identity can exist over any suitable region of the sequences, such as, for example, a region that is at least about 50 residues in length, a region that is at least about 100 residues, or a region that is at least about 150 residues. In certain embodiments, the sequences are substantially identical over the entire length of either or both comparison biopolymers.
The polynucleotide(s) encoding one or more enzyme activities for steps in the pathways of the invention may be derived from any source. Depending on the embodiment of the invention, the polynucleotide is isolated from a natural source such as bacteria, algae, fungi, plants, or animals; produced via a semi-synthetic route (e.g., the nucleic acid sequence of a polynucleotide is codon optimized for expression in a particular host cell, such as E. coli); or synthesized de novo. In certain embodiments, it is advantageous to select an enzyme from a particular source based on, e.g., the substrate specificity of the enzyme or the level of enzyme activity in a given host cell. In some embodiments of the invention, the enzyme and corresponding polynucleotide are naturally found in the host cell and over-expression of the polynucleotide is desired. In this regard, in some embodiments, additional copies of the polynucleotide are introduced in the host cell to increase the amount of enzyme. In some embodiments, over-expression of an endogenous polynucleotide may be achieved by upregulating endogenous promoter activity, or operably linking the polynucleotide to a more robust heterologous promoter.
Exogenous enzymes and their corresponding polynucleotides also are suitable for use in the context of the invention, and the features of the biosynthesis pathway or end product can be tailored depending on the particular enzyme used.
The invention contemplates that polynucleotides of the invention may be engineered to include alternative degenerate codons to optimize expression of the polynucleotide in a particular microorganism. For example, a polynucleotide may be engineered to include codons preferred in E. coli if the DNA sequence will be expressed in E. coli. Methods for codon-optimization are known in the art.
In certain embodiments, the microorganism produces an analog or variant of the polypeptide encoding an enzyme activity. Amino acid sequence variants of the polypeptide include substitution, insertion, or deletion variants, and variants may be substantially homologous or substantially identical to the unmodified polypeptides. In certain embodiments, the variants retain at least some of the biological activity, e.g., catalytic activity, of the polypeptide. Other variants include variants of the polypeptide that retain at least about 50%, preferably at least about 75%, more preferably at least about 90%, of the biological activity.
Substitutional variants typically exchange one amino acid for another at one or more sites within the protein. Substitutions of this kind can be conservative, that is, one amino acid is replaced with one of similar shape and charge. Conservative substitutions include, for example,
the changes of: alanine to serine; arginine to lysine; asparagine to glutamine; aspartate to glutamate; cysteine to serine; glutamine to asparagine; glutamate to aspartate; isoleucine to leucine or valine; leucine to valine or isoleucine; lysine to arginine; methionine to leucine or isoleucine; phenylalanine to tyrosine, leucine or methionine; serine to threonine; threonine to serine; tryptophan to tyrosine; tyrosine to tryptophan or phenylalanine; and valine to isoleucine or leucine. An example of the nomenclature used herein to indicate a amino acid substitution is “S345F ThrA” wherein the naturally occurring serine occurring at position 345 of the naturally occurring ThrA enzyme which has been substituted with a phenylalanine.
In some instances, the microorganism comprises an analog or variant of the exogenous or over-expressed polynucleotide(s) described herein. Nucleic acid sequence variants include one or more substitutions, insertions, or deletions, and variants may be substantially homologous or substantially identical to the unmodified polynucleotide. Polynucleotide variants or analogs encode mutant enzymes having at least partial activity of the unmodified enzyme. Alternatively, polynucleotide variants or analogs encode the same amino acid sequence as the unmodified polynucleotide. Codon optimized sequences, for example, generally encode the same amino acid sequence as the parent/native sequence but contain codons that are preferentially expressed in a particular host organism.
A polypeptide or polynucleotide “derived from” an organism contains one or more modifications to the naturally-occurring amino acid sequence or nucleotide sequence and exhibits similar, if not better, activity compared to the native enzyme (e.g., at least 70%, at least 80%, at least 90%, at least 95%, at least 100%, or at least 110% the level of activity of the native enzyme). For example, enzyme activity is improved in some contexts by directed evolution of a parent/naturally-occurring sequence. Additionally or alternatively, an enzyme coding sequence is mutated to achieve feedback resistance.
In some instances, enzymes with similar catalytic activities can be sourced and tested for propionyl-CoA oxidase activity from other organisms and used in this invention, an example being the short chain acyl-CoA oxidase from pumpkin (de Bellis, et. al. Plant Physiology 123: 327-334 (2000).
In some instances, the selected microorganism is modified to increase carbon flux through the metabolic pathway from glucose to propionyl-CoA, an example being the high flux through the threonine pathway engineered in E. coli (Lee, et. al, Molecular Systems Biology, 3: article 149 (2007). An organism so-modified to increase carbon flux overproduces propionyl-CoA compared to a wild-type organism. Modifications to the pyruvate and succinyl-CoA pathways can also be made to increase carbon flux. Carbon flux is the increase in rate of carbon flow through the metabolic pathways.
Expression Vectors/Transfer into Microorganisms
Expression vectors for recombinant genes can be produced in any suitable manner to establish expression of the genes in a microorganism. Expression vectors include, but are not limited to, plasmids and phage. The expression vector can include the exogenous polynucleotide operably linked to expression elements, such as, for example, promoters, enhancers, ribosome binding sites, operators and activating sequences. Such expression elements may be regulatable, for example, inducible (via the addition of an inducer). Alternatively or in addition, the expression vector can include additional copies of a polynucleotide encoding a native gene product operably linked to expression elements. Representative examples of useful heterologous promoters include, but are not limited to: the LTR (long terminal 35 repeat from a retrovirus) or SV40 promoter, the E. coli lac, tet, or trp promoter, the phage Lambda PL promoter, and other promoters known to control expression of genes in prokaryotic or eukaryotic cells or their viruses. In one aspect, the expression vector also includes appropriate sequences for amplifying expression. The expression vector can comprise elements to facilitate incorporation of polynucleotides into the cellular genome.
Introduction of the expression vector or other polynucleotides into cells can be performed using any suitable method, such as, for example, transformation, electroporation, microinjection, microprojectile bombardment, calcium phosphate precipitation, modified calcium phosphate precipitation, cationic lipid treatment, photoporation, fusion methodologies, receptor mediated transfer, or polybrene precipitation. Alternatively, the expression vector or other polynucleotides can be introduced by infection with a viral vector, by conjugation, by transduction, or by other suitable methods.
Microorganisms of the invention comprising recombinant genes are cultured under conditions appropriate for growth of the cells and expression of the gene(s). Microorganisms expressing the polypeptide(s) can be identified by any suitable methods, such as, for example, by PCR screening, screening by Southern blot analysis, or screening for the expression of the protein. In some embodiments, microorganisms that contain the polynucleotide can be selected by including a selectable marker in the DNA construct, with subsequent culturing of microorganisms containing a selectable marker gene, under conditions appropriate for survival of only those cells that express the selectable marker gene. The introduced DNA construct can be further amplified by culturing genetically modified microorganisms under appropriate conditions (e.g., culturing genetically modified microorganisms containing an amplifiable marker gene in the presence of a concentration of a drug at which only microorganisms containing multiple copies of the amplifiable marker gene can survive).
In some embodiments, the microorganisms (such as genetically modified bacterial cells) have an optimal temperature for growth, such as, for example, a lower temperature than normally encountered for growth and/or fermentation. In addition, in certain embodiments, cells of the invention exhibit a decline in growth at higher temperatures as compared to normal growth and/or fermentation temperatures as typically found in cells of the type.
Any cell culture condition appropriate for growing a microorganism and synthesizing a product of interest is suitable for use in the inventive method.
The methods of the invention optionally comprise a step of product recovery. Recovery of acrylate, 3-hydroxypropionyl-CoA, 3-hydroxypropionate or poly-3-hydroxypropionate can be carried out by methods known in the art. For example, acrylate can be recovered by distillation methods, extraction methods, crystallization methods, or combinations thereof; 3-hydroxypropionate can be recovered as described in U.S. Published Patent Application No. 2011/038364 or International Publication No. WO 2011/0125118; polyhydroxyalkanoates can be recovered as described in Yu and Chen, Biotechnol Prog, 22(2): 547-553 (2006); and 1,3 propanediol can be recovered as described in U.S. Pat. No. 6,428,992 or Cho et al., Process Biotechnology, 41(3): 739-744 (2006).
The following examples further describe and demonstrate embodiments within the scope of the present invention. The examples are given solely for the purpose of illustration and are not to be construed as limiting the present invention. Example 1 describes expression vectors for recombinant propionyl-CoA oxidase gene; Example 2 describes expression vectors for branched-chain alpha-ketoacid decarboxylase (KdcA); Example 3 describes expression vectors for Coenzyme-A acylating propionaldehyde dehydrogenase (PduP); Example 4 describes expression vectors for Acyl-CoA Thioesterase (TesB); Example 5 describes the transformation of E. coli; Example 6 describes the culturing of the E. coli; Example 7 describes the isolation of expressed proteins; Example 8 describes in vitro production of propionyl-CoA with 2-Keto acid dehydrogenases; Example 9 describes the assay for propionyl-CoA oxidase activity; Example 10 describes the production of acrylic acid from propionic acid using isolated enzymes; Example 11 describes increasing propionyl-CoA production by increasing carbon flow through the threonine-dependent pathway; Example 12 describes increasing 2-keto butyrate production by increasing carbon flow through the citramalate-dependent pathway; Example 13 describes the analytical procedures for the measurement of 2-ketobutyric acid, propionyl-CoA, acryloyl-CoA and acrylic acid; Example 14 describes the production of acrylic acid in engineered E. coli.
Expression Vector for Propionyl-CoA Oxidase Gene
An E. coli expression vector was constructed for production of a recombinant short chain acyl-CoA oxidase gene. A common cloning strategy was established utilizing the pET30a vector (Novagen [EMD Chemicals, Gibbstown, N.J.] #69909-30) providing for T7 promoter control and His-tagged recombinant proteins. Modifications to the pET30a vector were made by replacing the DNA sequence between the SphI and XhoI sites with a synthesized DNA sequence (SEQ ID NO: 107) (GenScript, Piscataway, N.J.). To facilitate cloning and expression, the synthesis design included the removal an XbaI site in the lac operator, streamlining the 5′ expression region by replacing the thrombin, S-tag and enterokinase site with an Factor Xa recognition site and modifying the multiple cloning site to include EcoRV, EcoRI, BamHI, Sad, and PstI sites. The resulting vector was designated pET30a-BB. A. thaliana acyl-CoA oxidase gene was codon-optimized for expression in E. coli and synthesized (GenScript, Piscataway, N.J.) (SEQ ID NO: 2). To facilitate cloning into the pET30a-BB vector, a 5′ prefix sequence (SEQ ID NO: 43) was added immediately upstream of the start codon and a SpeI, NotI and PstI restriction site 3′ suffix sequence (SEQ ID NO: 44) immediately downstream of the stop codon. The acyl-CoA oxidase gene sequence was further optimized by the removal of the common restriction sites: AvrII; BamHI; BglII; BstBI; EagI; EcoRI; EcoRV; HindIII; KpnI; NcoI; NheI; NotI; NspV; PstI; PvuII; SacI; SalI; SapI; SfuI; SpeI; XbaI; XhoI. The optimized sequence was cloned into the pET30a-BB vector at the KpnI and PstI sites. The resulting expression vector was designated pET30a-BB At ACO and the enzyme encoded (SEQ ID NO: 1).
Expression Vector for Branched-Chain Alpha-Ketoacid Decarboxylase (KdcA)
An E. coli expression vector was constructed for production of a recombinant branched-chain alpha-ketoacid decarboxylase (KdcA) gene. A common cloning strategy was established utilizing the modified pET30a-BB vector providing for T7 promoter control and His-tagged recombinant proteins. Lactococcus lactis branched-chain alpha-ketoacid decarboxylase gene was codon-optimized for expression in E. coli and synthesized (GenScript, Piscataway, N.J.). To facilitate cloning and expression, the synthesis design included the addition of EcoRI, NotI, XbaI restriction sites and a Ribosomal Binding Site (RBS) 5′ to the ATG start codon, and SpeI, NotI and PstI restriction sites 3′ to the stop codon. The branched-chain alpha-ketoacid decarboxylase gene sequence was further optimized by the removal of the common restriction sites: AvrII; BamHI; BglII; BstBI; EagI; EcoRI; EcoRV; HindIII; KpnI; NcoI; NheI; NotI; NspV; PstI; PvuII; SacI; SalI; SapI; SfuI; SpeI; XbaI; XhoI (SEQ ID NO: 24). The optimized sequence was cloned into the pET30a-BB vector at the EcoRI and PstI sites. The resulting expression vector was designated pET30a-BB Ll KDCA and the enzyme encoded (SEQ ID NO: 23).
Expression Vector for Coenzyme-A Acylating Propionaldehyde Dehydrogenase (PduP)
An E. coli expression vector was constructed for production of a recombinant Coenzyme-A acylating propionaldehyde dehydrogenase (PduP) gene. A common cloning strategy was established utilizing the modified pET30a-BB vector providing for T7 promoter control and His-tagged recombinant proteins. Salmonella enterica Coenzyme-A acylating propionaldehyde dehydrogenase gene was codon-optimized for expression in E. coli and synthesized (GenScript, Piscataway, N.J.). To facilitate cloning and expression, the synthesis design included the addition of EcoRI, NotI, XbaI restriction sites and a Ribosomal Binding Site (RBS) 5′ to the ATG start codon, and SpeI, NotI and PstI restriction sites 3′ to the stop codon. The Coenzyme-A acylating propionaldehyde dehydrogenase gene sequence was further optimized by the removal of the common restriction sites: AvrII; BamHI; BglII; BstBI; Eagl; EcoRI; EcoRV; HindIII; KpnI; NcoI; NheI; NotI; NspV; PstI; PvuII; SacI; SalI; SapI; SfuI; Spa; XbaI; XhoI (SEQ ID NO: 90). The optimized sequence was cloned into the pET30a-BB vector at the EcoRI and PstI sites. The resulting expression vector was designated pET30a-BB Se PDUP and the enzyme encoded (SEQ ID NO: 89).
Expression Vectors for Acyl-CoA Thioesterase Gene (tesB)
An E. coli expression vector was constructed for production of a recombinant short to medium-chain acyl-CoA thioesterase gene. A common cloning strategy was established utilizing the pET30a vector (Novagen [EMD Chemicals, Gibbstown, N.J.] #69909-30) providing for T7 promoter control and His-tagged recombinant proteins. E. coli acyl-CoA thioesterase II (TesB) gene was codon optimized for expression in E. coli and synthesized (GenScript, Piscataway, N.J.). To facilitate cloning, the synthesis design included the addition of BamHI and XbaI restriction sites 5′ to the ATG start codon, and SacI and HindIII restriction sites 3′ to the stop codon. The thioesterase gene sequences were further optimized by the removal of the common restriction sites: BamHI, BglII, BstBI, EcoRI, HindIII, KpnI, PstI, NcoI, NotI, SacI, SalI, XbaI, and XhoI (SEQ ID NO: 8). The optimized sequences were cloned into the pET30a vector at the BamHI and SacI sites. The resulting expression vector was designated pET30a Ec TesB and the enzyme encoded (SEQ ID NO: 7).
The recombinant plasmids were then used to transform chemically competent One ShotBL21 (DE3) pLysS E. coli cells (Invitrogen, Carlsbad, Calif.). Individual vials of cells were thawed on ice and gently mixed with 10 μg of plasmid DNA. The vials were incubated on ice for 30 minutes. The vials were briefly incubated at 42° C. for 30 seconds and quickly replaced back on ice for an additional 2 minutes. 250 μl of 37° C. SOC medium was added and the vials were secured horizontally on a shaking incubator platform and incubated for 1 hour at 37° C., 225 rpm. Aliquotes of 20 μl and 200 μl cells were plated onto selective LB agar (50 μg/ml kanamycin; 34 μg/ml chloramphenicol) plates to select for cells carrying the recombinant and pLysS plasmids respectively and incubated overnight at 37° C. Single colony isolates were isolated, cultured in 5 ml of selective LB broth and recombinant plasmids were isolated using a QIAPrep® Spin Miniprep Kit (Qiagen, Valencia, Calif.) spin plasmid miniprep kit. Plasmid DNAs were characterized by gel electrophoresis of restriction digests with AflIII.
Culture of E. coli
Overnight cultures of transformed strains (15 ml of LB broth; 34 μg/ml chloramphenicol; 50 μg/ml kanamycin) in 50 ml conical tubes were inoculated from a loop full of frozen glycerol stocks. Cultures were incubated overnight at 25° C. with 250 rpm shaking. LB broth (500 ml, containing 34 μg/ml chloramphenicol, 50 μg/ml kanamycin; equilibrated to 25° C.) in 2.8 L fluted Erlenmeyer flasks was inoculated from the overnight cultures at an optical density (OD) at 600 nm of ˜0.1. Cultures were continued at 25° C. with 250 rpm shaking and optical density monitored until A600 of ˜0.4. Plasmid recombinant gene protein expression was then induced by addition of 500 μL of 1M IPTG (Teknova, Hollister, Calif.; 1 mM final concentration). Cultures were further incubated for 24 hours at 25° C. with 250 rpm shaking before the cells were collected by centrifugationn and the pellets stored at −80° C.
His-tagged recombinant proteins were isolated by metal chelate affinity/gravity-flow chromatography utilizing nickel-nitrilotriacetic acid coupled Sepharose CL-6B resin (Ni-NTA, Qiagen, Valencia, Calif.) as follows: Cell pellets were thawed on ice and suspended in 20 ml of a 20 mM sodium phosphate, 500 mM NaCl, 20 mM imidazole (pH 7.4) binding buffer (with 1 mg/mL lysozyme and 1 Complete EDTA-free protease inhibitor pellet [Roche Applied Science, Indianapolis, Ind.]. Samples were incubated at 4° C. with 30 rpm rotation for 30 minutes. Cell lysates were disrupted 2× in a Thermo French Press; 1 inch cylinder; 1000 psi. Cell debris was pelleted by centrifugation for 1 hour at 15,000×g, 4° C. The supernatant was transferred to a 5 ml column bed of Ni-NTA equilibrated in binding buffer (20 mM sodium phosphate, 500 mM NaCl, 20 mM imidazole, pH 7.4). The Ni-NTA was suspended in the supernatant and incubated for 60 minutes with slow rocker mixing at 4° C. The bound media was then washed by gravity flow of 20× bed volumes (100 ml) of binding buffer followed by 10× bed volumes (50 ml) of rinse buffer (20 mM sodium phosphate, 500 mM NaCl, 100 mM imidazole, pH 7.4). Bound proteins were eluted by gravity-flow in 10× bed volumes (50 ml) of elution buffer (20 mM sodium phosphate, 500 mM NaCl, 500 mM imidazole, pH 7.4) and collected in fractions. Fraction samples were assayed for protein by SDS-PAGE analysis, pooled, and concentrated with Amicon Ultra-15 Centrifugal Filter Devices (EMD Millipore, Billerica, Mass.) with a 30K nominal molecular weight limit. The concentrated protein isolates were desalted and eluted into 3.5 ml of storage buffer (50 mM HEPES (pH 7.3-7.5); 300 mM NaCl; 20% glycerol) using PD-10 Desalting Columns (GE Healthcare Biosciences, Pittsburgh, Pa.)
In Vitro Production of Propionyl-CoA with 2-Keto acid Dehydrogenases
In a first assay, 2-ketobutyric acid (2 mM) was incubated with or without commercial porcine heart pyruvate dehydrogenase (1.4 mg/mL, Sigma) in the presence of coenzyme A (2 mM), β-NAD+ (2 mM), thiamine pyrophosphate (0.2 mM), MgCl2 (2 mM), and HEPES buffer (50 mM, pH 7.3). In a second assay, pyruvate dehydrogenase was substituted for porcine heart 2-ketoglutarate dehydrogenase (1.0 mg/mL, Sigma) while keeping the other components. In a third assay, purified 2-keto acid decarboxylase KdcA (1.8 μm) and propionaldehyde dehydrogenase PduP (1.8 μm) were used. The samples were incubated at room temperature for 17 h, followed by LC-MS analysis to determine concentrations of propionyl-CoA. Only when the dehydrogenases (and decarboxylase) were present, the product was detected in significant amounts (FIG. 7).
Propionyl-CoA Oxidase Activity Assay
To establish the enzymatic activity of purified acyl-CoA oxidase, solutions of propionyl-CoA (1 mM) were incubated with or without enzyme (11 μM) and commercial bovine liver catalse (60 μg/mL Sigma) in assay buffer (HEPES, 50 mM, pH 7.3) at room temperature for 3 h. Reaction and negative control samples lacking enzyme were analyzed by liquid chromatography coupled to mass spectrometry (LC-MS) to determine concentrations of propionyl-CoA and acryloyl-CoA (FIG. 8), confirming the activity of the purified enzyme.
In a different enzymatic assay, solutions of propionyl-CoA (1 mM) and 10-acetyl-3,7-dihydroxyphenoxazine (ADHP, 0.5 mM, Cell Biolabs) were incubated with commercial horseradish peroxidase (HRP, 1 U/mL, Cell Biolabs) and with or without purified acyl-CoA oxidase (11 μM) at room temperature. The formation of highly fluorescent resorufin, after reaction of ADHP with hydrogen peroxide generated during the enzymatic reaction, was followed by UV-Vis spectrophotometry (FIG. 9).
Production of Acrylic Acid from Propionic Acid Using Isolated Enzymes
Applying the strategy illustrated in FIG. 5, a 3 mL reaction mixture consisting of 10 mM propionic acid, 0.5 mM coenzyme A, 1 mM ATP, 1 mM MgCl2, 200 mM NaCl, 10% glycerol, 1 μM acyl-CoA oxidase, 0.5 U/mL acetyl-CoA synthetase (Sigma, Catalog #A1765-5MG: St. Louis, Mo.), 1,000 U/mL catalase (Sigma, Catalog #C40-100MG) and 50 mM HEPES, pH 7.3. The reaction was started with the addition of 0.5 μM propionyl-CoA transferase and incubated at 21° C. for 2 h. Aliquots of reaction mix were analyzed by high performance liquid chromatography (HPLC) using an Agilent 1100 system (Santa Clara, Calif.) monitoring absorbance at 196 nm and a Waters Atlantis T3 column (Catalog #186003748; Milford, Mass.). Mobile phases were 0.1% phosphoric acid in water (A) and 0.1% phosphoric acid in 80% acetonitrile/20% water (B). Analytes were eluted isocratically at 2% B in A over 12 min, followed by a linear gradient from 2% to 35% B in A over 18 min. The HPLC analysis indicates that acrylic acid was produced (FIG. 10). The identity of acrylic acid was confirmed by using external standards as well as by liquid chromatography-mass spectrometry (LC-MS) analysis as follows. Acrylic acid was quantitated by HPLC/negative electrospray ionization/isotope-dilution Fourier transform orbital trapping mass spectrometry using commercially available [13C]3-acrylic acid and a mixed mode ion exchange column (IMTAKT, SM-C18, 3 μM particle size). Gradient elution was performed (A=99/1 water:methanol, B=20 mM ammonium formate in 5/95 water:methanol, flow=300 μL/min, 100% A, 0-3 min, then ramp to 15% B over 3-10 min).
Increasing Propionyl-CoA Production by Increasing Carbon Flow Through the Threonine-Dependent Pathway
This example demonstrates that increasing carbon flow through a pathway utilizing threonine increases propionyl-CoA production in host cells. An E. coli strain was modified to increase production of threonine deaminase. Threonine deaminase promotes the conversion of threonine to 2-ketobutyrate. An expression vector comprising an E. coli threonine deaminase coding sequence, tdcB, operably linked to a trc promoter was constructed. To isolate tdcB, genomic DNA was prepared from E. coli BW25113 (E. coli Genetic Stock Center, Yale University, New Haven, Conn.) by picking an isolated colony from a Luria agar plate, suspending the colony in 100 μl Tris (1 mM; pH 8.0), 0.1 mM EDTA, boiling the sample for five minutes, and removing the insoluble debris by centrifugation. tdcB was amplified from the genomic DNA sample by PCR using primers GTGCCATGGCTCATA TTACATACGATCTGCCGGTTGC (SEQ ID NO: 47) and GATCGAATTCATCCTTAGGCGTCAACGAAACCGGTGATTTG (SEQ ID NO: 48). PCR was performed on samples having 1 μl of E. coli BW25113 genomic DNA, 1 μl of a 10 μM stock of each primer, 25 μl of Pfu Ultra II Hotstart 2× master mix (Agilent Technologies, Santa Clara, Calif.), and 22 μl of water. PCR conditions were as follows: the samples were initially incubated at 95° C. for two minutes, followed by three cycles at 95° C. for 20 seconds (strand separation), 56° C. for 20 seconds (primer annealing), and 72° C. primer extension for 30 seconds. In addition, 27 cycles were run at 95° C. for 20 seconds, 60° C. for 20 seconds, and 72° C. primer extension for 30 seconds. There was a three minute incubation at 72° C., and the samples were held at 4° C.
The PCR products were purified using a QIAquick® PCR Purification Kit (Qiagen), double digested with restriction enzymes HindIII and NcoI, and ligated (Fast-Link Epicentre Biotechnologies, Madison, Wis.) with HindIII/NcoI-digested pTrcHisA vector (Invitrogen, Carlsbad, Calif.). The ligation mix was used to transform OneShot Top10™ E. coli cells (Invitrogen, Carlsbad, Calif.). Individual vials of cells were thawed on ice and gently mixed with 2 μl of ligation mix. The vials were incubated on ice for 30 minutes. The vials were briefly incubated at 42° C. for 30 seconds and quickly replaced back on ice for an additional 2 minutes. 250 μl of 37° C. SOC medium was added and the vials were secured horizontally on a shaking incubator platform and incubated for 1 hour at 37° C., 225 rpm. Aliquots of 20 μl and 200 μl cells were plated onto selective LB agar (100 μg/ml ampicillin). Single colony isolates were isolated, cultured in 50 ml of selective LB broth and the recombinant plasmid was isolated using a Qiagen HiSpeed Plasmid Midi Kit and characterized by gel electrophoresis of restriction digests with HindIII and NcoI. DNA sequencing confirmed that the tdcB insert had been cloned and that the insert encoded the published amino acid sequence (Genbank number U00096.2) (SEQ ID NOs: 55 and 56). The resulting plasmid was designated pTrcHisA Ec tdcB.
Increasing 2-Keto Butyrate Production by Increasing Carbon Flow Through the Citramalate-Dependent Pathway
This example describes the generation of a recombinant microbe that produces exogenous citramalate synthase to further increase 2-keto butyrate production. A Methanococcus jannaschii citramalate synthase gene was codon optimized for enzyme activity in E. coli (Atsumi et al., Applied and Environmental Microbiology 74: 7802-8 (2008)). The native M. jannaschii citramalate synthase coding sequence also was mutated through directed evolution to improve enzyme activity and feedback resistance. E. coli is not known to have citramalate synthase activity, and a strain was engineered to produce exogenous citramalate synthase while overproducing three native E. coli enzymes: LeuB, LeuC, and LeuD. Citramalate synthase, LeuB, LeuC, and LeuD mediate the first four chemical conversions in the citramalate pathway to produce 2-keto butyrate.
To generate a synthetic CimA3.7 gene codon-optimized for E. coli expression, a DNA fragment (SEQ ID NO: 57) coding for the amino acid sequence (SEQ ID NO: 105) containing a restriction site BspHI (bases 1-6), codon-optimized cimA3. 7 fragment (bases 3-1118), stop codon TGA (bases 1119-1121), a fragment of 52 bases from the start of the E. coli leuB gene (bases 1121-1173), and a linker sequence (bases 1174-1209) containing NotI, PacI, PmeI, XbaI and EcoRI sites was synthesized (GenScript, Piscataway, N.J.). The stop codon of cimA3. 7 (TGA) and start codon (ATG) of leuB overlaps one base (A), presumably to enable translational coupling. This overlap mimics the native leuA and leuB coupling in E. coli. The synthesized fragment was digested with BspHI and EcoRI and cloned into pTricHisA (Invitrogen) at the NcoI and EcoRI sites, using the compatible ends generated by BspHI and NcoI. The end of the leuB fragment (bases 1168-1173) also contains a BspEI site for cloning for leuBCD. This vector was designated as pTrcHisA Mj cimA.
To fuse the three-gene complex leuBCD behind M. jannaschii cimA, E. coli leuBCD cDNA was amplified from an E. coli BW25113 genomic DNA sample using PCR primers (SEQ ID NO: 58 and SEQ ID NO: 59), which included a BspEI restriction site in leuB and incorporated a NotI restriction site 3′ of the stop codon of leuD during the PCR reaction. The PCR was performed with 50 μl of Pfu Ultra II Hotstart 2× master mix (Agilent Technologies, Santa Clara, Calif.), 1 μl of a mix of the two primers (10 μmoles of each), 1 μl of E. coli BW25113 genomic DNA, and 48 μl of water. The PCR began with a two minute incubation at 95° C., followed by 30 cycles of 20 seconds at 95° C. for denaturation, 20 seconds for annealing at 64° C., and two minutes at 72° C. for extension. The sample was incubated at 72° C. for three minutes and then held at 4° C. The PCR product (leuBCD insert, SEQ ID NO: 60) was purified using a QIAquick® PCR Purification Kit (Qiagen, Valencia, Calif.).
The leuBCD insert and the bacterial expression vector pTrcHisA Mj cimA were digested with BspEI. The digested vector and leuBCD insert were again purified using a QIAquick®PCR purification columns prior to being restriction digested with NotI. Following final column purification, the digested vector and insert were ligated using Fast-Link (Epicentre Biotechnologies, Madison, Wis.). The ligation mix was then used to transform E. coli TOP10 cells (Invitrogen, Carlsbad, Calif.). Individual vials of cells were thawed on ice and gently mixed with 2 μl of ligation mix. The vials were incubated on ice for 30 minutes. The vials were briefly incubated at 42° C. for 30 seconds and quickly replaced back on ice for an additional 2 minutes. 250 μl of 37° C. SOC medium was added and the vials were secured horizontally on a shaking incubator platform and incubated for 1 hour at 37° C., 225 rpm. Aliquotes of 20 μl and 200 μl cells were plated onto selective LB agar (100 μg/ml ampicillin). Single colony isolates were isolated, cultured in 5 ml of selective LB broth and the recombinant plasmids were isolated using a QIAPrep® Spin Miniprep Kit (Qiagen) and characterized by gel electrophoresis of restriction digests with AflIII. DNA sequencing confirmed that the leuBCD insert had been cloned and that the insert encoded the published amino acid sequences (GenBank Accession No. AAC73184 (Ec leuB) (SEQ ID NO: 61); GenBank Accession No. AAC73183 (Ec leuC) (SEQ ID NO: 62); and GenBank Accession No. AAC73182 (Ec leuD) (SEQ ID NO: 106). The resulting plasmid was designated pTrc Mj cimA Ec leuBCD.
Acyl-CoA and Organic Acid Assays for Cell Cultures
Coenzyme-A Analysis Sample Processing
Samples were prepared for CoA analysis. A stable-labeled (deuterium) internal standard containing master mix is prepared, comprising d3-3-hydroxymethylglutaryl-CoA (200 μl of 60 μg/ml stock in 10 ml of 15% trichloroacetic acid). An aliquot (500 μl) of the master mix is added to a 2-ml microcentrifuge tube. Silicone oil (AR200; Sigma catalog number 85419; 700 μl) is layered onto the master mix. An E. coli culture (700 μl) is layered gently on top of the silicone oil. The sample is subject to centrifugation at 20,000 g for five minutes at 4° in an Eppendorf 5417C centrifuge. A portion (˜240 μl) of the master mix-containing layer (lower layer) is transferred to an empty tube and frozen on dry ice for 30 minutes prior to storage at −80° C.
Culture Broth Processing for 2-Ketobyric Acid and Acrylic Acid Analyses
Culture samples were processed for metabolite analysis as follows: Cells were pelleted by centrifugation at 5000×g; 4° C. Supernatants were filtered through Acrodisc Syringe Filters (0.2 μm HT Tuffryn membrane; low protein binding; Pall Corporation, Ann Arbor, Mich.) and frozen on dry ice prior to storage at −80° C.
Measurement of Acyl-CoA Levels.
The following method was used to prepare samples for acyl-CoA analysis. A stable-labeled (deuterium) internal standard-containing master mix was prepared, comprising d3-3-hydroxymethylglutaryl-CoA (Cayman Chemical Co., 200 μl of 50 μg/ml stock in 10 ml of 15% trichloroacetic acid). An aliquot (500 μl) of the master mix was added to a 2-ml tube. Silicone oil (AR200; Sigma catalog number 85419; 800 μl) was layered onto the master mix. Clarified E. coli culture broth (800 μl) was layered gently on top of the silicone oil. The sample was subjected to centrifugation at 20,000 g for five minutes at 4° in an Eppendorf 5417C centrifuge. A portion (300 μl) of the master mix-containing layer was transferred to an empty tube and frozen on dry ice for 30 minutes.
The acyl-CoA content of samples was determined using LC/MS/MS. Individual CoA standards (CoA and acetyl-CoA) were purchased from Sigma Chemical Company (St. Louis, Mo.) and prepared as 500 μg/ml stocks in methanol. Acryloyl-CoA was synthesized and prepared similarly. The analytes were pooled, and standards with all of the analytes were prepared by dilution with 15% trichloroacetic acid. Standards for regression were prepared by transferring 500 μl of the working standards to an autosampler vial containing 10 μL of the 50 μg/ml internal standard. Sample peak areas (or heights) were normalized to the stable-labeled internal standard (d3-3-hydroxymethylglutaryl-CoA,). Samples were assayed by HPLC/MS/MS on a Sciex API5000 mass spectrometer in positive ion Turbo Ion Spray. Separation was carried out by reversed-phase high performance liquid chromatography using a Phenomenex Onyx Monolithic C18 column (2×100 mm) and mobile phases of 1) 5 mM ammonium acetate, 5 mM dimethylbutylamine, 6.5 mM acetic acid and 2) acetonitrile with 0.1% formic acid, with the following gradient at a flow rate of 0.6 ml/min:
0 min 97.5 2.5
1.0 min 97.5 2.5
2.5 min 91.0 9.0
5.5 min 45 55
6.0 min 45 55
6.1 min 97.5 2.5
7.5 min — —
9.5 min End Run
The conditions on the mass spectrometer were: DP 160, CUR 30, GS1 65, GS2 65, IS 4500, CAD 7, TEMP 650 C. The following transitions were used for the multiple reaction monitoring (MRM):
Compound Ion* Ion* Collision Energy CXP
n-Propionyl-CoA 824.3 317.2 41 32
Succinyl-CoA 868.2 361.1 49 38
Iso-Butyrl-CoA 838.3 331.2 43 21
Lactoyl-CoA 840.3 333.2 45 38
Acroyl-CoA 822.4 315.4 45 36
CoA 768.3 261.2 45 34
Isovaleryl-CoA 852.2 345.2 45 34
Malonyl-Coa 854.2 347.2 41 36
Acetyl-CoA 810.3 303.2 43 30
d3-3- 915.2 408.2 49 13
*Energies, in volts, for the MS/MS analysis
2-Ketobutyric Acid and Threonine Determination by Liquid Chromatograpny/Mass Spectometry
The 2-ketobutyrate and threonine content of samples was determined using LC/MS/MS. A threonine standard was purchased from Sigma Chemical Company (St. Louis, Mo.) and a 2-ketobutryate standard obtained from Sigma-Aldrich. Stocks were prepared at 1.0 mg/ml in 50/50 methanol/water then standards of individual analtyes were prepared by dilution with 50/50 acetonitrile/water. Standards for regression were prepared by transferring 1.0 ml of the working standards to an autosampler vial containing 25 μL of the 20 μg/ml internal standard (L-threonine U13C4 UD5 15N and 2-ketobutyric Acid 13C4 3,3-D2) Samples were prepared by a 1:10 dilution was prepared by taking 100 μL of sample to a vial with 25 μL IS and 900 μL of 50:50 acetonitrile/water, cap and vortex to mix.
Sample peak areas were normalized to the stable-labeled internal standard for each analyte. Samples were assayed by HPLC/MS/MS on a Sciex API5000 mass spectrometer in positive ion Turbo Ion Spray. Separation was carried out by reversed-phase high performance liquid chromatography using a ZIC-HILIC, 2.1×50 mm, 5-μm particles and mobile phases of 1) 0.754% formic acid in water and 2) acetonitrile with 0.754% formic acid, with the following gradient at a flow rate of 0.35 ml/min:
0 min 97.5 95
1.0 min 97.5 95
4.0 min 91.0 5
5.0 min 45 5
5.1 min 45 95
9.0 min End Run
The mass spectrometer was run in a two period mode with the first period configured in negative ionization to determine 2-ketobutryate and corresponding internal standard. The conditions on the mass spectrometer were: DP-60, CUR 30, GS1 60, GS2 60, IS-3500, CAD 12, TEMP 500 C. The following transitions were used for the multiple reaction monitoring (MRM):
Compound Ion* Product Ion* Collision Energy CXP
2-Ketobutyric Acid 101.1 56.9 −12 −23
2-Ketobutyric Acid 107.1 60.9 −12 −23
13C4 3,3-D2
The second period was configured in positive ionization to determine threonine and corresponding internal standard. The conditions on the mass spectrometer were: DP 30, CUR 30, GS1 60, GS2 60, IS 3500, CAD 12, TEMP 500 C. The following transitions were used for the multiple reaction monitoring (MRM):
Compound Ion* Ion* Energy CXP
Threonine 120.1 57.0 17 15
L-Threonine U13C4 UD5 15N 125.1 60.1 17 15
Acrylic Acid Determination
An internal Standard solution of 100 μg/mL of 13C3-labelled acrylic acid in 1:1 MeOH:H2O was prepared. External Standard solutions were prepared at acrylic acid concentrations of 2.5 μg/mL, 5 μg/mL and 10 μg/mL in 1:1 MeOH:H2O. 900 μL of filtered supernatant or External Standard was added to 100 μL of the Internal Standard solution. These solutions were subjected to Ion Exclusion LC separations and MS detection.
The LC separation conditions were as follows: 10 μL of sample/standard were injected onto a Thermo Fisher Dionex ICE-AS1 (4×250 mm) column (with guard) running an isocratic mobile phase of 1 mM heptafluorbutyric acid at a flow rate of 0.15 mL/min. 20 mM NH4OH in MeCN at 0.15 mL/min was teed into the column effluent.
The MS detection conditions were as follows: A Sciex API-4000 MS was run in negative ion mode and monitored the m/z 71 (unit resolution) ion of acrylic acid and the m/z 74 (unit resolution) ion of 13C3-labelled acrylic acid. The dwell time used was 300 ms, the declustering potential was set at −38, the entrance potential was set at −10, the collision energy was set at −8, the collision set exit potential was set at −8, the collision gas was set at 12, the curtain gas was set at 15, the ion source gas 1 was set at 55, the ion source gas 2 was set at 55, the ionspray voltage was set at −3500, the temperature was set at 650, the interface heater was on. An elution profile is shown in FIG. 14.
Production of Acrylic Acid in Engineered E. coli
This example demonstrates that increasing carbon flow through a pathway utilizing threonine increases propionyl-CoA production in host cells which can then be converted to acrylic acid. An E. coli strain was established to overexpress E. coli threonine deaminase (SEQ ID NO: 56), L. lactis branched-chain 2-keto acid decarboxylase (KdcA) set out in SEQ ID NO: 23), S. enterica Coenzyme-A acylating propionaldehyde dehydrogenase (PduP) set out in SEQ ID NO: 89, A. thaliana acryl-CoA oxidase set out in amino acid SEQ ID NO: 1, and the E. coli thioesterase II (TesB), set out in amino acid SEQ ID NO: 7.
In this example threonine deaminase (SEQ ID NO: 56) promotes the conversion of threonine to 2-ketobutyrate. The L. lactis branched-chain 2-keto acid decarboxylase (KdcA) set out in SEQ ID NO: 46) and a S. enterica Coenzyme-A acylating propionaldehyde dehydrogenase (PduP) set out in SEQ ID NO: 89 catalyzes a reaction to convert 2-keto-butyrate to propionyl-CoA. The A. thaliana acryl-CoA oxidase catalyzes a reaction to convert propionyl-CoA to acryloyl-CoA. The E. coli thioesterase II (TesB), set out in amino acid SEQ ID NO: 7 catalyzes a reaction to convert acryloyl-CoA to acrylate.
An E. coli expression vector was constructed for overexpression of a recombinant A. thaliana acryloyl-CoA oxidase and E. coli threonine dehydratase (TdcB). The E. coli tdcB was PCR amplified from the vector pTrcHisA Ec tdcB (Example 11) (SEQ ID NOs: 55 and 56) using the following primers:
Ec tdcB-BB fwd [5′→3′]:
TCGAATTCGCGGCCGCTTCTAGAAGGAGATATACATATGGCTCATATTAC
ATACGATCTGCCG;
Ec tdcB-BB rev [5′→3′]:
AGCTGCAGCGGCCGCTACTAGTATTAGGCGTCAACGAAACCGGTG.
PCR was performed on samples having 30 ng of pTrcHisA Ec tdcB plasmid DNA, 1 μl of a 10 μM stock of each primer, 50 μl of Pfu Ultra II Hotstart 2× master mix (Agilent Technologies, Santa Clara, Calif.), and 47 μl of water. PCR conditions were as follows: the samples were initially incubated at 95° C. for two minutes, followed by thirty cycles at 95° C. for 20 seconds (strand separation), 58° C. for 20 seconds (primer annealing), and 72° C. primer extension for 90 seconds. There was a three minute incubation at 72° C., and the samples were held at 10° C.
The PCR product was purified using a QIAquick® PCR Purification Kit (Qiagen), double digested with restriction enzymes Xba I and Pst I, and ligated (Fast-Link Epicentre Biotechnologies, Madison, Wis.) with SpeI/PstI-digested pET30a-BB At ACO vector (SEQ ID NO: 1 and 2). The ligation mix was used to transform OneShot Top10™ E. coli cells (Invitrogen, Carlsbad, Calif.). Individual vials of cells were thawed on ice and gently mixed with 2 μl of ligation mix. The vials were incubated on ice for 30 minutes. The vials were briefly incubated at 42° C. for 30 seconds and quickly replaced back on ice for an additional 2 minutes. 250 μl of 37° C. SOC medium was added and the vials were secured horizontally on a shaking incubator platform and incubated for 1 hour at 37° C., 225 rpm. Aliquotes of 20 μl and 200 μl cells were plated onto selective LB agar (50 μg/ml kanamycin). Single colony isolates were isolated, cultured in 5 ml of selective LB broth and the recombinant plasmid was isolated using a Qiagen Plasmid Mini Kit and characterized by gel electrophoresis of restriction digests with AflIII. DNA sequencing confirmed that the tdcB insert had been cloned and that the insert encoded the published amino acid sequence (Genbank number U00096.2) (SEQ ID NOs: 55 and 56). The resulting plasmid was designated pET30a-BB At ACO_Ec TdcB.
An E. coli expression vector was constructed for overexpression of a recombinant A. thaliana Acryl CoA oxidase, E. coli threonine dehydratase (TdcB), and E. coli thioesterase II (TesB). The codon optimized E. coli thioesterase II (TesB) gene was PCR amplified from the vector pET30a Ec TesB (Example 4) for cloning into the vector pET30a-BB At ACO_Ec TdcB using the following primers:
Ec TesB-BB fwd [5′→3′]:
TCGAATTCGCGGCCGCTTCTAGAAGGAGATATACATATGAGCCAAGCCCT
GAAAAAC;
Ec TesB-BB rev [5′→3′]:
AGCTGCAGCGGCCGCTACTAGTATTAGTTGTGATTACGCATAACGCC.
PCR was performed on samples having 30 ng of pET30a Ec tesB plasmid DNA, 1 μl of a 10 μM stock of each primer, 50 μl of Pfu Ultra II Hotstart 2× master mix (Agilent Technologies, Santa Clara, Calif.), and 47 μl of water. PCR conditions were as follows: the samples were initially incubated at 95° C. for two minutes, followed by thirty cycles at 95° C. for 20 seconds (strand separation), 58° C. for 20 seconds (primer annealing), and 72° C. primer extension for 90 seconds. There was a three minute incubation at 72° C., and the samples were held at 10° C.
The PCR product was purified using a QIAquick® PCR Purification Kit (Qiagen), double digested with restriction enzymes Xba I and Pst I, and ligated (Fast-Link Epicentre Biotechnologies, Madison, Wis.) with SpeI/PstI-digested pET30a-BB At ACO_Ec TdcB vector. The ligation mix was used to transform OneShot Top10™ E. coli cells (Invitrogen, Carlsbad, Calif.). Individual vials of cells were thawed on ice and gently mixed with 2 μl of ligation mix. The vials were incubated on ice for 30 minutes. The vials were briefly incubated at 42° C. for 30 seconds and quickly replaced back on ice for an additional 2 minutes. 250 μl of 37° C. SOC medium was added and the vials were secured horizontally on a shaking incubator platform and incubated for 1 hour at 37° C., 225 rpm. Aliquotes of 20 μl and 200 μl cells were plated onto selective LB agar (50 μg/ml kanamycin). Single colony isolates were isolated, cultured in 5 ml of selective LB broth and the recombinant plasmid was isolated using a Qiagen Plasmid Mini Kit and characterized by gel electrophoresis of restriction digests with AflIII. DNA sequencing confirmed that the tesB insert had been cloned and that the insert encoded the published amino acid sequence (SEQ ID NOs: 7 and 8). The resulting plasmid was designated pET30a-BB At ACO_Ec TdcB_Ec TesB.
An E. coli expression vector was constructed for overexpression of a recombinant S. enterica Coenzyme-A acylating propionaldehyde dehydrogenase (PduP) and L. lactis branched-chain 2-keto acid decarboxylase (KdcA). The codon optimized L. lactis branched-chain 2-keto acid decarboxylase (kdcA) from pET30a-BB Ll KDCA (Example 2) was cloned into pET30a-BB Se PDUP (Example 3) by double digestion of pET30a-BB Ll KDCA with restriction enzymes Xba I and Pst I. The Ll KDCA fragment was band isolated, purified using a QIAquick Gel Extraction Kit (Qiagen, Carlsbad, Calif.) and ligated (Fast-Link Epicentre Biotechnologies, Madison, Wis.) with SpeI/PstI-digested pET30a-BB Se PDUP vector. The ligation mix was used to transform OneShot Top10™ E. coli cells (Invitrogen, Carlsbad, Calif.). Individual vials of cells were thawed on ice and gently mixed with 2 μl of ligation mix. The vials were incubated on ice for 30 minutes. The vials were briefly incubated at 42° C. for 30 seconds and quickly replaced back on ice for an additional 2 minutes. 250 μl of 37° C. SOC medium was added and the vials were secured horizontally on a shaking incubator platform and incubated for 1 hour at 37° C., 225 rpm. Aliquots of 20 μl and 200 μl cells were plated onto selective LB agar (50 μg/ml kanamycin). Single colony isolates were isolated, cultured in 5 ml of selective LB broth and the recombinant plasmid was isolated using a Qiagen Plasmid Mini Kit and characterized by gel electrophoresis of restriction digests with AflIII. The resulting plasmid was designated pET30a-BB Se PDUP_Ll KDCA.
To facilitate cotransformation with pET30a-BB At ACO_Ec TdcB_Ec TesB the codon optimized S. enterica Coenzyme-A acylating propionaldehyde dehydrogenase (PduP) and L. lactis Branched-chain 2-keto acid decarboxylase (KdcA) gene pair was subcloned from pET30a-BB Se PDUP_Ll KDCA into the pCDFDuet-1 vector (Novagen [EMD Chemicals, Gibbstown, N.J.] #71340-3) by double digestion of pET30a-BB Se PDUP_Ll KDCA with restriction enzymes EcoRI and Pst I. The Se PDUP_Ll KDCA fragment was band isolated, purified using a QIAquick Gel Extraction Kit (Qiagen, Carlsbad, Calif.) and ligated (Fast-Link Epicentre Biotechnologies, Madison, Wis.) with EcoRI/PstI-digested pCDFDuet-1. The ligation mix was used to transform OneShot Top10™ E. coli cells (Invitrogen, Carlsbad, Calif.). Individual vials of cells were thawed on ice and gently mixed with 2 μl of ligation mix. The vials were incubated on ice for 30 minutes. The vials were briefly incubated at 42° C. for 30 seconds and quickly replaced back on ice for an additional 2 minutes. 250 μl of 37° C. SOC medium was added and the vials were secured horizontally on a shaking incubator platform and incubated for 1 hour at 37° C., 225 rpm. Aliquots of 20 μl and 200 μl cells were plated onto selective LB agar (50 μg/ml spectinomycin). Single colony isolates were isolated, cultured in 5 ml of selective LB broth and the recombinant plasmid was isolated using a Qiagen Plasmid Mini Kit and characterized by gel electrophoresis of restriction digests with AflIII. The resulting plasmid was designated pCDFDuet-1 Se PDUP_Ll KDCA.
Co-Transformation of E. coli
The recombinant plasmids and empty parent vectors were used to co-transform chemically competent BL21 (DE3) pLysS E. coli cells (Invitrogen, Carlsbad, Calif.) in the following combinations:
pET30a-BB At ACO_Ec TdcB_Ec TesB and pCDFDuet-1 Se PDUP_Ll KDCA
pET30a-BB At ACO_Ec TdcB and pCDFDuet-1 Se PDUP_Ll KDCA
pET30a-BB and pCDFDuet-1
Individual vials of cells were thawed on ice and gently mixed with 50 μs of plasmid DNA. The vials were incubated on ice for 30 minutes. The vials were briefly incubated at 42° C. for 30 seconds and quickly replaced back on ice for an additional 2 minutes. 250 μl of 37° C. SOC medium was added and the vials were secured horizontally on a shaking incubator platform and incubated for 1 hour at 37° C., 225 rpm. Aliquotes of 20 μl and 200 μl cells were plated onto selective LB agar (50 μg/ml kanamycin; 50 μg/ml spectinomycin; 34 μg/ml chloramphenicol) plates to select for cells carrying the recombinant pET30a-BB, pCDFDuet-1 and pLysS plasmids respectively and incubated overnight at 37° C. Single colony isolates were isolated, cultured in 5 ml of selective LB broth and the recombinant plasmids were isolated using a QIAPrep® Spin Miniprep Kit (Qiagen, Valencia, Calif.) and characterized by gel electrophoresis of restriction digests with AvaI.
Overnight cultures of the co-transformed BL21 (DE3) pLysS strains (10 ml of minimal M9 media; 34 μg/ml chloramphenicol; 50 μg/ml kanamycin and 50 μg/ml spectinomycin) in 50 ml conical tubes were inoculated from single colony forming units from minimal M9 agar plates. Cultures were incubated overnight at 37° C. with 250 rpm shaking. Fresh cultures (30 ml of minimal M9 media; 34 μg/ml chloramphenicol; 50 μg/ml kanamycin and 50 μg/ml spectinomycin) in 250 ml Erlenmeyer flasks were inoculated from the overnight cultures at an optical density at 600 nm (OD600) of ˜0.01. The second cultures were incubated at 37° C. with 250 rpm shaking overnight. Two sets of test cultures (50 ml of minimal M9 media; 34 μg/ml chloramphenicol; 50 μg/ml kanamycin and 50 μg/ml spectinomycin) in 500 ml Erlenmeyer flasks were inoculated from the second overnight cultures at an OD600 of ˜0.2. One set of these cultures was further supplemented with 1 g/L L-threonine (Sigma-Adlrich). All cultures were incubated at 25° C. with 250 rpm shaking and optical density monitored until OD600 of ˜0.4. All cultures were then supplemented with 100×BME vitamins (Sigma-Aldrich) at a 10× final concentration and plasmid recombinant gene protein expression was then induced by addition of 50 μL of 1M IPTG (Teknova, Hollister, Calif.; 1 mM final concentration). Cultures were further incubated for 18 hours at 25° C. with 250 rpm shaking before the cells were processed for analysis and stored at −80° C.
Minimal M9 Media Component 1X Base Recipe
CaCl2* 2H2O 0.1 mM
Dextrose 80 mM
Chloramphenicol 34 μg/mL
100X BME Vitamins (added as 10X; Sigma-Aldrich,
D-Biotin (0.1 g/L) 10 mg/L
Choline Chloride (0.1 g/L) 10 mg/L
Folic Acid (0.1 g/L) 10 mg/L
myo-Inositol (0.2 g/L) 20 mg/L
Niacinamide (0.1 g/L) 10 mg/L
p-Amino Benzoic Acid (0.1 g/L) 10 mg/L
D-Pantothenic Acid•½Ca (0.1 g/L) 10 mg/L
Pyridoxal•HCl (0.1 g/L) 10 mg/L
Riboflavin (0.01 g/L) 1 mg/L
Thiamine•HCl (0.1 g/L) 10 mg/L
NaCl (8.5 g/L) 0.85 g/L
Production of Acrylic Acid by Engineered E. coli
The data shows that the presence of intermediates and acrylic acid in the threonine to acrylic acid pathway are dependent upon the expression of the genes. Endogenous threonine likely supports production when no exogenous threonine was added to the culture medium. When threonine is added, an increase in 2-ketobutyrate and acrylic acid was observed.
Expressed Threonine Acrylic Acid
Heterologous Addition 2-Ketobutyrate Propionyl- Acryloyl- in Broth*
Genes (g/L) in Broth (μg/ml) CoA (ng/mL) CoA (ng/mL) (μg/ml)
tdcB, kdcA, pduP, 0 <0.25 204 7.3 0.44
ACO, tesB
tdcB, kdcA, pduP, 0 5.1 415 75 0.21
None 0 <0.25 9.3 <2.5 0.03
tdcB, kdcA, pduP, 1 14.7 317 9.1 0.62
tdcB, kdcA, pduP, 1 31.0 425 85 0.27
None 1 1.0 8.8 1.9 0.08
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