Method for the preparation of 2,4-dihydroxybutyrate

• US 11,505,811 B2
• Filed: 01/13/2020
• Issued: 11/22/2022
• Est. Priority Date: 07/11/2012
• Status: Active Grant

• Current Assignee: Adisseo France S.A.S. (China National Chemical Corporation)
• Original Assignee: Adisseo France S.A.S. (China National Chemical Corporation)
• Inventors: Walther, Thomas, Cordier, Helene, Dressaire, Clementine, Francois, Jean Marie, Huet, Robert
• Primary Examiner(s): Tsay, Marsha
• Application Number:
  US16/740,598
• Publication Number:
  US 20200131542A1
• Time in Patent Office: 1,044 Days
• Field of Search: None
• CPC Class Codes: C12N 15/70 Vectors or expression systems specially adapted for E. coli
• CPC Class Codes: C12N 9/0006 acting on CH-OH groups as donors (1.1)
• CPC Class Codes: C12N 9/1096 transferring nitrogenous groups (2.6)
• CPC Class Codes: C12P 7/42 Hydroxy-carboxylic acids
• CPC Class Codes: C12Y 101/01027 L-Lactate dehydrogenase (1.1.1.27)
• CPC Class Codes: C12Y 101/01028 D-Lactate dehydrogenase (1.1.1.28)
• CPC Class Codes: C12Y 101/01037 Malate dehydrogenase (1.1.1.37)
• CPC Class Codes: C12Y 101/01082 Malate dehydrogenase (NADP+) (1.1.1.82)
• CPC Class Codes: C12Y 101/01272 (R)-2-Hydroxyacid dehydrogenase (1.1.1.272)
• CPC Class Codes: C12Y 101/01299 Malate dehydrogenase (NAD(P)+)(1.1.1.299)
• CPC Class Codes: C12Y 206/01001 Aspartate transaminase (2.6.1.1), i.e. aspartate-aminotransferase
• CPC Class Codes: C12Y 206/01042 Branched-chain-amino-acid transaminase (2.6.1.42)
• CPC Class Codes: C12Y 206/01057 Aromatic-amino-acid transaminase (2.6.1.57)

Abstract

A method for the preparation of 2,4-dihydroxybutyric acid from homoserine includes a first step of conversion of the primary amino group of homoserine to a carbonyl group to obtain 2-oxo-4-hydroxybutyrate, and a second step of reduction of the obtained 2-oxo-4-hydroxybutyrate (OHB) to 2,4-dihydroxybutyrate.

Claims

1. A method for the preparation of 2,4-dihydroxybutyrate (2,4-DHB) from homoserine comprising:

deaminating homoserine to form 2-oxo-4-hydroxybutyrate (OHB), where the deamination of homoserine is catalyzed by an enzyme having homoserine transaminase activity, wherein

the enzyme having homoserine transaminase activity is produced via a transformed host microorganism that comprises a first chimeric gene including a first nucleic acid sequence encoding the enzyme having homoserine transaminase activity for converting the primary amino group of homoserine to a carbonyl group to obtain OHB, and

the enzyme having homoserine transaminase activity is selected from the group consisting of aspC from Escherichia coli (SEQ ID NO;

     64), ilvE from Escherichia coli (SEQ ID NO;

     60), bcaT from Lactococcus lactis (SEQ ID NO;

     68), tyrB from Escherichia coli (SEQ ID NO;

     62), araT from Lactococcus lactis (SEQ ID NO;

     66), and ARO8 from Saccharomyces cerevisiae (SEQ ID NO;

     70), or is selected from any sequence sharing a sequence identity of at least 90% with at least one of the sequences of said enzymes having homoserine transaminase activity; and

reducing the OHB to form 2,4-DHB, where the reduction of OHB is catalyzed by an enzyme having OHB reductase activity, wherein

the enzyme having OHB reductase activity is produced via the transformed host microorganism, which further comprises a second chimeric gene including a second nucleic acid sequence encoding the enzyme having OHB reductase activity for reducing OHB to 2,4-DHB, and

the enzyme having OHB reductase activity is selected from the group consisting of (L)-malate dehydrogenase from Escherichia coli (SEQ ID NO;

     2), (D)-lactate dehydrogenase from Escherichia coli (SEQ ID NO;

     4), (L)-lactate dehydrogenase from Lactococcus lactis (SEQ ID NO;

     6), (L)-lactate dehydrogenase from Bacillus subtilis (SEQ ID NO;

     8), (L)-lactate dehydrogenase from Geobacillus stearothermophilus (SEQ ID NO;

     10), the two isoforms of (L)-lactate dehydrogenase from Oryctalagus cuniculus (SEQ ID NO;

12 and SEQ ID NO;

     14), or is selected from any sequence sharing a sequence identity of at least 90% with at least one of said enzymes having OHB reductase activity.

2. The method of claim 1, wherein

the enzyme having homoserine transaminase activity is selected from the group consisting of aspC from Escherichia coli (SEQ ID NO:

64), ilvE from Escherichia coli (SEQ ID NO;

     60), bcaT from Lactococcus lactis (SEQ ID NO;

     68), tyrB from Escherichia coli (SEQ ID NO;

     62), araT from Lactococcus lactis (SEQ ID NO;

     66), and ARO8 from Saccharomyces cerevisiae (SEQ ID NO;

     70), and

wherein the enzyme having OHB reductase activity is selected from the group consisting of (L)-malate dehydrogenase from Escherichia coli (SEQ ID NO;

     2), (D)-lactate dehydrogenase from Escherichia coli (SEQ ID NO;

     4), (L)-lactate dehydrogenase from Lactococcus lactis (SEQ ID NO;

     6), (L)-lactate dehydrogenase from Bacillus subtilis (SEQ ID NO;

     8), (L)-lactate dehydrogenase from Geobacillus stearothermophilus (SEQ ID NO;

     10), the two isoforms of (L)-lactate dehydrogenase from Oryctalagus cuniculus (SEQ ID NO;

12 and SEQ ID NO;

     14).

3. The method of claim 1, wherein the enzyme having OHB reductase activity is

a lactate dehydrogenase comprising at least one mutation in position V17, Q85, E89, I226, or A222, said positions being defined by reference to (L)-lactate dehydrogenase from Lactococcus lactis (SEQ. ID NO:

6);

or

a malate dehydrogenase comprising at least one mutation in position I12, R81, M85, D86, V93, G179, T211, or M227, said positions being defined by reference to (L)-malate dehydrogenase from Escherichia coli (SEQ ID NO;

     2).

4. The method of claim 3, wherein the enzyme having OHB reductase activity is selected from the group consisting of SEQ ID NO:

30, SEQ ID NO;

32, SEQ ID NO;

102, SEQ ID NO;

104, SEQ ID NO;

106, SEQ ID NO;

108, SEQ ID NO;

110, SEQ ID NO;

112, SEQ ID NO;

114, SEQ ID NO;

116 and SEQ ID NO;

118.

5. A modified microorganism for the preparation of 2,4-dihydroxybutyrate (2,4-DHB) from homoserine via a two-step pathway comprising:

deaminating homoserine to form 2-oxo-4-hydroxybutyrate (OHB), where the deamination of homoserine is catalyzed by an enzyme having homoserine transaminase activity selected from the group consisting of aspC from Escherichia coli (SEQ ID NO;

     64), ilvE from Escherichia coli (SEQ ID NO;

     60), bcaT from Lactococcus lactis (SEQ ID NO;

     68), tyrB from Escherichia coli (SEQ ID NO;

     62), araT from Lactococcus lactis (SEQ ID NO;

     66), and ARO8 from Saccharomyces cerevisiae (SEQ ID NO;

     70), or is selected from any sequence sharing a sequence identity of at least 90% with at least one of the sequences of said enzymes having homoserine transaminase activity, and

reducing the OHB to form 2,4-DHB, where the reduction of OHB is catalyzed by an enzyme having OHB reductase activity, wherein the enzyme having OHB reductase activity is selected from the group consisting of (L)-malate dehydrogenase from Escherichia coli (SEQ ID NO;

     2), (D)-lactate dehydrogenase from Escherichia coli (SEQ ID NO;

     4), (L)-lactate dehydrogenase from Lactococcus lactis (SEQ ID NO;

     6), (L)-lactate dehydrogenase from Bacillus subtilis (SEQ ID NO;

     8), (L)-lactate dehydrogenase from Geobacillus stearothermophilus (SEQ ID NO;

     10), and the two isoforms of (L)-lactate dehydrogenase from Oryctalagus cuniculus (SEQ ID NO;

12 and SEQ ID NO;

     14), or is selected from any sequence sharing a sequence identity of at least 90% with at least one of said enzymes having homoserine transaminase activity;

wherein

the modified microorganism is a host microorganism that has been transformed to enhance production of 2,4-DHB compared to a non-transformed host microorganism, the transformed host microorganism comprising;

a first chimeric gene including a first nucleic acid sequence encoding the enzyme having homoserine transaminase activity for converting the primary amino group of homoserine to a carbonyl group to obtain OHB, and

a second chimeric gene including a second nucleic acid sequence encoding the enzyme having OHB reductase activity for reducing OHB in 2,4-DHB.

6. The modified microorganism of claim 5, wherein the transformed host microorganism has been further transformed to enhance production of homoserine compared to the non-transformed host microorganism.

7. The modified microorganism of claim 6, wherein the enhanced production of homoserine comprises overexpressing one or more additional enzymes selected from the group consisting of aspartate kinase, aspartate semialdehyde dehydrogenase and homoserine dehydrogenase, wherein the overexpression of said one or more enzymes is realized by expressing the enzymes from a multicopy plasmid.

8. The modified microorganism of claim 7, wherein the modified microorganism is a bacterium, a yeast, or a fungus.

9. The modified microorganism of claim 7, wherein

the expression of at least of one the enzymatic activities chosen among phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase, isocitrate lyase, pyruvate carboxylase, and hexose symporter permease is increased, and/or

at least one of the enzymatic activities chosen among lactate dehydrogenase, alcohol dehydrogenase, acetate kinase, phosphate acetyltransferase, pyruvate oxidase, isocitrate lyase, fumarase, 2-oxoglutarate dehydrogenase, pyruvate kinase, malic enzyme, phosphoglucose isomerase, phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase, pyruvate-formate lyase, succinic semialdehyde dehydrogenase, sugar-transporting phosphotransferase, ketohydroxyglutarate aldolase, homoserine-O-succinyl transferase, homoserine kinase, homoserine efflux transporter, diaminopimelate decarboxylase, and/or methylglyoxal synthase is decreased.

10. The modified microorganism of claim 8, the modified microorganism being Escherichia coli, which

overexpresses at least one of the genes chosen among ppc (phosphoenol pyruvate carboxylase), pck, aceA, galP, asd, thrA, metL, lysC all E coli;

pycA from L lactis, and/or

has at least one of the genes deleted chosen among ldhA, adhE, ackA, pta, poxB, focA, pfIB, sad, gabABC, sfcA, maeB, ppc, pykA, pykF, mgsA, sucAB, ptsl, ptsG, pgi, fumABCaldA, HdD, iclR, metA, thrB, lysA, eda, rthA, rthB, and rthC.

11. The modified microorganism of claim 5, wherein the enzyme having homoserine transaminase activity is selected from the group consisting of aspC from Escherichia coli (SEQ ID NO:

64), ilvE from Escherichia coli (SEQ ID NO;

     60), bcaT from Lactococcus lactis (SEQ ID NO;

     68), tyrB from Escherichia coli (SEQ ID NO;

     62), araT from Lactococcus lactis (SEQ ID NO;

     66), and ARO8 from Saccharomyces cerevisiae (SEQ ID NO;

     70), and

wherein the enzyme having OHB reductase activity is selected from the group consisting of (L)-malate dehydrogenase from Escherichia coli (SEQ ID NO;

     2), (D)-lactate dehydrogenase from Escherichia coli (SEQ ID NO;

     4), (L)-lactate dehydrogenase from Lactococcus lactis (SEQ ID NO;

     6), (L)-lactate dehydrogenase from Bacillus subtilis (SEQ ID NO;

     8), (L)-lactate dehydrogenase from Geobacillus stearothermophilus (SEQ ID NO;

     10), and the two isoforms of (L)-lactate dehydrogenase from Oryctalagus cuniculus (SEQ ID NO;

12 and SEQ ID NO;

     14).

12. A method of production of 2,4-DHB comprising the steps of

culturing the modified microorganism of claim 5 in an appropriate culture medium,

recovering 2,4-DHB from the culture medium.

13. The method of claim 12 wherein the 2,4-DHB is further purified.