Metabolic engineering for microbial production of terpenoid products

12227,783

17/729056

April 26, 2022

In various aspects and embodiments, the invention relates to bacterial strains and methods for making terpene and terpenoid products. The invention provides bacterial strains with improved carbon flux through the MEP pathway, to thereby increase terpene and/or terpenoid product yield by fermentation with carbon sources such as glucose.

MANUS BIO INC. (Cambridge, MA, US)

Manus Bio Inc. (Waltham, MA, US)

1. A method for production of a terpene or terpenoid, comprising: providing a bacterial strain that produces isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) through an upstream methylerythritol pathway (MEP) and converts the IPP and DMAPP to a terpene or terpenoid through a downstream synthesis pathway; and culturing the bacterial strain in culture media to produce the terpene or terpenoid, wherein greater than 15% of carbon entering glycolysis becomes MEP carbon; wherein the bacterial strain overexpresses 1-deoxy-D-xylulose-5-phosphate reductoisomerase (Dxr) and 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE), such that expression levels of Dxr and IspE in the bacterial strain limits accumulation of each of 1-deoxy-D-xylulose (DOX) and 2-C-methyl-D-erythritol (ME) in the culture media to 1 g/L or less; wherein the bacterial strain further overexpresses 1-hydroxy-2-methyl-2-E-butenyl 4-diphosphate synthase (IspG) and 1-hydroxy-2-methyl-2-(E) 4-diphosphate reductase (IspH), such that expression levels of IspG and IspH in the bacterial cell limits accumulation of 2C-methyl-D-erythritol 2,4-cyclodiphosphate (MEcPP) in the culture media.

2. The method of claim 1 , wherein the ubiquinone biosynthesis pathway is downregulated.

3. The method of claim 2 , wherein the strain has reduced expression or activity of IspB.

4. The method of claim 3 , wherein IspB expression is reduced by a modified ribosome binding sequence (RBS).

5. The method of claim 3 , wherein a Shine-Dalgarno (SD) sequence of the ispB gene is CGTGCT or CGTGCC or a modification thereof having one or two nucleotide changes in CGTGCT or CGTGCC.

6. The method of claim 1 , wherein the strain has an inducible or constitutive expression of the isc operon.

7. The method of claim 6 , wherein the iscR gene is deleted in whole or in part, or is inactivated, optionally by modification to an RBS.

8. The method of claim 6 , wherein the iscR gene is replaced with a inducible or constitutive promoter.

9. The method of claim 1 , wherein the strain comprises a ryhB deletion or inactivation.

10. The method of claim 1 , wherein the strain overexpresses Dxr by complementation with a recombinant gene or operon comprising dxr.

11. The method of claim 10 , wherein the strain has a modified Dxr enzyme or Dxr ortholog having increased activity with respect to the wild type E. coli Dxr.

12. The method of claim 10 , wherein the strain overexpresses IspE by complementation with a recombinant gene or operon comprising ispE.

13. The method of claim 10 , wherein the strain overexpresses ispG and ispH by complementation with a recombinant gene or operon comprising ispG and ispH.

14. The method of claim 13 , wherein the strain has a modified IspG enzyme or ortholog having increased activity with respect to the wild type E. coli IspG.

15. The method of claim 14 , wherein the IspG enzyme contains one or more mutations at positions with respect to SEQ ID NO: 5 selected from V30, S32, T34, N35, R37, V59, V61, S62, V63, L83, V84, C104, L105, P131, I132, I134, A138, K143, F176, K177, V178, V180, A182, L205, I207, A210, G212, A213, L236, V238, A241, A242, D243, R259, S262, R263, I265, N266, F267, I268, A269, T272, S274, Q276, E277, F278, D289, S301, I302, I303, V306.

16. The method of claim 15 , wherein the IspG has a modification at a plurality of positions with respect to SEQ ID NO: 5 selected from: (1) V30, S32, T34, N35, R37; or (2) V59, V61, S62, V63, L83, V84; or (3) C104, L105, S301, I302, I303, V306; or (4) P131, I132, I134, A138, K143; or (5) F176, K177, V178, V180, A182; or (6) L205, I207, A210, G212, A213; or (7) L236, V238, A241, A242, D243; or (8) R259, S262, R263, I265, N266; or (9) F267, I268, A269, T272, S274, Q276, E277, F278, D289.

17. The method of claim 15 , wherein the IspG enzyme has one, two, three or all of the following mutations with respect to SEQ ID NO: 5: L205V, A210S, G212T, and A213I.

18. The method of claim 1 , wherein the bacterial strain has at least one additional copy of dxs and idi expressed as an operon or module; or dxs, ispD, ispF, and idi expressed as an operon or module.

19. The method of claim 1 , wherein the strain is cultured with a C1, C2, C3, C4, C5, and/or C6 carbon source under microaerobic conditions.

20. The method of claim 19 , wherein the culture is at least about 100 L.

21. The method of claim 20 , comprising, monitoring the accumulation of DOX, ME, or MEcPP in the culture.

22. The method of claim 1 , further comprising, recovering the terpene or terpenoid.

23. A method for making an industrial or consumer product, comprising, incorporating the terpene or terpenoid made according to the method of claim 1 into said industrial or consumer product.

24. The method of claim 11 , wherein the strain overexpresses deoxyxylulose-5-phosphate reductoisomerase-like (DRL) enzyme optionally by complementation with a recombinant gene or operon comprising DRL.

25. The method of claim 1 , wherein DOX, ME, and MEcPP metabolites are found at reduced levels in the culture medium as compared to a parent strain.

26. The method of claim 25 , wherein the bacterial strain has a gene complementation of dxs, ispD, ispF, and idi genes.

27. The method of claim 1 , wherein the culture is at least 1000 L.

28. The method of claim 1 , wherein the culture is at least 10,000 L.

29. The method of claim 1 , wherein DOX and ME each accumulate in the culture at less than about 500 mg/L.

30. The method of claim 1 , wherein the bacterial strain is Escherichia coli, Bacillus subtilis, Rhodobacter capsulatus, Rhodobacter sphaeroides, Zymomonas mobilis , or Pseudomonas putida.

31. The method of claim 1 , wherein the bacterial strain is Escherichia coli.

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