Production of acetyl-coenzyme A derived isoprenoids
View Patent ↗Provided herein are compositions and methods for the heterologous production of acetyl-CoA-derived isoprenoids in a host cell. In some embodiments, the host cell is genetically modified to comprise a heterologous nucleotide sequence encoding an acetaldehyde dehydrogenase, acetylating (ADA, E.C. 1.2.1.10) and an MEV pathway comprising an NADH-using HMG-CoA reductase. In some embodiments, the host cell is genetically modified to comprise a heterologous nucleotide sequence encoding an ADA and an MEV pathway comprising an acetoacetyl-CoA synthase. In some embodiments, the genetically modified host cell further comprises one or more heterologous nucleotide sequences encoding a phosphoketolase and a phosphotransacetylase. In some embodiments, the genetically modified host cell further comprises a functional disruption of the native PDH-bypass. The compositions and methods described herein provide an energy-efficient yet redox balanced route for the heterologous production of acetyl-CoA-derived isoprenoids.
1. A genetically modified yeast cell capable of producing an isoprenoid, the cell comprising:
(a) a nucleic acid encoding an enzyme that condenses acetyl-CoA with malonyl-CoA to form acetoacetyl-CoA, and optionally one or more heterologous nucleic acids encoding one or more enzymes of a mevalonate (MEV) pathway for making isopentenyl pyrophosphate;
(b) a heterologous nucleic acid encoding an acylating acetylaldehyde dehydrogenase (ADA, EC 1.2.1.10); and
(c) a functional disruption of one or more enzymes of the native pyruvate dehydrogenase (PDH)-bypass selected from the group consisting of acetyl-CoA synthetase 1 (ACS1), acetyl-CoA synthetase 2 (ACS2), and aldehyde dehydrogenase 6 (ALD6),
wherein the genetically modified yeast cell produces an increased amount of an isoprenoid compound compared to an yeast cell not comprising a nucleic acid encoding an enzyme that condenses acetyl-CoA with malonyl-CoA to form acetoacetyl-CoA.
2. The genetically modified yeast cell of claim 1 , wherein the enzyme that condenses acetyl-CoA with malonyl-CoA to form acetoacetyl-CoA is an acetyl-CoA:malonyl-CoA acyltransferase.
3. The genetically modified yeast cell of claim 1 , wherein the one or more enzymes of the MEV pathway comprise an NADH-using enzyme that converts 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) to mevalonate.
4. The genetically modified yeast cell of claim 1 , wherein the one or more enzymes of the MEV pathway comprise an NADH-using HMG-CoA reductase (HMGr).
5. The genetically modified yeast cell of claim 1 , further comprising a heterologous nucleic acid encoding a phosphoketolase (PK).
6. The genetically modified yeast cell of claim 1 , further comprising a heterologous nucleic acid encoding a phosphotransacetylase (PTA).
7. The genetically modified yeast cell of claim 1 , wherein ACS1 is functionally disrupted.
8. The genetically modified yeast cell of claim 1 , wherein ACS2 is functionally disrupted.
9. The genetically modified yeast cell of claim 1 , wherein ALD6 is functionally disrupted.
10. The genetically modified yeast cell of claim 1 , wherein ACS1 and ACS2 are functionally disrupted.
11. The genetically modified yeast cell of claim 1 , wherein ACS1, ACS2 and ALD6 are functionally disrupted.
12. The genetically modified yeast cell of claim 1 , wherein the one or more enzymes of the MEV pathway comprise an enzyme that condenses two molecules of acetyl-CoA to form acetoacetyl-CoA.
13. The genetically modified yeast cell of claim 1 , wherein the one or more enzymes of the MEV pathway comprise an enzyme that condenses acetoacetyl-CoA with acetyl-CoA to form HMG-CoA.
14. The genetically modified yeast cell of claim 1 , wherein the one or more enzymes of the MEV pathway comprise an NAPDH-using enzyme that converts HMG-CoA to mevalonate.
15. The genetically modified yeast cell of claim 1 , wherein the one or more enzymes of the MEV pathway comprise an enzyme that phosphorylates mevalonate to mevalonate 5-phosphate.
16. The genetically modified yeast cell of claim 1 , wherein the one or more enzymes of the MEV pathway comprise an enzyme that converts mevalonate 5-phosphate to mevalonate 5-pyrophosphate.
17. The genetically modified yeast cell of claim 1 , wherein the one or more enzymes of the MEV pathway comprise an enzyme that converts mevalonate 5-pyrophosphate to isopentenyl pyrophosphate.
18. The genetically modified yeast cell of claim 1 , wherein the one or more enzymes of the MEV pathway are selected from HMG-CoA synthase, mevalonate kinase, phosphomevalonate kinase and mevalonate pyrophosphate decarboxylase.
19. The genetically modified yeast cell of claim 1 , wherein the cell comprises a plurality of heterologous nucleic acids encoding all of the enzymes of the MEV pathway.
20. The genetically modified yeast cell of claim 1 , wherein the one or more heterologous nucleic acids encoding one or more enzymes of the MEV pathway are under control of a single transcriptional regulator.
21. The genetically modified yeast cell of claim 1 , further comprising a heterologous nucleic acid encoding an enzyme that can convert isopentenyl pyrophosphate (IPP) into dimethylallyl pyrophosphate (DMAPP).
22. The genetically modified yeast cell of claim 1 , further comprising a heterologous nucleic acid encoding an enzyme that can condense IPP and/or DMAPP molecules to form a polyprenyl compound.
23. The genetically modified yeast cell of claim 1 , further comprising a heterologous nucleic acid encoding an enzyme that can modify IPP or a polyprenyl to form an isoprenoid compound.
24. The genetically modified yeast cell of claim 23 , wherein the enzyme that can modify IPP or a polyprenyl to form an isoprenoid compound is selected from the group consisting of carene synthase, geraniol synthase, linalool synthase, limonene synthase, myrcene synthase, ocimene synthase, α-pinene synthase, β-pinene synthase, γ-terpinene synthase, terpinolene synthase, amorphadiene synthase, α-farnesene synthase, β-farnesene synthase, farnesol synthase, nerolidol synthase, patchouliol synthase, nootkatone synthase, and abietadiene synthase.
25. The genetically modified yeast cell of claim 23 , wherein the isoprenoid is selected from the group consisting of a hemiterpene, monoterpene, diterpene, triterpene, tetraterpene, sesquiterpene, and polyterpene.
26. The genetically modified yeast cell of claim 23 , wherein the isoprenoid is a C 5 -C 20 isoprenoid.
27. The genetically modified yeast cell of claim 23 , wherein the isoprenoid is selected from the group consisting of abietadiene, amorphadiene, carene, α-farnesene, β-farnesene, farnesol, geraniol, geranylgeraniol, isoprene, linalool, limonene, myrcene, nerolidol, ocimene, patchoulol, β-pinene, sabinene, γ-terpinene, terpinolene, and valencene.
28. The genetically modified yeast cell of claim 1 , wherein the yeast is Saccharomyces cerevisiae.
29. A method for producing an isoprenoid comprising:
(a) culturing a population of the genetically modified yeast cell of claim 1 in a medium with a carbon source under conditions suitable for making said isoprenoid compound; and
(b) recovering said isoprenoid compound from the medium.
30. The method of claim 29 , wherein the genetically modified yeast cell produces an increased amount of an isoprenoid compound compared to the same genetically modified yeast cell not comprising a nucleotide sequence encoding an enzyme that condenses acetyl-CoA with malonyl-CoA to form acetoacetyl-CoA.