Advanced biofuel production in microbes

Biotechnology Journal

Volumn 5, Issue 2, 2010, Pages 147-162

  Peralta Yahya, Pamela P ^a,b   Keasling, Jay D ^a,b,c,d  

^a JOINT BIOENERGY INSTITUTE   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c University of California at Berkeley   (United States)

^d University of California   (United States)

Author keywords

Alcohols; Biofuels; Fatty acids; Isoprenoids; Metabolic engineering

Indexed keywords

BIOFUEL PRODUCTION; COST-EFFECTIVE PRODUCTION; ECONOMIC USE; ENERGY SECURITY; FUEL DISTRIBUTION; ISOPRENOIDS; LONG CHAINS; LOW ENERGIES; METABOLIC ENGINEERING; METABOLIC PATHWAYS; PETROLEUM-DERIVED FUELS; RENEWABLE MATERIALS; SACCHAROMYCES CEREVISIAE; STORAGE INFRASTRUCTURE; TRANSPORTATION SECTOR;

ACIDS; CLIMATE CHANGE; ESCHERICHIA COLI; ETHANOL; FATTY ACIDS; FUEL STORAGE; FUELS; METABOLISM; MICROORGANISMS; PLANTS (BOTANY);

RENEWABLE ENERGY RESOURCES;

ALCOHOL; FATTY ACID; ISOPRENOID; PETROLEUM;

BIOFUEL PRODUCTION; BIOSYNTHESIS; CLIMATE CHANGE; COST EFFECTIVENESS ANALYSIS; ESCHERICHIA COLI; METABOLIC ENGINEERING; MICROORGANISM; NONHUMAN; PRIORITY JOURNAL; REVIEW; SACCHAROMYCES CEREVISIAE; SUPPLEMENTATION;

BIOELECTRIC ENERGY SOURCES; CLOSTRIDIUM; ESCHERICHIA COLI; METABOLIC NETWORKS AND PATHWAYS; SACCHAROMYCES CEREVISIAE;

ESCHERICHIA COLI; SACCHAROMYCES CEREVISIAE;

EID: 76649111044     PISSN: 18606768     EISSN: 18607314     Source Type: Journal    
DOI: 10.1002/biot.200900220     Document Type: Review

References (70)

1. Decker, J., Going against the grain: Ethanol from lignocellulosics. Renewable Energy World Magazine 2009, 11.
2. Lee, S. K., Chou, H., Ham, T. S., Lee, T. S., Keasling, J.D., Metabolic engineering of microorganisms for biofuels production: From bugs to synthetic biology to fuels. Curr. Opin. Biotechnol. 2008, 19, 556-563.
3. Fischer, C. R., Klein-Marcuschamer, D., Stephanopoulos, G., Selection and optimization of microbial hosts for biofuels production. Metab. Eng. 2008, 10, 295-304.
4. Yan, Y., Liao, J. C., Engineering metabolic systems for production of advanced fuels. J. Ind. Microbiol. Biotechnol. 2009, 36, 471-479
5. Chen, J. S., Hiu, S. F., Acetone butanol isopropanol production by Clostridium-beijerinckii (synonym, Clostridiumbutylicum). Biotechnol. Lett. 1986, 8, 371-376.
6. Lee, S.Y., Park, J. H., Jang, S. H., Nielsen, L. K. et al., Fermentative butanol production by Clostridia. Biotechnol. Bioeng. 2008, 101, 209-228.
7. Qureshi, N., Blaschek, H. P., Production of acetone butanol ethanol (ABE) by a hyper-producing mutant strain of Clostridium beijerinckii BA101 and recovery by pervaporation. Biotechnol. Prog. 1999, 15, 594-602.
8. Atsumi, S., Cann, A. F., Connor, M. R., Shen, C. R. et al., Metabolic engineering of Escherichia coli for 1-butanol production. Metab. Eng. 2008, 10, 305-311.
9. Hanai, T., Atsumi, S., Liao, J. C., Engineered synthetic pathway for isopropanol production in Escherichia coli. Appl. Environ. Microbiol. 2007, 73, 7814-7818.
10. Bermejo, L. L., Welker, N. E., Papoutsakis, E. T., Expression of Clostridium acetobutylicum ATCC 824 genes in Escherichia coli for acetone production and acetate detoxification. Appl. Environ. Microbiol. 1998, 64, 1079-1085.
11. Jojima, T., Inui, M., Yukawa, H., Production of isopropanol by metabolically engineered Escherichia coli. Appl. Microbiol. Biotechnol. 2008, 77, 1219-1224.
12. Inui, M., Suda, M., Kimura, S., Yasuda, K. et al., Expression of Clostridium acetobutylicum butanol synthetic genes in Escherichia coli. Appl. Microbiol. Biotechnol. 2008, 77, 1305-1316.
13. Nielsen, D. R., Leonard, E., Yoon, S. H., Tseng, H. C. et al., Engineering alternative butanol production platforms in heterologous bacteria. Metab. Eng. 2009, 11, 262-273.
14. Steen, E. J., Chan, R., Prasad, N., Myers, S. et al., Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol. Microb. Cell Fact. 2008, 7, 36.
15. Shiba, Y., Paradise, E. M., Kirby, J., Ro, D. K., Keasling, J. D., Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae for high-level production of isoprenoids. Metab. Eng. 2007, 9, 160-168.
16. Hazelwood, L. A., Daran, J. M., van Maris, A. J., Pronk, J. T., Dickinson, J. R., The Ehrlich pathway for fusel alcohol production: A century of research on Saccharomyces cerevisiae metabolism. Appl. Environ. Microbiol. 2008, 74, 2259-2266.
17. Atsumi, S., Hanai, T., Liao, J. C., Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 2008, 451, 86-89.
18. Shen, C. R., Liao, J. C., Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the ketoacid pathways. Metab. Eng. 2008, 10, 312-320.
19. Atsumi, S., Liao, J. C., Directed evolution of Methanococcus jannaschii citramalate synthase for biosynthesis of 1-propanol and 1-butanol by Escherichia coli. Appl. Environ. Microbiol. 2008, 74, 7802-7808.
20. Connor, M. R., Liao, J. C., Engineering of an Escherichia coli strain for the production of 3-methyl-1-butanol. Appl. Environ. Microbiol. 2008, 74, 5769-5775.
21. Cann, A. F., Liao, J. C., Production of 2-methyl-1-butanol in engineered Escherichia coli. Appl. Microbiol. Biotechnol. 2008, 81, 89-98.
22. Zhang, K., Sawaya, M. R., Eisenberg, D. S., Liao, J. C., Expanding metabolism for biosynthesis of nonnatural alcohols. Proc. Natl. Acad. Sci. USA 2008, 105, 20653-20658.
23. Renninger, N., McPhee, D., Fuel compositions comprising farnesane and farnesane derivatives and method of making and using same, WO2008045555, 2008.
24. Rude, M., Schirmer, A., New microbial fuels: A biotech perspechtive. Curr. Opin. Microbiol. 2009, 12, 274-281.
25. Renninger, N. S., Ryder, J. A., Fischer, K. J., Jetfuel compositions and methods of making and using same, WO2008130492, 2008.
26. Farmer, W. R., Liao, J. C., Improving lycopene production in Escherichia coli by engineering metabolic control. Nat. Biotechnol. 2000, 18, 533-537.
27. Alper, H., Miyaoku, K., Stephanopoulos, G., Construction of lycopene-overproducing E-coli strains by combining systematic and combinatorial gene knockout targets. Nat. Biotechnol. 2005, 23, 612-616.
28. Alper, H., Miyaoku, K., Stephanopoulos, G., Characterization of lycopene-overproducing E-coli strains in high cell density fermentations. Appl. Microbiol. Biotechnol. 2006, 72, 968-974.
29. Yuan, L. Z., Rouviere, P. E., LaRossa, R. A., Suh, W., Chromosomal promoter replacement of the isoprenoid pathway for enhancing carotenoid production in E-coli. Metab. Eng. 2006, 8, 79-90.
30. Martin, V. J., Pitera, D. J., Withers, S. T., Newman, J. D., Keasling, J. D., Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 2003, 21, 796-802.
31. Newman, J. D., Marshall, J., Chang, M., Nowroozi, F. et al., High-level production of amorpha-4,11-diene in a two-phase partitioning bioreactor of metabolically engineered Escherichia coli. Biotechnol. Bioeng. 2006, 95, 684-691.
32. Glick, B. R., Metabolic load and heterologous gene-expression. Biotechnol. Adv. 1995, 13, 247-261.
33. Goff, S. A., Goldberg, A. L., Production of abnormal proteins in Escherichia-coli stimulates transcription of ion and other heat-shock genes. Cell 1985, 41, 587-595.
34. Pitera, D. J., Paddon, C. J., Newman, J. D., Keasling, J. D., Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli. Metab. Eng. 2007, 9, 193-207.
35. Dueber, J. E., Wu, G.C., Malmirchegini, G. R., Moon, T.S. et al., Synthetic protein scaffolds provide modular control over metabolic flux. Nat. Biotechnol. 2009, 27, 753-759.
36. Anthony, J. R., Anthony, L. C., Nowroozi, F., Kwon, G. et al., Optimization of the mevalonate-based isoprenoid biosynthetic pathway in Escherichia coli for production of the antimalarial drug precursor amorpha-4,11-diene. Metab. Eng. 2009, 11, 13-19.
37. Tsuruta, H., Paddon, C. J., Eng, D., Lenihan, J. R. et al., High-level production of amorpha-4,11-diene, a precursor of the antimalarial agent artemisinin, in Escherichia coli. PLoS One 2009, 4, e4489.
38. Pitera, D. J., Paddon, C. J., Newman, J. D., Keasling, J. D., Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli. Metab. Eng. 2007, 9, 193-207.
39. Ro, D. K., Paradise, E. M., Ouellet, M., Fisher, K. J. et al., Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 2006, 440, 940-943.
40. Chang, M. C., Eachus, R. A., Trieu, W., Ro, D. K., Keasling, J. D., Engineering Escherichia coli for production of functionalized terpenoids using plant P450s. Nat. Chem. Biol. 2007, 3, 274-277.
41. Yoshikuni, Y., Ferrin, T. E., Keasling, J.D., Designed divergent evolution of enzyme function. Nature 2006, 440, 1078-1082.
42. Withers, S.T., Gottlieb, S.S., Lieu, B., Newman, J.D., Keasling, J. D., Identification of isopentenol biosynthetic genes from Bacillus subtilis by a screening method based on isoprenoid precursor toxicity. Appl. Environ. Microbiol. 2007, 73, 6277-6283.
43. Cheesbrough, T. M., Kolattukudy, P. E., Alkane biosynthesis by decarbonylation of aldehydes catalyzed by a particulate preparation from Pisum sativum. Proc. Natl. Acad. Sci. USA 1984, 81, 6613-6617.
44. Dennis, M., Kolattukudy, P. E., A cobalt-porphyrin enzyme converts a fatty aldehyde to a hydrocarbon and CO. Proc. Natl. Acad. Sci. USA 1992, 89, 5306-5310.
45. Park, M. O., New pathway for long-chain n-alkane synthesis via 1-alcohol in Vibrio furnissii M1. J. Bacteriol. 2005, 187, 1426-1429.
46. Wackett, L. P., Frias, J. A., Seffernick, J. L., Sukovich, D. J., Cameron, S. M., Genomic and biochemical studies demonstrating the absence of an alkane-producing phenotype in Vibrio furnissii M1. Appl. Environ. Microbiol. 2007, 73, 7192-7198.
47. Kalscheuer, R., Stolting, T., Steinbuchel, A., Microdiesel: Escherichia coli engineered for fuel production. Microbiology 2006, 152, 2529-2536.
48. Michinaka, Y., Shimauchi, T., Aki, T., Nakajima, T. et al., Extracellular secretion of free fatty acids by disruption of a fatty acyl-CoA synthetase gene in Saccharomyces cerevisiae. J. Biosci. Bioeng. 2003, 95, 435-440.
49. Scharnewski, M., Pongdontri, P., Mora, G., Hoppert, M., Fulda, M., Mutants of Saccharomyces cerevisiae deficient in acyl-CoA synthetases secrete fatty acids due to interrupted fatty acid recycling. FEBS J. 2008, 275, 2765-2778.
50. Campbell, J., A new Escherichia coli metabolic competency: Growth on fatty acids by a novel anaerobic beta oxidation pathway. Mol. Microbiol. 2003, 47, 793-805.
51. Davis, M. S., Solbiati, J., Cronan, J. E., Jr., Overproduction of acetyl-CoA carboxylase activity increases the rate of fatty acid biosynthesis in Escherichia coli. J. Biol. Chem. 2000, 275, 28593-28598.
52. Lu, X., Vora, H., Khosla, C., Overproduction of free fatty acids in E. coli: Implications for biodiesel production. Metab. Eng. 2008, 10, 333-339.
53. Kalscheuer, R., Luftmann, H., Steinbuchel, A., Synthesis of novel lipids in Saccharomyces cerevisiae by heterologous expression of an unspecific bacterial acyltransferase. Appl. Environ. Microbiol. 2004, 70, 7119-7125.
54. Keasling, J., Hu, Z., Somerville, C., Church, G. et al., Production of fatty acids and derivatives thereof, WO2007136762, 2007.
55. Steen, E., Keasling, J., Host cells and methods for producing fatty acid derived compounds, WO2009006430, 2009.
56. Hu, Z., Valle, F., Enhanced production of fatty acid derivatives, WO2008119082, 2008.
57. Friedman, L., Rude, M., Process for producing low molecular weight hydrocarbons from renewable resources, WO2008113041, 2008.
58. Alibhai, M., Rude, M., Schirmer, A., Methods and compositions for producing olefins, WO2009085278, 2009.
59. Mukhopadhyay, A., Redding, A., Rutherford, B., Keasling, J. D., Importance of systems biology in engineering microbes for biofuel production. Curr. Opin. Biotechnol. 2008, 19, 228-234.
60. Nakamura, C., Whited, G. M., Metabolic engineering for the microbial production of 1,3-propanediol. Curr. Opin. Biotechnol. 2003, 14, 454-459.
61. Kizer, L., Pitera, D. J., Pfleger, B.F., Keasling, J.D., Application of functional genomics to pathway optimization for increased isoprenoid production. Appl. Environ. Microbiol. 2008, 74, 3229-3241.
62. Brynildsen, M.P., Liao, J.C., An integrated network approach identifies the isobutanol response network of Escherichia coli. Mol. Syst. Biol. 2009, 5, 277.
63. Gustafsson, C., Govindarajan, S., Minshull, J., Codon bias and heterologous protein expression. Trends Biotechnol. 2004, 22, 346-353.
64. Santos, C. N., Stephanopoulos, G., Combinatorial engineering of microbes for optimizing cellular phenotype. Curr. Opin. Chem. Biol. 2008, 12, 168-176.
65. Landrain, T. E., Carrera, J., Kirov, B., Rodrigo, A., Jaramillo, A., Modular model-based design for heterologous bioproduction in bacteria. Curr. Opin. Biotechnol. 2009, 20, 272-279.
66. Gardner, T. S., Cantor, C. R., Collins, J. J., Construction of a genetic toggle switch in Escherichia coli. Nature 2000, 403, 339-342.
67. Pfleger, B. F., Pitera, D., Smolke, C. D., Keasling, J. D., Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat. Biotechnol. 2006, 24, 1027-1032.
68. Alper, H., Stephanopoulos, G., Global transcription machinery engineering: A new approach for improving cellular phenotype. Metab. Eng. 2007, 9, 258-267.
69. Martin, C. H., Nielsen, D. R., Solomon, K. V., Prather, K. L., Synthetic metabolism: Engineering biology at the protein and pathway scales. Chem. Biol. 2009, 16, 277-286.
70. Yoshikuni, Y., Keasling, J. D., Pathway engineering by designed divergent evolution. Curr. Opin. Chem. Biol. 2007, 11, 233-239.