Redesigning Escherichia coli metabolism for anaerobic production of isobutanol

Applied and Environmental Microbiology

Volumn 77, Issue 14, 2011, Pages 4894-4904

  Trinh, Cong T ^a,b   Li, Johnny ^a   Blanch, Harvey W ^a   Clark, Douglas S ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of Tennessee Knoxville   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANAEROBIC CONDITIONS; ANAEROBIC GROWTH; E. COLI; ELEMENTARY MODE; ENZYME COMPLEXES; ETHANOL PRODUCTION; EXPERIMENTAL DATA; FERMENTABLE SUGARS; GENERAL APPROACH; GLYCOLYTIC FLUX; HETEROLOGOUS GENES; HIGH YIELD; ISOBUTANOL; KEY ENZYMES; MODEL PREDICTION; OVER-EXPRESSION; PYRUVATES;

BIOFUELS; ENZYMES; ETHANOL; FORECASTING; GENES; GLUCOSE; METABOLISM; METABOLITES; PHYSIOLOGY;

ESCHERICHIA COLI;

ALDEHYDE DEHYDROGENASE; BUTANOL; ESCHERICHIA COLI PROTEIN; ISOBUTANOL; OXIDOREDUCTASE; PYRUVATE DEHYDROGENASE (NADP+); PYRUVATE DEHYDROGENASE COMPLEX;

ALCOHOL; ANOXIC CONDITIONS; BIOFUEL; COLIFORM BACTERIUM; ENZYME ACTIVITY; FERMENTATION; GENE; GROWTH RATE; INHIBITION; METABOLITE; OPTIMIZATION;

ANAEROBIC GROWTH; ARTICLE; ESCHERICHIA COLI; GENE INACTIVATION; GENETIC ENGINEERING; GENETICS; METABOLISM;

ALDEHYDE DEHYDROGENASE; ANAEROBIOSIS; BUTANOLS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE KNOCKOUT TECHNIQUES; GENETIC ENGINEERING; KETONE OXIDOREDUCTASES; PYRUVATE DEHYDROGENASE COMPLEX;

ESCHERICHIA COLI;

EID: 79961084093     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00382-11     Document Type: Article

References (41)

1. Alper, H., and G. Stephanopoulos. 2009. Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential? Nat. Rev. Microbiol. 7:715-723.
2. Atsumi, S., et al. 2008. Metabolic engineering of Escherichia coli for 1-butanol production. Metab. Eng. 10:305-311.
3. Atsumi, S., T. Hanai, and J. C. Liao. 2008. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451:86-89.
4. Atsumi, S., Z. Li, and J. C. Liao. 2009. Acetolactate synthase from Bacillus subtilis serves as a 2-ketoisovalerate decarboxylase for isobutanol biosynthesis in Escherichia coli. Appl. Environ. Microbiol. 75:6306-6311.
5. Atsumi, S., et al. 2010. Engineering the isobutanol biosynthetic pathway in Escherichia coli by comparison of three aldehyde reductase/alcohol dehydrogenase genes. Appl. Microbiol. Biotechnol. 85:651-657.
6. Baba, T., et al. 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio Collection. Mol. Syst. Biol. 2:2006.0008.
7. Bastian, S., et al. 2011. Engineered ketol-acid reductoisomerase and alcohol dehydrogenase enable anaerobic 2-methylpropan-1-ol production at theoretical yield in Escherichia coli. Metab. Eng. 13:345-352.
8. Birkmann, A., F. Zinoni, G. Sawers, and A. Böck. 1987. Factors affecting transcriptional regulation of the formate-hydrogen-lyase pathway of Escherichia coli. Arch. Microbiol. 148:44-51.
9. Blanch, H. W., et al. 2008. Addressing the need for alternative transportation fuels: the Joint BioEnergy Institute. ACS Chem. Biol. 3:17-20.
10. Cann, A., and J. Liao. 2010. Pentanol isomer synthesis in engineered microorganisms. Appl. Microbiol. Biotechnol. 85:893-899.
11. Cherepanov, P. P., and W. Wackernagel. 1995. Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant. Gene 158:9-14.
12. Datsenko, K. A., and B. L. Wanner. 2000. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. U. S. A. 97:6640-6645.
13. de Graef, M. R., S. Alexeeva, J. L. Snoep, and M. J. Teixeira de Mattos. 1999. The steady-state internal redox state (NADH/NAD) reflects the external redox state and is correlated with catabolic adaptation in Escherichia coli. J. Bacteriol. 181:2351-2357.
14. Dickinson, J. R., S. J. Harrison, and M. J. E. Hewlins. 1998. An investigation of the metabolism of valine to isobutyl alcohol in Saccharomyces cerevisiae. J. Biol. Chem. 273:25751-25756.
15. Hädicke, O., and S. Klamt. 2010. CASOP: a computational approach for strain optimization aiming at high productivity. J. Biotechnol. 147:88-101.
16. Herrera, S. 2006. Bonkers about biofuels. Nat. Biotechnol. 24:755-760.
17. Ho, N. W., Z. Chen, and A. P. Brainard. 1998. Genetically engineered Saccharomyces yeast capable of effective cofermentation of glucose and xylose. Appl. Environ. Microbiol. 64:1852-1859.
18. Inui, M. 2008. Expression of Clostridium acetobutylicum butanol synthetic genes in Escherichia coli. Appl. Microbiol. Biotechnol. 77:1305-1316.
19. Murarka, A., J. M. Clomburg, S. Moran, J. V. Shanks, and R. Gonzalez. 2010. Metabolic analysis of wild-type Escherichia coli and a pyruvate dehydrogenase complex (PDHC)-deficient derivative reveals the role of PDHC in the fermentative metabolism of glucose. J. Biol. Chem. 285:31548-31558.
20. Ohta, K., D. S. Beall, J. P. Mejia, K. T. Shanmugam, and L. O. Ingram. 1991. Genetic improvement of Escherichia coli for ethanol production: chromosomal integration of Zymomonas mobilis genes encoding pyruvate decarboxylase and alcohol dehydrogenase II. Appl. Environ. Microbiol. 57:893-900.
21. Park, J. H., K. H. Lee, T. Y. Kim, and S. Y. Lee. 2007. Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation. Proc. Natl. Acad. Sci. U. S. A. 104:7797-7802.
22. Pecher, A., et al. 1983. On the redox control of synthesis of anaerobically induced enzymes in enterobacteriaceae. Arch. Microbiol. 136:131-136.
23. Pfeiffer, T., I. Sanchez-Valdenebro, J. C. Nuno, F. Montero, and S. Schuster. 1999. METATOOL: for studying metabolic networks. Bioinformatics 15:251-257.
24. Ragauskas, A. J., et al. 2006. The path forward for biofuels and biomaterials. Science 311:484-489.
25. Schirmer, A., M. A. Rude, X. Li, E. Popova, and S. B. del Cardayre. 2010. Microbial biosynthesis of alkanes. Science 329:559-562.
26. Schubert, C. 2006. Can biofuels finally take center stage? Nat. Biotechnol. 24:777-784.
27. Schuster, S., D. A. Fell, and T. Dandekar. 2000. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol. 18:326-332.
28. Schuster, S., C. Hilgetag, J. H. Woods, and D. A. Fell. 1994. Elementary modes of functioning in biochemical networks, p. 151-165. In R. Cuthbertson, M. Holcombe, and R. Paton (ed.), Computation in cellular and molecular biological systems. World Scientific, Singapore.
29. Schuster, S., C. Hilgetag, J. H. Woods, and D. A. Fell. 2002. Reaction routes in biochemical reaction systems: algebraic properties, validated calculation procedure and example from nucleotide metabolism. J. Math. Biol. 45:153-181.
30. Sillers, R., A. Chow, B. Tracy, and E. T. Papoutsakis. 2008. Metabolic engineering of the non-sporulating, non-solventogenic Clostridium acetobutylicum strain M5 to produce butanol without acetone demonstrate the robustness of the acid-formation pathways and the importance of the electron balance. Metab. Eng. 10:321-332.
31. Steen, E. J., et al. 2010. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463:559-562.
32. Trinh, C., A. Wlaschin, and F. Srienc. 2009. Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism. Appl. Microbiol. Biotechnol. 81:813-826.
33. Trinh, C. T., R. Carlson, A. Wlaschin, and F. Srienc. 2006. Design, construction and performance of the most efficient biomass producing E. coli bacterium. Metab. Eng. 8:628-638.
34. Trinh, C. T., S. Huffer, M. E. Clark, H. W. Blanch, and D. S. Clark. 2010. Elucidating mechanisms of solvent toxicity in ethanologenic Escherichia coli. Biotechnol. Bioeng. 106:721-730.
35. Trinh, C. T., and F. Srienc. 2009. Metabolic engineering of Escherichia coli for efficient conversion of glycerol to ethanol. Appl. Environ. Microbiol. 75:6696-6705.
36. Trinh, C. T., P. Unrean, and F. Srienc. 2008. Minimal Escherichia coli cell for the most efficient production of ethanol from hexoses and pentoses. Appl. Environ. Microbiol. 74:3634-3643.
37. Unden, G., and J. Bongaerts. 1997. Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors. Biochim. Biophys. Acta 1320:217-234.
38. Unrean, P., C. T. Trinh, and F. Srienc. 2010. Rational design and construction of an efficient E. coli for production of diapolycopendioic acid. Metab. Eng. 12:112-122.
39. U.S. Energy Information Administration. 2010. International energy outlook 2010. U.S. Energy Information Administration, U.S. Department of Energy, Washington, DC.
40. Zhang, M., C. Eddy, K. Deanda, M. Finkelstein, and S. Picataggio. 1995. Metabolic engineering of a pentose metabolism pathway in ethanologenic Zymomonas mobilis. Science 267:240-243.
41. Zinoni, F., A. Beier, A. Pecher, R. Wirth, and A. Böck. 1984. Regulation of the synthesis of hydrogenase (formate hydrogen-lyase linked) of E. coli. Arch. Microbiol. 139:299-304.