Model-driven rebalancing of the intracellular redox state for optimization of a heterologous n-butanol pathway in Escherichia coli

Metabolic Engineering

Volumn 20, Issue , 2013, Pages 56-62

  Lim, Jae Hyung ^a   Seo, Sang Woo ^a   Kim, Se Yeon ^a   Jung, Gyoo Yeol ^a  

^a Pohang University of Science and Technology (POSTECH)   (South Korea)

Author keywords

Metabolic engineering; Metabolic imbalance; N butanol; Redox rebalancing; Synthetic biology

Indexed keywords

ENZYME ACTIVITY; ESCHERICHIA COLI; METABOLIC ENGINEERING; OPTIMIZATION; PHYSIOLOGY; YEAST;

5'-UNTRANSLATED REGIONS; CONSTITUTIVE PROMOTERS; FORMATE DEHYDROGENASE; METABOLIC IMBALANCE; MICROBIAL CELL FACTORIES; N-BUTANOL; REBALANCING; SYNTHETIC BIOLOGY;

SUBSTRATES;

BUTANOL; FORMATE DEHYDROGENASE; GALACTOSE; GLUCOSE; PYRUVATE DEHYDROGENASE;

5' UNTRANSLATED REGION; ARTICLE; ESCHERICHIA COLI; METABOLIC ENGINEERING; NONHUMAN; OXIDATION REDUCTION STATE; PRIORITY JOURNAL; REACTION OPTIMIZATION; SACCHAROMYCES CEREVISIAE; STRAIN IMPROVEMENT; SYNTHETIC BIOLOGY;

ESCHERICHIA COLI; SACCHAROMYCES CEREVISIAE;

METABOLIC ENGINEERING; METABOLIC IMBALANCE; N-BUTANOL; REDOX REBALANCING; SYNTHETIC BIOLOGY;

1-BUTANOL; 5' UNTRANSLATED REGIONS; ANAEROBIOSIS; ESCHERICHIA COLI; FORMATE DEHYDROGENASES; MODELS, BIOLOGICAL; OXIDATION-REDUCTION; RECOMBINANT PROTEINS; RNA, BACTERIAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84884927626     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2013.09.003     Document Type: Article

References (42)

1. Ajikumar P.K., Xiao W.H., Tyo K.E.J., Wang Y., Simeon F., Leonard E., Mucha O., Phon T.H., Pfeifer B., Stephanopoulos G. Isoprenoid pathway optimization for taxol precursor overproduction in Escherichia coli. Science 2010, 330:70-74.
2. Ashok S., Raj S.M., Ko Y., Sankaranarayanan M., Zhou S.F., Kumar V., Park S. Effect of puuC overexpression and nitrate addition on glycerol metabolism and anaerobic 3-hydroxypropionic acid production in recombinant Klebsiella pneumoniae δglpK δdhaT. Metab. Eng. 2013, 15:10-24.
3. Atsumi S., Cann A.F., Connor M.R., Shen C.R., Smith K.M., Brynildsen M.P., Chou K.J.Y., Hanai T., Liao J.C. Metabolic engineering of Escherichia coli for 1-butanol production. Metab. Eng. 2008, 10:305-311.
4. Bastian S., Liu X., Meyerowitz J.T., Snow C.D., Chen M.M.Y., Arnold F.H. Engineered ketol-acid reductoisomerase and alcohol dehydrogenase enable anaerobic 2-methylpropan-1-ol production at theoretical yield in Escherichia coli. Metab. Eng. 2011, 13:345-352.
5. Berrios-Rivera S.J., Bennett G.N., San K.Y. Metabolic engineering of Escherichia coli: Increase of NADH availability by overexpressing an NAD(+)-dependent formate dehydrogenase. Metab. Eng. 2002, 4:217-229.
6. Bond-Watts B.B., Bellerose R.J., Chang M.C.Y. Enzyme mechanism as a kinetic control element for designing synthetic biofuel pathways. Nat. Chem. Biol. 2011, 7:222-227.
7. Boyle P.M., Silver P.A. Parts plus pipes: synthetic biology approaches to metabolic engineering. Metab. Eng. 2012, 14:223-232.
8. Chemler J.A., Fowler Z.L., McHugh K.P., Koffas M.A.G. Improving NADPH availability for natural product biosynthesis in Escherichia coli by metabolic engineering. Metab. Eng. 2010, 12:96-104.
9. Curran K.A., Alper H.S. Expanding the chemical palate of cells by combining systems biology and metabolic engineering. Metab. Eng. 2012, 14:289-297.
10. Datsenko K.A., Wanner B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. U.S.A. 2000, 97:6640-6645.
11. Farmer W.R., Liao J.C. Improving lycopene production in Escherichia coli by engineering metabolic control. Nat. Biotechnol. 2000, 18:533-537.
12. Foster J.W., Moat A.G. Nicotinamide adenine dinucleotide biosynthesis and pyridine nucleotide cycle metabolism in microbial systems. Microbiol. Rev. 1980, 44:83-105.
13. Holtz W.J., Keasling J.D. Engineering static and dynamic control of synthetic pathways. Cell 2010, 140:19-23.
14. Isaacs F.J., Dwyer D.J., Ding C.M., Pervouchine D.D., Cantor C.R., Collins J.J. Engineered riboregulators enable post-transcriptional control of gene expression. Nat. Biotechnol. 2004, 22:841-847.
15. Keasling J.D. Synthetic biology and the development of tools for metabolic engineering. Metab. Eng. 2012, 14:189-195.
16. Kim Y., Ingram L.O., Shanmugam K.T. Construction of an Escherichia coli K-12 mutant for homoethanologenic fermentation of glucose or xylose without foreign genes. Appl. Environ. Microbiol. 2007, 73:1766-1771.
17. Kim Y., Ingram L.O., Shanmugam K.T. Dihydrolipoamide dehydrogenase mutation alters the NADH sensitivity of pyruvate dehydrogenase complex of Escherichia coli K-12. J. Bacteriol. 2008, 190:3851-3858.
18. Lim H.G., Seo S.W., Jung G.Y. Engineered Escherichia coli for simultaneous utilization of galactose and glucose. Bioresour. Technol. 2013, 135:564-567.
19. Lim J.H., Seo S.W., Kim S.Y., Jung G.Y. Refactoring redox cofactor regeneration for high-yield biocatalysis of glucose to butyric acid in Escherichia coli. Bioresour. Technol. 2013, 135:568-573.
20. Lim S.I., Min B.E., Jung G.Y. Lagging strand-biased initiation of Red recombination by linear double-stranded DNAs. J. Mol. Biol. 2008, 384:1098-1105.
21. Lo T.M., Teo W.S., Ling H., Chen B., Kang A., Chang M.W. Microbial engineering strategies to improve cell viability for biochemical production. Biotechnol. Adv. 2013.
22. Lynch S.A., Gill R.T. Synthetic biology: new strategies for directing design. Metab. Eng. 2012, 14:205-211.
23. Martin V.J.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.
24. Michener J.K., Thodey K., Liang J.C., Smolke C.D. Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. Metab. Eng. 2012, 14:212-222.
25. Nielsen D.R., Leonard E., Yoon S.H., Tseng H.C., Yuan C., Prather K.L.J. Engineering alternative butanol production platforms in heterologous bacteria. Metab. Eng. 2009, 11:262-273.
26. Peralta-Yahya P.P., Zhang F.Z., del Cardayre S.B., Keasling J.D. Microbial engineering for the production of advanced biofuels. Nature 2012, 488:320-328.
27. Pfleger B.F., Pitera D.J., Smolke D., Keasling, J.D.C. Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat. Biotechnol. 2006, 24:1027-1032.
28. Saito, I., Kanegae, Y., 2001. DNA containing variant FRT sequences. Int. Patent Appl., WO/2001/023545.
29. Salis H.M., Mirsky E.A., Voigt C.A. Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol. 2009, 27. (946-U112).
30. Seo S.W., Kim S.C., Jung G.Y. Synthetic regulatory tools for microbial engineering. Biotechnol. Bioprocess Eng. 2012, 17:1-7.
31. Seo S.W., Yang J., Jung G.Y. Quantitative correlation between mRNA secondary structure around the region downstream of the initiation codon and translational efficiency in Escherichia coli. Biotechnol. Bioeng. 2009, 104:611-616.
32. Seo S.W., Yang J.S., Kim I., Yang J., Min B.E., Kim S., Jung G.Y. Predictive design of mRNA translation initiation region to control prokaryotic translation efficiency. Metab. Eng. 2013, 15:67-74.
33. Shen C.R., Lan E.I., Dekishima Y., Baez A., Cho K.M., Liao J.C. Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli. Appl. Environ. Microbiol. 2011, 77:2905-2915.
34. Singh A., Lynch M.D., Gill R.T. Genes restoring redox balance in fermentation-deficient E. coli NZN111. Metab. Eng. 2009, 11:347-354.
35. Slusarczyk H., Felber S., Kula M.R., Pohl M. Stabilization of NAD-dependent formate dehydrogenase from Candida boidinii by site-directed mutagenesis of cysteine residues. Eur. J. Biochem. 2000, 267:1280-1289.
36. Stephanopoulos G. Challenges in engineering microbes for biofuels production. Science 2007, 315:801-804.
37. Stephens P.E., Darlison M.G., Lewis H.M., Guest J.R. The pyruvate dehydrogenase complex of Escherichia coli K12. Nucleotide sequence encoding the pyruvate dehydrogenase component. Eur. J. Biochem. 1983, 133:155-162.
38. Wang Q.Z., Ou M.S., Kim Y., Ingram L.O., Shanmugam K.T. Metabolic flux control at the pyruvate node in an anaerobic Escherichia coli strain with an active pyruvate dehydrogenase. Appl. Environ. Microbiol. 2010, 76:2107-2114.
39. Wilkinson K.D., Williams C.H. NADH inhibition and NAD activation of Escherichia coli lipoamide dehydrogenase catalyzing the NADH-lipoamide reaction. J. Biol. Chem. 1981, 256:2307-2314.
40. Xu P., Gu Q., Wang W.Y., Wong L., Bower A.G.W., Collins C.H., Koffas M.A.G. Modular optimization of multi-gene pathways for fatty acids production in E. coli. Nat. Commun. 2013, 4:1409.
41. Yadav V.G., De Mey M., Lim C.G., Ajikumar P.K., Stephanopoulos G. The future of metabolic engineering and synthetic biology: towards a systematic practice. Metab. Eng. 2012, 14:233-241.
42. Zhang F.Z., Carothers J.M., Keasling J.D. Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat. Biotechnol. 2012, 30:354-359.