Optimizing cofactor specificity of oxidoreductase enzymes for the generation of microbial production strains - OptSwap

Industrial Biotechnology

Volumn 9, Issue 4, 2013, Pages 236-246

  King, Zachary A ^a   Feist, Adam M ^a,b  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b Chalmers University of Technology   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

COFACTOR SPECIFICITY; GENOME-SCALE METABOLIC MODELS; MICROBIAL METABOLISM; MICROBIAL PRODUCTION; OXIDATIVE PHOSPHORYLATION; OXIDOREDUCTASE REACTION; PREFERENTIAL BINDING; SUCCINATE PRODUCTION;

AMINO ACIDS; DESIGN; ENZYMES; ESCHERICHIA COLI; METABOLISM; METABOLITES; OPTIMIZATION; PRODUCTIVITY; STRAIN; VOLATILE FATTY ACIDS;

SUBSTRATES;

EID: 84881496214     PISSN: 15509087     EISSN: None     Source Type: Journal    
DOI: 10.1089/ind.2013.0005     Document Type: Article

References (45)

1. Russell J, Cook G. Energetics of bacterial growth: Balance of anabolic and catabolic reactions. Microbiol Rev 1995;59(1).
2. Sauer U, Canonaco F, Heri S, et al. The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli. J Biol Chem 2004;279(8):6613-6619. (Pubitemid 38248798)
3. Gottschalk G. Bacterial Metabolism (2nd ed.). New York: Springer-Verlag, 1986.
4. Lunzer M, Miller SP, Felsheim R, Dean AM. The biochemical architecture of an ancient adaptive landscape. Science 2005;310(5747):499-501. (Pubitemid 41507965)
5. Rodríguez-Arnedo A, Camacho M, Llorca F, Bonete M-J. Complete reversal of coenzyme specificity of isocitrate dehydrogenase from Haloferax volcanii. Protein J 2005;24(5):259-266. (Pubitemid 41609498)
6. Bocanegra J, Scrutton N, Perham R. Creation of an NADP-dependent pyruvate dehydrogenase multienzyme complex by protein engineering. Biochemistry 1993;32(11):2737-2740. (Pubitemid 23102793)
7. Kim S, Lee CH, Nam SW, Kim P. Alteration of reducing powers in an isogenic phosphoglucose isomerase (pgi)-disrupted Escherichia coli expressing NAD(P)- dependent malic enzymes and NADP-dependent glyceraldehyde 3-phosphate dehydrogenase. Lett Appl Microbiol 2011;52(5):433-440.
8. Fuhrer T, Sauer U. Different biochemical mechanisms ensure network-wide balancing of reducing equivalents in microbial metabolism. J Bacteriol 2009;191(7):2112-2121.
9. Guest J, Abdel-Hamid A, Auger G, et al. Physiological effects of replacing the PDH complex of E. Coli by genetically engineered variants or by pyruvate oxidase. In: Gordon F, Mulchand S, eds. Thiamine: Catalytic Mechanisms in Normal and Disease States. New York: CRC Press, 2003:387-407.
10. Hurley J, Chen R, Dean AM. Determinants of cofactor specificity in isocitrate dehydrogenase: Structure of an engineering NADP+/NAD+ specificityreversal mutant. Biochemistry 1996;2960(95):5670-5678. (Pubitemid 26143662)
11. Zhu G, Golding GB, Dean AM. The selective cause of an ancient adaptation. Science 2005;307(5713):1279-1282. (Pubitemid 40299972)
12. Martínez I, Zhu J, Lin H, et al. Replacing Escherichia coli NAD-dependent glyceraldehyde 3-phosphate dehydrogenase (GAPDH) with a NADP-dependent enzyme from Clostridium acetobutylicum facilitates NADPH dependent pathways. Metab Eng 2008;10(6):352-359.
13. Verho R, Londesborough J, PenttilaM, Richard P. Engineering redox cofactor regeneration for improved pentose fermentation in Saccharomyces cerevisiae. Appl Environ Microbiol 2003;69(10):5892.
14. Feist AM, Palsson BO. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol 2008;26(6):659-667. (Pubitemid 351824691)
15. McCloskey D, Palsson BO, Feist AM. Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Mol Syst Biol 2013;9(661):1-15.
16. Price ND, Reed JL, Palsson BO. Genome-scale models of microbial cells: Evaluating the consequences of constraints. Nat Rev Microbiol 2004;2(11): 886-897. (Pubitemid 39567269)
17. Lewis NE, Nagarajan H, Palsson BO. Constraining the metabolic genotypephenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol 2012;10(4):291-305.
18. Ibarra RU, Edwards JS, Palsson BO. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 2002;420: 186-189. (Pubitemid 35340123)
19. Fong SS, Nanchen A, Palsson BO, Sauer U. Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzyme. J Biol Chem 2006;281(12):8024-8033. (Pubitemid 43847420)
20. Fong SS, Palsson BO. Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet 2004;36(10):1056-1058. (Pubitemid 41184464)
21. Fong SS, Burgard AP, Herring CD, et al. In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol Bioeng 2005;91(5):643-648. (Pubitemid 41335499)
22. Feist AM, Zielinski DC, Orth JD, et al. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab Eng 2010;12(3):173-186.
23. Burgard AP, Pharkya P, Maranas CD. Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 2003;84(6):647-657. (Pubitemid 37420336)
24. Tepper N, Shlomi T. Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways. Bioinformatics 2010;26(4):536-543.
25. Patil KR, Rocha I, Forster J, Nielsen J. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 2005;6:308.
26. Ghosh A, Zhao H, Price ND. Genome-scale consequences of cofactor balancing in engineered pentose utilization pathways in Saccharomyces cerevisiae. PLoS One 2011;6(11):e27316.
27. Orth JD, Conrad TM, Na J, et al. A comprehensive genome-scale reconstruction of Escherichia coli metabolism - 2011. Mol Syst Biol 2011;7(535):535.
28. Blaschkowski H, Neuer G, Ludwig-Festl M, Knappe J. Routes of flavodoxin and ferredoxin reduction in Escherichia coli. Eur J Biochem 1982;123(3):563-569.
29. Kauffman KJ, Prakash P, Edwards JS. Advances in flux balance analysis. Curr Opin Biotechnol 2003;14(5):491-496. (Pubitemid 37298033)
30. Lewis NE, Hixson KK, Conrad TM, et al. Omic data from evolved E. Coli are consistent with computed optimal growth from genome-scale models. Mol Syst Biol 2010;6:390.
31. Mahadevan R, Schilling CH. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng 2003;5(4):264-276. (Pubitemid 38122488)
32. Becker S a, Feist AM, Mo ML, et al. Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox. Nat Protoc 2007;2(3):727-738. (Pubitemid 47040034)
33. Varma A, Boesch BW, Palsson B. Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates. Appl Environ Microbiol 1993;59(8):2465-2473. (Pubitemid 23222983)
34. Varma A, Palsson BO. Metabolic flux balancing: Basic concepts, scientific and practical use. Nat Biotechnol 1994;12:994-998.
35. Palsson BO. Systems Biology: Properties of Reconstructed Networks. Cambridge, UK: Cambridge University Press, 2006.
36. Almaas E, Kovács B, Vicsek T, et al. Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 2004;427(6977):839- 843. (Pubitemid 38297745)
37. Zhang X, Jantama K, Moore JC, et al. Production of L -alanine by metabolically engineered Escherichia coli. Appl Microbiol Biotechnol 2007;77(2):355-366. (Pubitemid 350029450)
38. Wang B, Wang P, Zheng E, et al. Biochemical properties and physiological roles of NADP-dependent malic enzyme in Escherichia coli. J Microbiol 2011;49(5):797-802.
39. Stols L, Donnelly M. Production of succinic acid through overexpression of NAD (+) -dependent malic enzyme in an Escherichia coli mutant. Appl Environ Microbiol 1997;63(7):2695-2701. (Pubitemid 27292862)
40. Marx A, Eikmanns BJ, Sahm H, et al. Response of the central metabolism in Corynebacterium glutamicum to the use of an NADH-dependent glutamate dehydrogenase. Metab Eng 1999;1(1):35-48. (Pubitemid 129499370)
41. Kalinina O, Gelfand M. Amino acid residues that determine functional specificity of NADP-and NAD-dependent isocitrate and isopropylmalate dehydrogenases. Proteins 2006;64(4):1001-1009. (Pubitemid 44424337)
42. Yaoi T, Miyazaki K, Oshima T, et al. Conversion of the coenzyme specificity of isocitrate dehydrogenase by module replacement. J Biochem 1996;119(5):1014-1018. (Pubitemid 26182385)
43. Auriol C, Bestel-Corre G, Claude J-B, et al. Stress-induced evolution of Escherichia coli points to original concepts in respiratory cofactor selectivity. Proc Natl Acad Sci 2011;108(4):1278-1283.
44. Baba T, Ara T, Hasegawa M, et al. Construction of Escherichia coli K-12 inframe, single-gene knockout mutants: The Keio collection. Mol Syst Biol 2006;2: doi: 10.1038/msb4100050 (Pubitemid 43948152)
45. Heavner BD, Smallbone K, Barker B, et al. Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. BMC Syst Biol 2012;6(1):55.