Improving NADPH availability for natural product biosynthesis in Escherichia coli by metabolic engineering

Metabolic Engineering

Volumn 12, Issue 2, 2010, Pages 96-104

  Chemler, Joseph A ^a   Fowler, Zachary L ^a   McHugh, Kyle P ^a   Koffas, Mattheos A G ^a  

^a the State University of New York   (United States)

Author keywords

Catechins; Constraint based modeling; Flavonoids; NADPH

Indexed keywords

BATCH CULTURE; COFACTORS; CONSTRAINT-BASED MODELING; DIHYDROFLAVONOL 4 REDUCTASE; EFFICIENT PRODUCTION; FLAVONOIDS; GENE DELETION; GENE KNOCKOUT; METABOLIC ENGINEERING; MICROBIAL PRODUCTION; NADPH AVAILABILITY; NATURAL PRODUCT SYNTHESIS; NATURAL PRODUCTS; POLYPHENOLS; WILD-TYPE CONTROLS;

BATCH CELL CULTURE; BIOCHEMISTRY; DRILLING PLATFORMS; ESCHERICHIA COLI; GLUCOSE; ORGANIC COMPOUNDS; PRODUCTION PLATFORMS; SYNTHESIS (CHEMICAL); VITAMINS;

PHENOLS;

CATECHIN; NATURAL PRODUCT; POLYPHENOL DERIVATIVE; PYCNOGENOL; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; TAXIFOLIN;

ARTICLE; CONTROLLED STUDY; ESCHERICHIA COLI; GENE DELETION; GENOTYPE; METABOLIC ENGINEERING; MICROBIAL BIOMASS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MODELS, BIOLOGICAL; NADP; PROTEIN ENGINEERING;

ESCHERICHIA COLI;

EID: 76749151341     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2009.07.003     Document Type: Article

References (56)

1. Alper H., et al. Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab. Eng. 7 (2005) 155-164
2. Alper H., et al. Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets. Nat. Biotechnol. 23 (2005) 612-616
3. Bastos F.D., et al. Three different coupled enzymatic systems for in situ regeneration of NADPH. Biotechnol. Tech. 13 (1999) 661-664
4. Bonarius H.P.J., et al. Flux analysis of underdetermined metabolic networks: the quest for the missing constraints. Trends Biotechnol. 15 (1997) 308-314
5. Boonstra B., et al. Cofactor regeneration by a soluble pyridine nucleotide transhydrogenase for biological production of hydromorphone. Appl. Environ. Microbiol. 66 (2000) 5161-5166
6. Burgard A.P., et al. OptKnock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng. 84 (2003) 647-657
7. Chemler J.A., et al. Standardized biosynthesis of flavan-3-ols with effects on pancreatic beta-cell insulin secretion. Appl. Environ. Microbiol. 77 (2007) 797-807
8. Chin J.W., et al. Analysis of NADPH supply during xylitol production by engineered Escherichia coli. Biotechnol. Bioeng. 102 (2009) 209-220
9. Cirino P.C., and Sun L. Advancing biocatalysis through enzyme, cellular, and platform engineering. Biotechnol. Prog. 24 (2008) 515-519
10. Covert M.W., et al. Metabolic modeling of microbial strains in silico. Trends Biochem. Sci. 26 (2001) 179-186
11. Datsenko K.A., and Wanner B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97 (2000) 6640-6645
12. De Maeseneire S.L., et al. Metabolic characterisation of E-coli citrate synthase and phosphoenolpyruvate carboxylase mutants in aerobic cultures. Biotechnol. Lett. 28 (2006) 1945-1953
13. Dean A.M., and Koshland D.E. Kinetic mechanism of Escherichia coli isocitrate dehydrogenase. Biochemistry 32 (1993) 9302-9309
14. Edwards J.S., et al. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol. 19 (2001) 125-130
15. Fong S.S., et al. In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol. Bioeng. 91 (2005) 643-648
16. Fowler, Z.L., Gikandi, W.W., Koffas, M.A.G., 2009. Increasing malonyl-CoA biosynthesis by tuning the Escherichia coli metabolic network and its application to flavanone production. Appl. Environ. Microbiol.75 (18), doi:10.1128/AEM.00270-09.
17. Giorgetti, N., 2005. A C Matlab MEX interface for the CPLEX callable library. Control and Optimization of Hybrid and Embedded Systems Group, University of Siena, Siena, Italy.
18. Hannum S.M. Potential impact of strawberries on human health: a review of the science. Crit. Rev. Food Sci. 44 (2004) 1-17
19. Ichinose H., et al. Enzymatic redox cofactor regeneration in organic media: functionalization and application of glycerol dehydrogenase and soluble transhydrogenase in reverse micelles. Biotechnol. Prog. 21 (2005) 1192-1197
20. Irani M., and Maitra P.K. Isolation and characterization of Escherichia coli mutants defective in enzymes of glycolysis. Biochem. Biophys. Res. Commun. 56 (1974) 127-133
21. Johannes T.W., et al. Directed evolution of a thermostable phosphite dehydrogenase for NAD(P)H regeneration. Appl. Environ. Microbiol. 71 (2005) 5728-5734
22. Johannes T.W., et al. Efficient regeneration of NADPH using an engineered phosphite dehydrogenase. Biotechnol. Bioeng. 96 (2007) 18-26
23. Kabir M.M., and Shimizu K. Fermentation characteristics and protein expression patterns in a recombinant Escherichia coli mutant lacking phosphoglucose isomerase for poly(3-hydroxybutyrate) production. Appl. Microbiol. Biotechnol. 62 (2003) 244-255
24. Kahkonen M.P., and Heinonen M. Antioxidant activity of anthocyanins and their aglycons. J .Agric. Food Chem. 51 (2003) 628-633
25. Kanehisa M. A database for post-genome analysis. Trends Genet. 13 (1997) 375-376
26. Kauffman K.J., et al. Advances in flux balance analysis. Curr. Opin. Biotechnol. 14 (2003) 491-496
27. Keseler I.M., et al. EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res. 33 (2005) D334-D337
28. Kim T.Y., et al. Strategies for systems-level metabolic engineering. Biotechnol. J. 3 (2008) 612-623
29. Kubo T., et al. Enantioselective epoxidation of terminal alkenes to (R)- and (S)-epoxides by engineered cytochromes P450BM-3. Chem. Eur. J. 12 (2006) 1216-1220
30. Lee K.H., et al. Systems metabolic engineering of Escherichia coli for l-threonine production. Mol. Syst. Biol. 3 (2007) (Article 149)
31. Lee W.H., et al. Enhanced production of e-caprolactone by overexpression of NADPH-regenerating glucose 6-phosphate dehydrogenase in recombinant Escherichia coli harboring cyclohexanone monooxygenase gene. Appl. Microbiol. Biotechnol. 76 (2007) 329-338
32. Leonard E., et al. Characterization of dihydroflavonol 4-reductases for recombinant plant pigment biosynthesis applications. Biocatal. Biotransform. 26 (2008) 243-251
33. Lila M.A. Interactions between flavonoids that benefit human health. In: Gould K., et al. (Ed). Anthocyanins: Biosynthesis, Functions, and Applications (2009), Springer, New York 305-323
34. Lilius E.M., et al. Quantitative extraction and estimation of intracellular nicotinamide nucleotides of Escherichia coli. Anal. Biochem. 99 (1979) 22-27
35. Lim S.J., et al. Amplification of the NADPH-related genes zwf and gnd for the oddball biosynthesis of PHB in an E. coli transformant harboring a cloned phbCAB operon. J. Biosci. Bioeng. 93 (2002) 543-549
36. Matsushita K., et al. Escherichia coli is unable to produce pyrroloquinoline quinone (PQQ). Microbiology 143 (1997) 3149-3156
37. Middleton E., et al. The effects of plant flavonoids on mammalian cells: Implications for inflammation, heart disease, and cancer. Pharmacol. Rev. 52 (2000) 673-751
38. Nielsen J. Metabolic engineering: techniques for analysis of targets for genetic manipulations. Biotechnol. Bioeng. 58 (1998) 125-132
39. Nimmo H.G. Kinetic mechanism of Escherichia coli isocitrate dehydrogenase and its inhibition by glyoxylate and oxaloacetate. Biochem. J. 234 (1986) 317-323
40. Park J.H., et al. 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. USA 104 (2007) 7797-7802
41. Park J.H., et al. Application of systems biology for bioprocess development. Trends Biotechnol. 26 (2008) 404-412
42. Patil K.R., et al. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinf. 6 (2005) (Article 308)
43. 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements. FEMS Microbiol. Lett. 235 (2004) 17-23
44. Pharkya P., et al. OptStrain: a computational framework for redesign of microbial production systems. Genome Res. 14 (2004) 2367-2376
45. Reed J.L., et al. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 4 (2003) (Article R54)
46. Sauer U., et al. The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli. J. Biol. Chem. 279 (2004) 6613-6619
47. Segre D., et al. Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. USA 99 (2002) 15112-15117
48. Shlomi T., et al. Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc. Natl. Acad. Sci. USA 102 (2005) 7695-7700
49. + using malic enzyme of Achromobacter parvulus IFO-13182. Enzyme Microb. Technol. 7 (1985) 418-424
50. Tanner G.J., et al. Proanthocyanidin biosynthesis in plants: Purification of legume leucoanthocyanidin reductase and molecular cloning of its cDNA. J. Biol. Chem. 278 (2003) 31647-31656
51. Tishkov V.I., and Popov V.O. Protein engineering of formate dehydrogenase. Biomol. Eng. 23 (2006) 89-110
52. Tyo K.E., et al. Expanding the metabolic engineering toolbox: more options to engineer cells. Trends Biotechnol. 25 (2007) 132-137
53. Varma A., and Palsson B.O. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl. Environ. Microbiol. 60 (1994) 3724-3731
54. Walton A.Z., and Stewart J.D. Understanding and improving NADPH-dependent reactions by nongrowing Escherichia coli cells. Biotechnol. Prog. 20 (2004) 403-411
55. +-dependent formate dehydrogenase. Biotechnol. Lett. 26 (2004) 1739-1744
56. Zha W., et al. Improving cellular malonyl-CoA level in Escherichia coli via metabolic engineering. Metab. Eng. 11 (2009) 192-198