Metabolic capacity estimation of Escherichia coli as a platform for redox biocatalysis: Constraint-based modeling and experimental verification

Biotechnology and Bioengineering

Volumn 100, Issue 6, 2008, Pages 1050-1065

  Blank, Lars M ^a,b   Ebert, Birgitta E ^a   Bühler, Bruno ^a   Schmid, Andreas ^a,b  

^a TU DORTMUND UNIVERSITY   (Germany)

^b LEIBNIZ INSTITUT FÜR ANALYTISCHE WISSENSCHAFTEN ISAS E V   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; EPOXIDATION; ESCHERICHIA COLI; GLUCOSE; METABOLISM; OPTIMIZATION;

A-PRIORI; BIOCATALYSIS; BIOCATALYTIC ACTIVITY; BIOTRANSFORMATION PROCESSES; BY-PRODUCT FORMATION; CARBON METABOLISM; COFACTOR REGENERATION; CONSTRAINT BASED MODELLING; ENERGY DEMANDS; EXPERIMENTAL VERIFICATION; FLUX BALANCE ANALYSIS; FLUX DISTRIBUTIONS; FORMATION RATES; GLUCOSE UPTAKE; HIGH RATES; IN-SILICO; LINEAR CORRELATIONS; LINEAR DEPENDENCIES; METABOLIC CAPACITIES; METABOLIC NETWORKS; MICROBIAL CELLS; NADH REGENERATION; OPTIMIZATION CRITERION; PENTOSE PHOSPHATE PATHWAY; QUANTITATIVE COMPARISON; WILD-TYPE CELLS;

ESTIMATION;

REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE;

ANIMAL EXPERIMENT; ARTICLE; BACTERIAL STRAIN; BIOCATALYST; BIOTRANSFORMATION; CARBON METABOLISM; CONTROLLED STUDY; EPOXIDATION; ESCHERICHIA COLI; GLUCOSE TRANSPORT; GLYCOLYSIS; METABOLIC CAPACITY; NONHUMAN; SYSTEM ANALYSIS; WILD TYPE;

BACTERIAL PROTEINS; CATALYSIS; COMPUTER SIMULATION; ESCHERICHIA COLI; FEEDBACK, BIOCHEMICAL; GENE EXPRESSION REGULATION, BACTERIAL; GLUCOSE; GLYCOLYSIS; KINETICS; MODELS, BIOLOGICAL; NAD; OXIDATION-REDUCTION; PENTOSE PHOSPHATE PATHWAY; PROTEIN ENGINEERING;

ESCHERICHIA COLI;

EID: 48649109598     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.21837     Document Type: Article

References (52)

1. Alper H, Jin YS, Moxley JF, Stephanopoulos G. 2005. Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab Eng 7(3):155-164.
2. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H. 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection. Mol Syst Biol 2:0008.
3. 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast. Genome Biol 6(6):R49.
4. Boonstra B, French CE, Wainwright I, Bruce NC. 1999. The udhA gene of Escherichia coli encodes a soluble pyridine nucleotide transhydrogenase. J Bacteriol 181(3):1030-1034.
5. Bro C, Regenberg B, Forster J, Nielsen J. 2006. In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production. Metab Eng 8(2):102-111.
6. Buhler B, Schmid A, Hauer B, Witholt B. 2000. Xylene monooxygenase catalizes the multistep oxygenation of toluene and pseudocumene to corresponding alcohols, aldehydes, and acids in Escherichia coli JM101. J Biol Chem 275(14):10085-10092.
7. Buhler B, Schmid A. 2004. Process implementation aspects for biocatalytic hydrocarbon oxyfunctionalization. J Biotechnol 113(1-3): 183-210.
8. Bühler B, Straathof AJJ, Witholt B, Schmid A. 2006. Analysis of two-liquid-phase multistep biooxidation based on a process model: Indications for biological energy shortage. Org Process Res Dev 10(3):628-643.
9. Bühler B, Park JB, Blank LM, Schmid A. 2008. NADH availability limits asymmetric biocatalytic epoxidation in growing recombinant Escherichia coli. Appl Environ Microbiol. 2008 Jan 11 [Epub ahead of print].
10. Clarke DM, Loo TW, Gillam S, Bragg PD. 1986. Nucleotide sequence of the pntA and pntB genes encoding the pyridine nucleotide transhydrogenase of Escherichia coli. Eur J Biochem 158(3):647-653.
11. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. 2004. Integrating high-throughput and computational data elucidates bacterial networks. Nature 429(6987):92-96.
12. Datsenko KA, Wanner BL. 2000. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 97(12):6640-6645.
13. Dawes EA, Ribbons DW. 1965. Studies on endogenous metabolism of Escherichia coli. Biochem J 95(2):332-343.
14. Duetz WA, van Beilen JB, Witholt B. 2001. Using proteins in their natural environment: Potential and limitations of microbial whole-cell hydroxylations in applied biocatalysis. Curr Opin Biotechnol 12(4):419-425.
15. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO. 2007. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3:121.
16. Fischer E, Sauer U. 2003a. Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS. Eur J Biochem 270(5):880-891.
17. Fischer E, Sauer U. 2003b. A novel metabolic cycle catalyzes glucose oxidation and anaplerosis in hungry Escherichia coli. J Biol Chem 278(47):46446-46451.
18. Fischer E, Sauer U. 2005. Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism. Nat Genet 37(6):636-640.
19. Flores S, Flores N, de Anda R, Gonzalez A, Escalante A, Sigala JC, Gosset G, Bolivar F. 2005. Nutrient-scavenging stress response in an Escherichia coli strain lacking the phosphoenolpyruvatexarbohydrate phosphotransferase system, as explored by gene expression profile analysis. J Mol Microbiol Biotechnol 10(l):51-63.
20. Gonzalez-Lergier J, Broadbelt LJ, Hatzimanikatis V. 2006. Analysis of the maximum theoretical yield for the synthesis of erythromycin precursors in Escherichia coli. Biotechnol Bioeng 95(4):638-644.
21. Gottschalk G. 1979. Bacterial metabolism. New York: Springer. 281 p.
22. Harris LM, Blank L, Desai RP, Welker NE, Papoutsakis ET. 2001. Fermentation characterization and flux analysis of recombinant strains of Clostridium acetobutylicum with an inactivated solR gene. J Ind Microbiol Biotechnol 27(5):322-328.
23. Irani MH, Maitra PK. 1977. Properties of Escherichia coli mutants deficient in enzymes of glycolysis. J Bacteriol 132(2):398-410.
24. Kantz A, Chin F, Nallamothu N, Nguyen T, Gassner GT. 2005. Mechanism of flavin transfer and oxygen activation by the two-component flavoenzyme styrene monooxygenase. Arch Biochem Biophys 442(1): 102-116.
25. Karp PD, Riley M, Saier M, Paulsen IT, Paley M, Pellegrini-Toole A. 2000. The EcoCyc and MetaCyc databases. Nucleic Acids Res 28(1):56-59.
26. Koffas M, Stephanopoulos G. 2005. Strain improvement by metabolic engineering: Lysine production as a case study for systems biology. Curr Opin Biotechnol 16(3):361-366.
27. Laemmli UK. 1970. Cleavage of structural proteins during assembly of head of bacteriophage-T4. Nature 227(5259):680-685.
28. Li M, Ho PY, Yao SJ, Shimizu K. 2006. Effect of sucA or sucC gene knockout on the metabolism in Escherichia coli based on gene expressions, enzyme activities, intracellular metabolite concentrations and metabolic fluxes by C-13-labeling experiments. Biochem Eng J 30(3):286-296.
29. Ma H, Zeng AP. 2003. Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 19(2):270-277.
30. Majewski RA, Domach MM. 1990. Simple constrained-optimization view of acetate overflow in Escherichia coli. Biotechnol Bioeng 35(7):732-738.
31. Meyer D, Buehler B, Schmid A. 2006. Process and catalyst design objectives for specific redox biocatalysis. Adv Appl Microbiol 59:53-91.
32. Neidhardt FC, Ingraham JL. 1987. Escherichia coli and Salmonella typhimurium cellular and molecular biology, 2 vols. Washington, DC: American Society for Microbiology.
33. Nelson DL, Cox MM, Lehninger AL. 2005. Lehninger principles of biochemistry. New York: W.H. Freeman. 1119 p.
34. 31P NMR using a circulating fermentation system. J Biochem (Tokyo) 136(4):509-515.
35. Otto K, Hofstetter K, Rothlisberger M, Witholt B, Schmid A. 2004. Biochemical characterization of StyAB from Pseudomonas sp. strain VLB 120 as a two-component flavin-diffusible monooxygenase. J Bacteriol 186(16):5292-5302.
36. Panke S, Meyer A, Huber CM, Witholt B, Wubbolts MG. 1999. An alkane-responsive expression system for the production of fine chemicals. Appl Environ Microbiol 65(6):2324-2332.
37. Panke S, Wubbolts MG, Schmid A, Witholt B. 2000. Production of enantiopure styrene oxide by recombinant Escherichia coli synthesizing a two-component styrene monooxygenase. Biotechnol Bioeng 69(1): 91-100.
38. Papoutsakis ET. 1984. Equations and calculations for fermentations of butyric-acid bacteria. Biotechnol Bioeng 26(2):174-187.
39. Park JB, Buehler B, Habicher T, Hauer B, Panke S, Witholt B, Schmid A. 2006. The efficiency of recombinant Escherichia coli as biocatalyst for stereospecific epoxidation. Biotechnol Bioeng 95(3):501-512.
40. Pharkya P, Burgard AP, Maranas CD. 2004. OptStrain: A computational framework for redesign of microbial production systems. Genome Res 14(11):2367-2376.
41. Phue JN, Noronha SB, Bhattacharyya R, Wolfe AJ, Shiloach J. 2005. Glucose metabolism at high density growth of E. coli B and E. coli K: Differences in metabolic pathways are responsible for efficient glucose utilization in E. coli B as determined by microarrays and northern blot analyses. Biotechnol Bioeng 91(5):649-649.
42. Russell JB, Cook GM. 1995. Energetics of bacterial growth - Balance of anabolic and catabolic reactions. Microbiol Rev 59(1):48-62.
43. Sahm H, Eggeling L, de Graaf AA. 2000. Pathway analysis and metabolic engineering in Corynebacterium glutatnicum. Biol Chem 381(9-10): 899-910.
44. Sambrook J, Russell DW. 2001. Molecular cloning a laboratory manual, 3 vols. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
45. Sauer U, Cameron DC, Bailey JE. 1998. Metabolic capacity of Bacillus subtilis for the production of purine nucleosides, riboflavin, and folic acid. Biotechnol Bioeng 59(2):227-238.
46. Sauer U, Canonaco F, Heri S, Perrenoud A, Fischer E. 2004. The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli. J Biol Chem 279(8):6613-6619.
47. Sawers G, Watson G. 1998. A glycyl radical solution: Oxygen-dependent interconversion of pyruvate formate-lyase. Mol Microbiol 29(4):945-954.
48. Vallino JJ, Stephanopoulos G. 1994. Carbon flux distributions at the pyruvate branch point in Corynebacterium glutamicum during lysine overproduction. Biotechnol Progr 10(3):320-326.
49. Varma A, Palsson BO. 1994. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol 60(10):3724-3731.
50. Walton AZ, Stewart JD. 2004. Understanding and improving NADPH-dependent reactions by nongrowing Escherichia coli cells. Biotechnol Progr 20(2):403-411.
51. Witholt B. 1972. Method for isolating mutants overproducing nicotinamide adenine dinucleotide and its precursors. J Bacteriol 109(1):350-364.
52. Zeng AP, Ross A, Deckwer WD. 1990. A method to estimate the efficiency of oxidative-phosphorylation and biomass yield from ATP of a facultative anaerobe in continuous culture. Biotechnol Bioeng 36(9):965-969.