Genetically constrained metabolic flux analysis

Metabolic Engineering

Volumn 7, Issue 5-6, 2005, Pages 445-456

  Cox, Steven J ^a   Shalel Levanon, Sagit ^b   Bennett, George N ^b   San, Ka Yiu ^a  

^a Rice University   (United States)

^b RICE UNIVERSITY   (United States)

Author keywords

Genetic regulatory network; Metabolic flux analysis; Metabolic network

Indexed keywords

DATABASE SYSTEMS; ESCHERICHIA COLI; GENES; GENETIC ENGINEERING; OXYGEN; REDOX REACTIONS;

GENETIC REGULATORY NETWORK; METABOLIC FLUXES; METABOLIC NETWORK;

METABOLISM;

OXYGEN;

ADAPTATION; ANALYSIS; ARTICLE; CITRIC ACID CYCLE; DATA BASE; DNA MICROARRAY; ESCHERICHIA COLI; GENE ACTIVATION; GENE CONTROL; GENE EXPRESSION; GENE REPRESSION; GENOMICS; GLYCOLYSIS; METABOLISM; OXIDATION REDUCTION REACTION; PRIORITY JOURNAL; REGULATORY MECHANISM; STIMULUS RESPONSE;

CITRIC ACID CYCLE; COMPUTER SIMULATION; ENERGY METABOLISM; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; GLYCOLYSIS; MODELS, BIOLOGICAL; OXYGEN; SIGNAL TRANSDUCTION;

ESCHERICHIA COLI;

EID: 29044438437     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2005.07.004     Document Type: Article

References (32)

1. S. Alexeeva, K.J. Hellingwerf, Teixeira, and M.J. de Mattos Requirement of ArcA for redox regulation in Escherichia coli under microaerobic but not anaerobic or aerobic conditions J. Bacteriol. 185 2003 204 209
2. L.M. Blank, and U. Sauer TCA cycle activity in Saccharomyces cerevisiae is a function of the environmentally determined specific growth and glucose uptake rates Microbiology 150 2004 1085 1093
3. A.P. Burgard, and C.D. Maranas Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions Biotechnol. Bioeng. 74 2001 364 375
4. A.P. Burgard, P. Pharkya, and C.D. Maranas Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization Biotechnol. Bioeng. 84 2003 647 657
5. G. Chao, J. Shen, C.P. Tseng, S.J. Park, and R.P. Gunsalus Aerobic regulation of isocitrate dehydrogenase gene (icd) expression in Escherichia coli by the arcA and fnr gene products J. Bacteriol. 179 1997 4299 4304
6. H. De Jong Modeling and simulation of genetic regulatory systems: a literature review J. Comput. Biol. 9 2002 67 103
7. J.S. Edwards, M. Covert, and B. Palsson Metabolic modelling of microbes: the flux-balance approach Environ. Microbiol. 4 2002 133 140
8. D. Georgellis, O. Kwon, P. De Wulf, and E.C.C. Lin Signal decay through a reverse phosphorelay in the Arc two-component signal transduction system J. Biol. Chem. 273 1998 32864 32869
9. D. Georgellis, O. Kwon, and E.C.C. Lin Amplification of signaling activity of the Arc two-component system of Escherichia coli by anaerobic metabolites: an in vitro study with different protein modules J. Biol. Chem. 274 1999 35950 35954
10. D. Georgellis, O. Kwon, and E.C.C. Lin Quinones as the redox signal for the Arc two-component system of bacteria Science 292 2001 2314 2316
11. J.R. Guest, J. Green, A.S. Irvine, and S. Spiro The FNR modulon and FNR-regulated gene expression E.C.C. Lin A.S. Lynch Regulation of gene expression in Escherichia coli 1996 Chapman & Hall New York
12. R.P. Gunsalus Control of electron flow in Escherichia coli: coordinated transcription of respiratory pathway genes J. Bacteriol. 174 1992 7069 7074
13. Y. Kang, K.D. Weber, Y. Qiu, P.J. Kiley, and F.R. Blattner Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function J. Bacteriol. 187 2005 1135 1160
14. M.I. Klapa, S.M. Park, A.J. Sinskey, and G. Stephanopoulos Metabolite and isotopomer balancing in the analysis of metabolic cycles: I. Theory Biotechnol. Bioeng. 62 1999 375 391
15. M.I. Klapa, J.C. Aon, and G. Stephanopoulos Ion-trap mass spectrometry used in combination with gas chromatography for high-resolution metabolic flux determination Biotechniques 34 2003 832 836
16. S. Kauffman The large scale structure and dynamics of gene control circuits J. Theor. Biol. 44 1974 167 190
17. E.C.E. Lin, and A.S. Iuchi Regulation of gene expression in fermentative and respiratory systems in Escherichia coli and related bacteria Ann. Rev. Genet. 25 1991 361 387
18. A.S. Lynch, and E.C.C. Lin Regulation of aerobic and anaerobic metabolism by the Arc system E.C.C. Lin A.S. Lynch Regulation of gene expression in Escherichia coli 1996 Chapman & Hall New York
19. D.L. Nelson, and M.M. Cox Lehninger Principles of Biochemistry third ed 2000 Worth Publishers New York
20. S.J. Park, and R.P. Gunsalus Oxygen, iron, carbon, and superoxide control of the fumarase fumA and fumC genes of Escherichia coli: Role of the arcA, fnr, and soxR gene products J. Bacteriol. 177 1995 6255 6262
21. S.J. Park, G. Chao, and R.P. Gunsalus Aerobic regulation of the sucABCD genes of Escherichia coli, which encode α-ketoglutarate dehydrogenase and succinyl coenzyme A synthetase: Roles of ArcA, Fnr, and upstream sdhCDAB promoter J. Bacteriol. 179 1997 4138 4142
22. H. Salgado, S. Gama-Castro, A. Martinez-Antonio, E. Diaz-Peredo, F. Sanchez-Solano, M. Peralta-Gil, D. Garcia-Alonso, V. Jimenez-Jacinto, A. Santos-Zavaleta, C. Bonavides-Martinez, and J. Collado-Vides RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12 Nucleic Acids Res. 32 2004 (Database issue D303±D306)
23. San, K.-Y., Cox, S., Shalel Levanon, S., Bennett, G.N., 2003. Metabolic flux analysis based on dynamic genomic information. In: 225th American Chemical Society National Meeting, New Orleans, LA.
24. G. Sawers The aerobic/anaerobic interface Curr. Opin. Microbiol. 2 1999 181 187
25. C.H. Schilling, J.S. Edwards, D. Letscher, and B.O. Palsson Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems Biotechnol. Bioeng. 71 2001 286 306
26. S. Schuster, D.A. Fell, and T. Dandekar A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks Nature Biotech. 18 2000 326 332
27. S. Shalel Levanon, K.Y. San, and G.N. Bennett Effect of oxygen on the Escherichia coli ArcA and FNR regulation systems and metabolic responses Biotechnol. Bioeng. 89 2005 556 564
28. G. Sriram, and J.V. Shanks Improvements in metabolic flux analysis using carbon bond labeling experiments: bondomer balancing and Boolean function mapping Metab. Eng. 6 2004 116 132
29. C.P. Tseng, J. Albrecht, and R.P. Gunsalus Effect of microaerophilic cell growth conditions on expression of the aerobic (cyoABCDE and cydAB) and anaerobic (narGHJI, frdABCD, and dmsABC) respiratory pathway genes in Escherichia coli J. Bacteriol. 178 1996 1094 1098
30. 2 dependent gene regulation in facultatively anaerobic bacteria Arch. Microbiol. 164 1995 81 90
31. S.J. Wiback, R. Mahadevan, and B.O. Palsson Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum Biotechnol. Bioeng. 86 2004 317 331
32. J. Zhao, T. Baba, H. Mori, and K. Shimizu Effect of zwf gene knockout on the metabolism of Escherichia coli grown on glucose or acetate Metab. Eng. 6 2004 164 174