Effect of weight-added regulatory networks on constraint-based metabolic models of Escherichia coli

BioSystems

Volumn 90, Issue 3, 2007, Pages 843-855

  Lee, Sung Gun ^a   Park, Jun Hyung ^b   Hou, Bo Kyeng ^c   Kim, Young Han ^d   Kim, Cheol Min ^e   Hwang, Kyu Suk ^a  

^a Pusan National University   (South Korea)

^b Insilicogen Inc R and D Center: 16006 SK Hubblue   (South Korea)

^c Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^d Dong A University   (South Korea)

^e Pusan National University School of Medicine   (South Korea)

Author keywords

Central metabolic pathway; Flux balance analysis; If then rule; Linear programming; Weight added regulatory networks

Indexed keywords

ACETIC ACID; GLUCOSE; REGULATOR PROTEIN; TRANSCRIPTION FACTOR;

COLIFORM BACTERIUM; ENVIRONMENTAL CHANGE; EXPERIMENTAL STUDY; GENE EXPRESSION; GLUCOSE; LINEAR PROGRAMING; METABOLISM; NUMERICAL MODEL; PROTEIN; STOICHIOMETRY;

ARTICLE; BACTERIUM CULTURE; ESCHERICHIA COLI; GENE; GENE EXPRESSION; INFORMATION SCIENCE; METABOLISM; MOLECULAR INTERACTION; NONHUMAN; SENSOR; STIMULUS;

ESCHERICHIA COLI;

EID: 35648979008     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2007.05.003     Document Type: Article

References (53)

1. Adhya S. The lac and gal operons today. In: Lin E.C.C., and Lynch A.S. (Eds). In Regulation of Gene Expression in Escherichia coli (1996), Chapman & Hall, New York 181-200
2. Babu M.M., Luscombe N.M., Aravind L., Gerstein M., and Teichmann S.A. Structure and evolution of transcriptional regulatory networks. Curr. Opin. Struct. Biol. 14 (2004) 283-291
3. Cotter P.A., and Gunsalus R.P. Contribution of the fnr and arcA gene products in coordinate regulation of cytochrome o and d oxidase (cyoABCDE and cydAB) genes in Escherichia coli. FEMS Microbiol. Lett. 70 (1992) 31-36
4. Cotter P.A., Melville S., Albrecht J.A., and Gunsalus R.P. Aerobic Regulation of Cytochrome d Oxidase (cydAB) Operon Expression in Escherichia coli: Roles of FNR and ArcA in Activation and Repression. Mol. Microbiol. 25 (1997) 605-615
5. Covert M.W., Schilling C.H., and Palsson B. Regulation of gene expression in flux balance models of metabolism. J. Theor. Biol. 213 (2001) 73-88
6. Covert M.W., and Palsson. Transcriptional regulation in constraints-based metabolic models of Escherichio coli. J. Biol. Chem. 277 (2002) 28058-28064
7. Covert M.W., and Palsson B.O. Constraints-based models: Regulation of gene expression reduces the steady-state solution space. J. Theor. Biol. 221 (2003) 309-325
8. Covert M.C., Knight E.M., Reed J.L., Herrgard M.J., and Palsson B.O. Integrating high-throughput and computational data elucidates bacterial networks. Nature 429 (2004) 92-96
9. Cox S.J., Shalel Levanon S., Bennett G.N., and San K.Y. Genetically constrained metabolic flux analysis. Metab. Eng. 7 (2005) 445-456
10. Cunningham L., and John R.G. Transcription and transcript processing in the sdhCDAB-sucABCD operon of Escherichia coli. Microbiology 144 (1998) 2113-2123
11. Dasika M.S., Gupta A., and Maranas C.D. DEMSIM: a discrete event based mechanistic simulation platform for gene expression and regulation dynamics. J. Theor. Biol. 232 (2005) 55-69
12. Deborah L.W., Nicola W., and Timothy J.L. Structure and regulation of the glpFK operon encoding glycerol diffusion facilitator and glycerol kinase of Escherichia coli K-12. J. Biol. Chem. (1992) 6122-6131
13. De Reuse H., and Danchin A. The ptsH, ptsI, and crr gnes of the Esherichia coli posphoenolpyruvate-dpendent posphotransferase system: a complex operon with several modes of transcription. J. Bacteriol. 170 (1988) 3827-3837
14. Dongling Z., Chrystala C., Jon L.H., and Stephen D.M. Identification of the CRP regulon using in vitro and in vivo transcriptional profiling. Nucleic. Acids Res. 32 (2004) 5874-5893
15. Evelyn Z., Johannes B., and Gottfried U. Fumarate regulation of gene expression in Escherichia coli by the DcuSR (dcuSR Genes) two-component regulatory system. J. Bacteriol. 180 (1998) 5421-5425
16. Gunsalus R.P., and Park S.J. Aerobic-anaerobic gene regulation in Escherichia coli: control by the ArcAB and Fnr regulons. Res. Microbial. 145 (1994) 437-450
17. Helen M.J., and Robert P.G. Regulation of Escherichia coli fumarate reductase (frdABCD) operon expression by respiratory electron acceptors and the fnr gene product. J. Bacteriol. 169 (1987) 3340-3349
18. Holtman C.K., Pawlyk A.C., Meadow N.D., and Pettigrew D.T. Reverse genetics of Escherichia coli glycerol kinase allosteric regulation and glucose control of glycerol utilization in vivo. J. Bacteriol. 183 (2001) 3336-3344
19. Iuchi S., Cole S.T., and Lin E.C.C. Multiple regulatory elements for the glpA Operon encoding anaerobic glycerol-3-phosphate eehydrogenase and the glpD operon encoding aerobic glycerol-3-phosphate dehydrogenase in Escherichia coli: further characterization of respiratory control. J. Bacteriol. 172 (1990) 179-184
20. Iuchi S., and Lin E.C.C. areA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways. Proc. Natl. Acad. Sci. 85 (1988) 1888-1892
21. Jean-Claude C.S., Didier N., Bgre S., Mane Scarabel S., Tom M., Ramseier H., Narendra B., Vartak Q., Jonathan R., Milton H., Saier Jr., and Alain J.C. In Vitro asymmetric binding of the pleiotropic regulatory protein, FruR, to the ace operator controlling glyoxylate shunt enzyme synthesis. J. Biol. Chem. 269 (1994) 14885-14891
22. Kaiser M., and Sawers G. Overlapping promoters modulate Fnr- and ArcA-dependent anaerobic transcriptional activation of the focA-pfl operon in Escherichia coli. Microbiology 143 (1997) 775-783
23. Klaus B.A., and Kaspar V.M. Are growth rates of Escherichia coli in batch cultures limited by respiration?. J. Bacteriol. 144 (1980) 114-123
24. Koshland Jr. D.E. Bacterial chemotaxis in relation to neurobiology. Ann. Rev. Neurosci. 3 (1980) 43-75
25. Kremling A.K., Bettenbrock B., Laube J.W.L., and Gilles E.D. The organization of metabolic reaction networks: application for diauxic growth on glucose and lactose. Metab. Eng. 3 (2001) 362-379
26. Lee S.G., Hwang S.K., and Kim C.M. Dynamic behavior of regulatory elements in the hierarchical regulatory network of various carbon sources-grown Escherichia coli. J. Microbiol. Biotechnol. 15 (2005) 551-559
27. Lee S.G., Kim C.M., and Hwang K.S. Development of a software tool for in silico simulation of Escherichia coli using a visual programming environment. J. Biotechnol. 119 (2005) 87-92
28. Levanon S.S., San K.Y., and Bennett G.N. Effect of oxygen on the Escherichia coli ArcA and FNR regulation systems and metabolic responses. Biotechnol. Bioeng. 89 (2005) 556-564
29. Liao J.C., and Oh M.K. Toward predicting metabolic fluxes in metabolically engineered strains. Metab. Eng. 3 (1999) 214-223
30. Lizhen G., Alden S., Bin P., and David C.L. Autoregulation of iclR, the gene encoding the repressor of the glyoxylate bypass operon. J. Bacteriol. 178 (1996) 321-324
31. Martinez-Antonio A., and Collado-Vides J. Identifying global regulators in transcriptional regulatory networks in bacteria. Curr. Opin. Microbiol. 6 (2003) 482-489
32. Maxime S., and Agnes U. The use of gene fusions to study polar effects in the gal operon of Escherichia coli. FEMS Microbiol. Lett. 8 (1980) 147-150
33. Mendoza L., and Alvarez-Buylla E.R. Dynamics of the genetic regulatory network for Arabidopsis thaliana flower morphogenesis. J. Theor. Biol. 193 (1998) 307-319
34. Oh M.K., and Liao J.C. Gene expression profiling by DNA microarrays and metabolic fluxes in Escherichia coli. Biotechnol. Prog. 16 (2000) 278-286
35. Oh M.K., Rohlin L., Kao K.C., and Liao J.C. Global expression profiling of acetate-grown Escherichia coli. J. Biol. Chem. 277 (2002) 13175-13183
36. Park S.J., Chao G., and Gunsalus R.P. Aerobic regulation of the sucABCD genes of Escherichia coli, which encode a-ketoglutarate dehydrogenase and succinyl coenzyme a synthetase: Roles of ArcA, Fnr, and the upstream sdhCDAB promoter. Curr. Opin. Microbiol. 179 (1997) 4138-4142
37. Paul G., David J.K., John R.G., and Simon C.A. Transcriptional regulation and organization of the dcuA and dcuB genes, encoding homologous anaerobic C4-Dicarboxylate transporters in Escherichia coli. J. Bacteriol. 180 (1998) 6586-6596
38. Peggy A.C., Stephen B.M., Jeffrey A.A., and Robert P.G. Aerobic regulation of cytochrome d oxidase(cydAB) operon expression in Escherichia coli: roles of FNR and ArcA in repression and activation. Mol. Microbiol. 25 (1997) 605-615
39. Plumbridge J. Regulation of gene expression in the PTS in Escherichia coli: the role and interactions of Mlc. Curr. Opin. Microbiol. 5 (2002) 187-193
40. Plumbridge J. Expression of the phosphotransferase system both mediates and is mediated by Mlc regulation in Escherichia coli. Mol. Microbiol. 33 (1999) 260-273
41. Reed J.L., and Palsson B.O. Thirteen years of building constraint-based in silico models of Escherichia coli. J. Bacteriol. 185 (2003) 2692-2699
42. Resendis-Antonio O., Freyre-Gonzalez J.A., Menchaca-Mendez R., Gutierrez-Rios R.M., Martinez-Antonio A., Avila-Sanchez C., and Collado-Vides J. Modular analysis of the transcriptional regulatory network of E. coli. Trends Genet. 21 (2005) 16-20
43. Schmidt K., Nielsen J., and Villadsen J. Quantitative analysis of metabolic fluxes in Escherichia coli, using two-dimensional NMR spectroscopy and complete isotopomer models. J. Biotechnol. 71 (1999) 175-189
44. Shanzhang Y., and Timothy J.L. Structures of the promoter and operator of the glpD gene encoding Aerobic sn-glycerol-3-phosphate dehydrogenase of Escherichia coli K-12. J. Bacteriol. 170 (1988) 4209-4215
45. Stanley R.M., and William D.N. Role of Gene fadR in Escherichia coli acetate metabolism. J. Bacteriol. 148 (1981) 83-90
46. Stanley R.M., and William D.N. Genetic regulation of the glyoxylate shunt in Escherichia coli K-12. J. Bacteriol. 149 (1982) 173-180
47. Steffen K., and Hans-Joachim S. Carbon source-dependent regulation of the acetyl-coenzyme A synthetase encoding gene ACS1 from Saccharomyces cerevisiae. Gene 161 (1995) 75-79
48. Stephanopoulos G.N., Aristidou A.A., and Nielsen J. Metabolic engineering: Principles and Methodologies (1998), Acadomic Press, London, UK pp. 147-202
49. Suman K., Christine M.B., Douglas F.B., and Stephen J. Regulation of acetyl coenzyme a synthetase in Escherichia coli. J. Bacteriol. 182 (2000) 4173-4179
50. Suzanne, J.D., Paul, G., Davood, O., Susan, A.B., Vikki, L.H., John, R.G., David, J.K., Simon, C.A., 1999. Inactivation and regulation of the aerobic c4-dicarboxylate transport (dctA) gene of Escherichia coli. c. 181, 5624-5635.
51. Tseng C.P., Albrecht J., and Gunsalus R.P. 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
52. Varma A., and Palsson O.B. 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
53. Varma A., and Palsson O.B. Parametric sensitivity of stoichiometric flux balance models applied to wild-type Escherichia coli metabolism. Biotechnol. Bioeng. 45 (1994) 69-79