Regulatory network of Escherichia coli: Consistency between literature knowledge and microarray profiles

Genome Research

Volumn 13, Issue 11, 2003, Pages 2435-2443

  Gutiérrez Ríos, Rosa María ^a   Rosenblueth, David A ^c   Loza, José Antonio ^a   Huerta, Araceli M ^a   Glasner, Jeremy D ^b   Blattner, Fred R ^b   Collado Vides, Julio ^a  

^a INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

REGULATOR PROTEIN;

ANALYTIC METHOD; ANALYTICAL ERROR; ARTICLE; BACTERIAL CELL; CONTROLLED STUDY; CORRELATION ANALYSIS; DNA MICROARRAY; DNA MODIFICATION; ESCHERICHIA COLI; GENE CONTROL; GENE INTERACTION; GENETIC ANALYSIS; GENETIC DATABASE; GENETIC TRANSCRIPTION; GENOME ANALYSIS; INTERMETHOD COMPARISON; MEDICAL LITERATURE; METABOLITE; NONHUMAN; OPERON; PRIORITY JOURNAL; RANDOMIZATION; REDUNDANCY ANALYSIS; REGULONDB; STATISTICAL SIGNIFICANCE; THEORY; TRANSCRIPTION REGULATION;

DATABASES, GENETIC; ESCHERICHIA COLI; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OPERON; PREDICTIVE VALUE OF TESTS; REGULON; RESEARCH DESIGN;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0242407438     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1387003     Document Type: Article

References (40)

1. Aki, T. and Adhya, S. 1997. Repressor induced site-specific binding of HU for transcriptional regulation. EMBO J. 16: 3666-3674.
2. Brown, M.P., Grundy, W.N., Lin, D., Cristianini, N., Sugnet, C.W., Furey, T.S., Ares Jr., M., and Haussler, D. 2000. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc. Natl. Acad. Sci. 97: 262-267.
3. Browning, D.F., Cole, J.A., and Busby, S.J. 2000. Suppression of FNR-dependent transcription activation at the Escherichia coli nir promoter by Fis, IHF and H-NS: Modulation of transcription initiation by a complex nucleo-protein assembly. Mol. Microbiol. 37: 1258-1269.
4. Busby, S. and Ebright, R.H. 1997. Transcription activation at class II CAP-dependent promoters. Mol. Microbiol. 23: 853-859.
5. Cotter, P.A. and Gunsalus, R.P. 1992. 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: 31-36.
6. Covert, M.W., Schilling, C.H., Famili, I., Edwards, J.S., Goryanin, I.I., Selkov, E., and Palsson, B.C. 2001. Metabolic modeling of microbial strains in silico. Trends Biochem. Sci. 26: 179-186.
7. Darwin, A.J., Ziegelhoffer, E.C., Kiley, P.J., and Stewart, V. 1998. Fnr, NarP, and NarL regulation of Escherichia coli K-12 napF (periplasmic nitrate reductase) operon transcription in vitro. J. Bacteriol. 180: 4192-4198.
8. Dombrecht, B., Marchal, K., Vanderleyden, J., and Michiels, J. 2002. Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales. Genome Biol. 3: RESEARCH0076.
9. Eisen, M.B., Spellman, P.T., Brown, P.O., and Botstein, D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. 95: 14863-14868.
10. Goosen, N. and van de Putte, P. 1995. The regulation of transcription initiation by integration host factor. Mol. Microbiol. 16: 1-7.
11. Halfon, M.S., Grad, Y., Church, G.M., and Michelson, A.M. 2002. Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res. 12: 1019-1028.
12. Ishihama, A. 2000. Functional modulation of Escherichia coli RNA polymerase. Annu. Rev. Microbiol. 54: 499-518.
13. Jacobson, B.A. and Fuchs, J.A. 1998. Multiple cis-acting sites positively regulate Escherichia coli nrd expression. Mol. Microbiol. 28: 1315-1322.
14. Kauffman, S. 1974. The large scale structure and dynamics of gene control circuits: An ensemble approach. J. Theor. Biol. 44: 167-190.
15. Lamark, T., Rokenes, T.P., McDougall, J., and Strom, A.R. 1996. The complex bet promoters of Escherichia coli: Regulation by oxygen (ArcA), choline (BetI), and osmotic stress. J. Bacteriol. 178: 1655-1662.
16. Lawley, B. and Pittard, A.J. 1994. Regulation of aroL expression by TyrR protein and Trp repressor in Escherichia coli K-12. J. Bacteriol. 176: 6921-6930.
17. Lee, D.H., Huo, L., and Schleif, R. 1992. Repression of the araBAD promoter from araO1. J. Mol. Biol. 224: 335-341.
18. Lee, N.L., Gielow, W.O., and Wallace, R.G. 1981. Mechanism of araC autoregulation and the domains of two overlapping promoters, Pc and PBAD, in the L-arabinose regulatory region of Escherichia coli. Proc. Natl. Acad. Sci. 78: 752-756.
19. Lewis, M., Chang, G., Horton, N.C., Kercher, M.A., Pace, H.C., Schumacher, M.A., Brennan, R.G., and Lu, P. 1996. Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science 271: 1247-1254.
20. Maas, W.K. and Clark, A.J. 1964. Studies on the mechanism of repression of arginine biosynthesis in E. coli.II. Dominance of repressibility in diploids. J. Mol. Biol. 8: 365-370.
21. Martínez-Antonio, A. and Collado-Vides, J. 2003. Identifying global regulators in transcriptional regulatory networks in bacteria. Curr. Opin. Microbiol. 6: 1-8.
22. Matthews, K.S. 1996. The whole lactose repressor. Science 271: 1245-1246.
23. Neidhardt, F.C., Bloch, P.L., and Smith, D.F. 1974. Culture medium for enterobacteria. J. Bacteriol. 119: 736-747.
24. Neidhardt, F.S. and Savageau, M.A. 1996. Regulation beyond the operon. In Escherichia coli and Salmonella: Cellular and molecular biology, 2nd ed. (eds. F. Neidhardt et al.), vol. 2, pp. 1310-1324. ASM Press, Washington, DC.
25. Oh, M.K. and Liao, J.C. 2000. Gene expression profiling by DNA microarrays and metabolic fluxes in Escherichia coli. Biotechnol. Prog. 16: 278-286.
26. Oosawa, C. and Savageau, M.A. 2002. Effects of alternative connectivity on behavior of randomly constructed Boolean networks. Physica D: Nonlinear Phenomena 170: 143-161.
27. Palsson, S. 2001. The effects of deleterious mutations in cyclically parthenogenetic organisms. J. Theor. Biol. 208: 201-214.
28. Perez-Rueda, E. and Collado-Vides, J. 2000. The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res. 28: 1838-1847.
29. Pilpel, Y., Sudarsanam, P., and Church, G.M. 2001. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet. 29: 153-159.
30. Rasmussen, P.B., Holst, B., and Valentin-Hansen, P. 1996. Dual-function regulators: The cAMP receptor protein and the CytR regulator can act either to repress or to activate transtription depending on the context. Proc. Natl. Acad. Sci. 93: 10151-10155.
31. Ravasz, E., Somera, A.L., Mongru, D.A., Oltvai, Z.N., and Barabasi, A.L. 2002. Hierarchical organization of modularity in metabolic networks. Science 297: 1551-1555.
32. Richet, E., Vidal-Ingigliardi, D., and Raibaud, O. 1991. A new mechanism for coactivation of transcription initiation: Repositioning of an activator triggered by the binding of a second activator. Cell 66: 1185-1195.
33. Richmond, C.S., Glasner, J.D., Mau, R., Jin, H., and Blattner, F.R. 1999. Genome-wide expression profiling in Escherichia coli K-12. Nucleic Acids Res. 27: 3821-3835.
34. Salgado, H., Santos-Zavaleta, A., Gama-Castro, S., Millan-Zarate, D., Diaz-Peredo, E., Sanchez-Solano, F., Perez-Rueda, E., Bonavides-Martinez, C., and Collado-Vides, J. 2001. RegulonDB (version 3.2): Transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res. 29: 72-74.
35. Savageau, M.A. 1998. Rules for the evolution of gene circuits. Pac. Symp. Biocomput. 54-65.
36. Tao, H., Bausch, C., Richmond, C., Blattner, F.R., and Conway, T. 1999. Functional genomics: Expression analysis of Escherichia coli growing on minimal and rich media. J. Bacteriol. 181: 6425-6440.
37. Thieffry, D., Huerta, A.M., Perez-Rueda, E., and Collado-Vides, J. 1998. From specific gene regulation to genomic networks: A global analysis of transcriptional regulation in Escherichia coli. Bioessays 20: 433-440.
38. Thomas, R. and D'Ari, R. 1990. Biological Feedback. CRC Press, Boston, MA.
39. Wade, J.T., Belyaeva, T.A., Hyde, E.I., and Busby, S.J. 2001. A simple mechanism for co-dependence on two activators at an Escherichia coli promoter. EMBO J. 20: 7160-7167.
40. Wu, H., Tyson, K.L., Cole, J.A., and Busby, S.J. 1998. Regulation of transcription initiation at the Escherichia coli nir operon promoter: A new mechanism to account for co-dependence on two transcription factors. Mol. Microbiol. 27: 493-505.