Relation of Intracellular Signal Levels and Promoter Activities in the gal Regulon of Escherichia coli

Journal of Molecular Biology

Volumn 391, Issue 4, 2009, Pages 671-678

  Krishna, Sandeep ^a   Orosz, László ^b   Sneppen, Kim ^a   Adhya, Sankar ^c   Semsey, Szabolcs ^b  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b EÖTVÖS LORÁND UNIVERSITY   (Hungary)

^c NATIONAL CANCER INSTITUTE   (United States)

Author keywords

gal regulon,computational biology; regulatory network; signal integration; transcription

Indexed keywords

ARTICLE; BACTERIAL GENETICS; CONTROLLED STUDY; ESCHERICHIA COLI; GENE ACTIVITY; GENE REGULATORY NETWORK; GENETIC TRANSCRIPTION; IN VITRO STUDY; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; REGULON; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

ESCHERICHIA COLI;

EID: 68149166743     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.06.043     Document Type: Article

References (34)

1. Krishna S., Semsey S., and Sneppen K. Combinatorics of feedback in cellular uptake and metabolism of small molecules. Proc. Natl Acad. Sci. USA 104 (2007) 20815-20819
2. Monod J., Changeux J.P., and Jacob F. Allosteric proteins and cellular control systems. J. Mol. Biol. 6 (1963) 306-329
3. Chapon C. Role of the catabolite activator protein in the maltose regulon of Escherichia coli. J. Bacteriol. 150 (1982) 722-729
4. Dickson R.C., Abelson J., Barnes W.M., and Reznikoff W.S. Genetic regulation: the Lac control region. Science 187 (1975) 27-35
5. Schleif R. Regulation of the L-arabinose operon of Escherichia coli. Trends Genet. 16 (2000) 559-565
6. Weickert M.J., and Adhya S. The galactose regulon of Escherichia coli. Mol Microbiol 10 (1993) 245-251
7. Buchler N.E., Gerland U., and Hwa T. On schemes of combinatorial transcription logic. Proc. Natl Acad. Sci. USA 100 (2003) 5136-5141
8. Davidson E.H., Rast J.P., Oliveri P., Ransick A., Calestani C., Yuh C.H., et al. A genomic regulatory network for development. Science 295 (2002) 1669-1678
9. Pastan I., and Perlman R. Cyclic adenosine monophosphate in bacteria. Science 169 (1970) 339-344
10. Semsey S., Krishna S., Sneppen K., and Adhya S. Signal integration in the galactose network of Escherichia coli. Mol. Microbiol. 65 (2007) 465-476
11. Semsey S., Krishna S., Erdossy J., Horvath P., Orosz L., Sneppen K., and Adhya S. Dominant negative autoregulation limits steady-state repression levels in gene networks. J. Bacteriol. 191 (2009) 4487-4491
12. Mangan S., Itzkovitz S., Zaslaver A., and Alon U. The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. J. Mol. Biol. 356 (2006) 1073-1081
13. Covert M.W., Schilling C.H., Famili I., Edwards J.S., Goryanin I.I., Selkov E., and Palsson B.O. Metabolic modeling of microbial strains in silico. Trends Biochem. Sci. 26 (2001) 179-186
14. Gama-Castro S., Jimenez-Jacinto V., Peralta-Gil M., Santos-Zavaleta A., Penaloza-Spinola M.I., Contreras-Moreira B., et al. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res. 36 (2008) D120-D124
15. Ingram P.J., Stumpf M.P., and Stark J. Network motifs: structure does not determine function. BMC Genomics 7 (2006) 108
16. Knabe J.F., Nehaniv C.L., and Schilstra M.J. Do motifs reflect evolved function?-No convergent evolution of genetic regulatory network subgraph topologies. Biosystems 94 (2008) 68-74
17. Horecker B.L., Thomas J., and Monod J. Galactose transport in Escherichia coli. I. General properties as studied in a galactokinaseless mutant. J. Biol. Chem. 235 (1960) 1580-1585
18. Death A., and Ferenci T. Between feast and famine: endogenous inducer synthesis in the adaptation of Escherichia coli to growth with limiting carbohydrates. J. Bacteriol. 176 (1994) 5101-5107
19. Notley-McRobb L., Death A., and Ferenci T. The relationship between external glucose concentration and cAMP levels inside Escherichia coli: implications for models of phosphotransferase-mediated regulation of adenylate cyclase. Microbiology 143 (1997) 1909-1918
20. Buettner M.J., Spitz E., and Rickenberg H.V. Cyclic adenosine 3′,5′-monophosphate in Escherichia coli. J. Bacteriol. 114 (1973) 1068-1073
21. Peterkofsky A., and Gazdar C. Glucose inhibition of adenylate cyclase in intact cells of Escherichia coli B. Proc. Natl Acad. Sci. USA 71 (1974) 2324-2328
22. Kaplan S., Bren A., Dekel E., and Alon U. The incoherent feed-forward loop can generate non-monotonic input functions for genes. Mol. Syst. Biol. 4 (2008) 203
23. Kaplan S., Bren A., Zaslaver A., Dekel E., and Alon U. Diverse two-dimensional input functions control bacterial sugar genes. Mol. Cell 29 (2008) 786-792
24. Kuhlman T., Zhang Z., Saier Jr. M.H., and Hwa T. Combinatorial transcriptional control of the lactose operon of Escherichia coli. Proc. Natl Acad. Sci. USA 104 (2007) 6043-6048
25. Adhya S., and Echols H. Glucose effect and the galactose enzymes of Escherichia coli: correlation between glucose inhibition of induction and inducer transport. J. Bacteriol. 92 (1966) 601-608
26. Irani M., Orosz L., Busby S., Taniguchi T., and Adhya S. Cyclic AMP-dependent constitutive expression of gal operon: use of repressor titration to isolate operator mutations. Proc. Natl Acad. Sci. USA 80 (1983) 4775-4779
27. Semsey S., Geanacopoulos M., Lewis D.E., and Adhya S. Operator-bound GalR dimers close DNA loops by direct interaction: tetramerization and inducer binding. EMBO J. 21 (2002) 4349-4356
28. Aki T., Choy H.E., and Adhya S. Histone-like protein HU as a specific transcriptional regulator: co-factor role in repression of gal transcription by GAL repressor. Genes Cells 1 (1996) 179-188
29. Ryu S., Kim J., Adhya S., and Garges S. Pivotal role of amino acid at position 138 in the allosteric hinge reorientation of cAMP receptor protein. Proc. Natl Acad. Sci. USA 90 (1993) 75-79
30. Geanacopoulos M., and Adhya S. Functional characterization of roles of GalR and GalS as regulators of the gal regulon. J. Bacteriol. 179 (1997) 228-234
31. Choy H.E., and Adhya S. Control of gal transcription through DNA looping: inhibition of the initial transcribing complex. Proc. Natl Acad. Sci. USA 89 (1992) 11264-11268
32. Semsey S., Virnik K., and Adhya S. Three-stage regulation of the amphibolic gal operon: from repressosome to GalR-free DNA. J. Mol. Biol. 358 (2006) 355-363
33. Chatterjee S., Zhou Y.N., Roy S., and Adhya S. Interaction of Gal repressor with inducer and operator: induction of gal transcription from repressor-bound DNA. Proc. Natl Acad. Sci. USA 94 (1997) 2957-2962
34. Semsey S., Tolstorukov M.Y., Virnik K., Zhurkin V.B., and Adhya S. DNA trajectory in the Gal repressosome. Genes Dev. 18 (2004) 1898-1907