Genome-wide analysis of the general stress response network in Escherichia coli: sigma(S)-dependent genes, promoters, and sigma factor selectivity

Weber H, Polen T, Heuveling J, Wendisch VF, Hengge R (2005)
Journal of Bacteriology 187(5): 1591-1603.

Journal Article | Published | English

No fulltext has been uploaded

Author
; ; ; ;
Abstract
The sigma(s) (or RpoS) subunit of RNA polymerase is the master regulator of the general stress response in Escherichia coli. While nearly absent in rapidly growing cells, us is strongly induced during entry into stationary phase and/or many other stress conditions and is essential for the expression of multiple stress resistances. Genome-wide expression profiling data presented here indicate that up to 10% of the E. coli genes are under direct or indirect control of us and that us should be considered a second vegetative sigma factor with a major impact not only on stress tolerance but on the entire cell physiology under nonoptimal growth conditions. This large data set allowed us to unequivocally identify a us consensus promoter in silico. Moreover, our results suggest that us-dependent genes represent a regulatory network with complex internal control (as exemplified by the acid resistance genes). This network also exhibits extensive regulatory overlaps with other global regulons (e.g., the cyclic AMP receptor protein regulon). In addition, the global regulatory protein Lrp was found to affect sigma(s) and/or sigma(70) selectivity of many promoters. These observations indicate that certain modules of the us-dependent general stress response can be temporarily recruited by stress-specific regulons, which are controlled by other stress-responsive regulators that act together with sigma(70) RNA polymerase. Thus, not only the expression of genes within a regulatory network but also the architecture of the network itself can be subject to regulation.
Publishing Year
PUB-ID

Cite this

Weber H, Polen T, Heuveling J, Wendisch VF, Hengge R. Genome-wide analysis of the general stress response network in Escherichia coli: sigma(S)-dependent genes, promoters, and sigma factor selectivity. Journal of Bacteriology. 2005;187(5):1591-1603.
Weber, H., Polen, T., Heuveling, J., Wendisch, V. F., & Hengge, R. (2005). Genome-wide analysis of the general stress response network in Escherichia coli: sigma(S)-dependent genes, promoters, and sigma factor selectivity. Journal of Bacteriology, 187(5), 1591-1603.
Weber, H., Polen, T., Heuveling, J., Wendisch, V. F., and Hengge, R. (2005). Genome-wide analysis of the general stress response network in Escherichia coli: sigma(S)-dependent genes, promoters, and sigma factor selectivity. Journal of Bacteriology 187, 1591-1603.
Weber, H., et al., 2005. Genome-wide analysis of the general stress response network in Escherichia coli: sigma(S)-dependent genes, promoters, and sigma factor selectivity. Journal of Bacteriology, 187(5), p 1591-1603.
H. Weber, et al., “Genome-wide analysis of the general stress response network in Escherichia coli: sigma(S)-dependent genes, promoters, and sigma factor selectivity”, Journal of Bacteriology, vol. 187, 2005, pp. 1591-1603.
Weber, H., Polen, T., Heuveling, J., Wendisch, V.F., Hengge, R.: Genome-wide analysis of the general stress response network in Escherichia coli: sigma(S)-dependent genes, promoters, and sigma factor selectivity. Journal of Bacteriology. 187, 1591-1603 (2005).
Weber, H., Polen, T., Heuveling, J., Wendisch, Volker F., and Hengge, R. “Genome-wide analysis of the general stress response network in Escherichia coli: sigma(S)-dependent genes, promoters, and sigma factor selectivity”. Journal of Bacteriology 187.5 (2005): 1591-1603.
This data publication is cited in the following publications:
This publication cites the following data publications:

315 Citations in Europe PMC

Data provided by Europe PubMed Central.

First-Step Mutations during Adaptation Restore the Expression of Hundreds of Genes.
Rodriguez-Verdugo A, Tenaillon O, Gaut BS., Mol. Biol. Evol. 33(1), 2016
PMID: 26500250
Survival guide: Escherichia coli in the stationary phase.
Pletnev P, Osterman I, Sergiev P, Bogdanov A, Dontsova O., Acta Naturae 7(4), 2015
PMID: 26798489
Adaptation to sustained nitrogen starvation by Escherichia coli requires the eukaryote-like serine/threonine kinase YeaG.
Figueira R, Brown DR, Ferreira D, Eldridge MJ, Burchell L, Pan Z, Helaine S, Wigneshweraraj S., Sci Rep 5(), 2015
PMID: 26621053
Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella.
Papenfort K, Espinosa E, Casadesus J, Vogel J., Proc. Natl. Acad. Sci. U.S.A. 112(34), 2015
PMID: 26307765
Contribution of RpoS to metabolic efficiency and ectoines synthesis during the osmo- and heat-stress response in the halophilic bacterium Chromohalobacter salexigens.
Salvador M, Argandona M, Pastor JM, Bernal V, Canovas M, Csonka LN, Nieto JJ, Vargas C., Environ Microbiol Rep 7(2), 2015
PMID: 25417903
Concurrent conditional clustering of multiple networks: COCONETS.
Kleessen S, Klie S, Nikoloski Z., PLoS ONE 9(8), 2014
PMID: 25105292
Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters.
Goncalves GA, Oliveira PH, Gomes AG, Prather KL, Lewis LA, Prazeres DM, Monteiro GA., Appl. Microbiol. Biotechnol. 98(15), 2014
PMID: 24769900
Stress-Induced Mutagenesis.
Williams AB, Foster PL., EcoSal Plus 5(1), 2012
PMID: 26442828
An alkyltransferase-like protein from Thermus thermophilus HB8 affects the regulation of gene expression in alkylation response.
Morita R, Hishinuma H, Ohyama H, Mega R, Ohta T, Nakagawa N, Agari Y, Fukui K, Shinkai A, Kuramitsu S, Masui R., J. Biochem. 150(3), 2011
PMID: 21531768

71 References

Data provided by Europe PubMed Central.

Network motifs: simple building blocks of complex networks.
Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U., Science 298(5594), 2002
PMID: 12399590
GadY, a small-RNA regulator of acid response genes in Escherichia coli.
Opdyke JA, Kang JG, Storz G., J. Bacteriol. 186(20), 2004
PMID: 15466020
DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate.
Polen T, Rittmann D, Wendisch VF, Sahm H., Appl. Environ. Microbiol. 69(3), 2003
PMID: 12620868
Rapid confirmation of single copy lambda prophage integration by PCR.
Powell BS, Rivas MP, Court DL, Nakamura Y, Turnbough CL Jr., Nucleic Acids Res. 22(25), 1994
PMID: 7838735
Acid resistance in Escherichia coli.
Richard HT, Foster JW., Adv. Appl. Microbiol. 52(), 2003
PMID: 12964244

AUTHOR UNKNOWN, 1989
The Pseudomonas aeruginosa RpoS regulon and its relationship to quorum sensing.
Schuster M, Hawkins AC, Harwood CS, Greenberg EP., Mol. Microbiol. 51(4), 2004
PMID: 14763974
GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins.
Serres MH, Goswami S, Riley M., Nucleic Acids Res. 32(Database issue), 2004
PMID: 14681418

AUTHOR UNKNOWN, 1984
Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis.
Tani TH, Khodursky A, Blumenthal RM, Brown PO, Matthews RG., Proc. Natl. Acad. Sci. U.S.A. 99(21), 2002
PMID: 12374860
Genes of the GadX-GadW regulon in Escherichia coli.
Tucker DL, Tucker N, Ma Z, Foster JW, Miranda RL, Cohen PS, Conway T., J. Bacteriol. 185(10), 2003
PMID: 12730179
DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide.
Zheng M, Wang X, Templeton LJ, Smulski DR, LaRossa RA, Storz G., J. Bacteriol. 183(15), 2001
PMID: 11443091
Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation.
Zimmer DP, Soupene E, Lee HL, Wendisch VF, Khodursky AB, Peter BJ, Bender RA, Kustu S., Proc. Natl. Acad. Sci. U.S.A. 97(26), 2000
PMID: 11121068

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 15716429
PubMed | Europe PMC

Search this title in

Google Scholar