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.

Zeitschriftenaufsatz | Veröffentlicht| Englisch
 
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Autor*in
Weber, H.; Polen, T.; Heuveling, J.; Wendisch, Volker F.UniBi ; Hengge, R.
Abstract / Bemerkung
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.
Stichworte
gade yhie; inducible gene; receptor protein; signal-transduction; molecular analysis; protein h-ns; rpos rna-polymerase; dependent acid resistance; stationary-phase; regulatory protein
Erscheinungsjahr
2005
Zeitschriftentitel
Journal of Bacteriology
Band
187
Ausgabe
5
Seite(n)
1591-1603
ISSN
ARRAY(0x9b1fd20)
Page URI
https://pub.uni-bielefeld.de/record/1895332

Zitieren

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. doi:10.1128/Jb.1875.5.1591-1603.2005
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.

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Espina L, Gelaw TK, de Lamo-Castellví S, Pagán R, García-Gonzalo D., PLoS One 8(2), 2013
PMID: 23424676
Rate of environmental change determines stress response specificity.
Young JW, Locke JC, Elowitz MB., Proc Natl Acad Sci U S A 110(10), 2013
PMID: 23407164
Putrescine catabolism is a metabolic response to several stresses in Escherichia coli.
Schneider BL, Hernandez VJ, Reitzer L., Mol Microbiol 88(3), 2013
PMID: 23531166
Sulfur-34S stable isotope labeling of amino acids for quantification (SULAQ34) of proteomic changes in Pseudomonas fluorescens during naphthalene degradation.
Herbst FA, Taubert M, Jehmlich N, Behr T, Schmidt F, von Bergen M, Seifert J., Mol Cell Proteomics 12(8), 2013
PMID: 23603340
A comparative proteomic analysis of Vibrio cholerae O1 wild-type cells versus a phoB mutant showed that the PhoB/PhoR system is required for full growth and rpoS expression under inorganic phosphate abundance.
Lery LM, Goulart CL, Figueiredo FR, Verdoorn KS, Einicker-Lamas M, Gomes FM, Machado EA, Bisch PM, von Kruger WM., J Proteomics 86(), 2013
PMID: 23665147
Expression dynamics of RpoS/Crl-dependent genes in Escherichia coli.
Dudin O, Lacour S, Geiselmann J., Res Microbiol 164(8), 2013
PMID: 23867204
An RpoS-dependent sRNA regulates the expression of a chaperone involved in protein folding.
Silva IJ, Ortega AD, Viegas SC, García-Del Portillo F, Arraiano CM., RNA 19(9), 2013
PMID: 23893734
Synthetic tolerance: three noncoding small RNAs, DsrA, ArcZ and RprA, acting supra-additively against acid stress.
Gaida SM, Al-Hinai MA, Indurthi DC, Nicolaou SA, Papoutsakis ET., Nucleic Acids Res 41(18), 2013
PMID: 23892399
Dissecting the assays to assess microbial tolerance to toxic chemicals in bioprocessing.
Zingaro KA, Nicolaou SA, Papoutsakis ET., Trends Biotechnol 31(11), 2013
PMID: 24094862
A small RNA activates CFA synthase by isoform-specific mRNA stabilization.
Fröhlich KS, Papenfort K, Fekete A, Vogel J., EMBO J 32(22), 2013
PMID: 24141880
Engineering dynamic pathway regulation using stress-response promoters.
Dahl RH, Zhang F, Alonso-Gutierrez J, Baidoo E, Batth TS, Redding-Johanson AM, Petzold CJ, Mukhopadhyay A, Lee TS, Adams PD, Keasling JD., Nat Biotechnol 31(11), 2013
PMID: 24142050
DNA, cell wall and general oxidative damage underlie the tellurite/cefotaxime synergistic effect in Escherichia coli.
Molina-Quiroz RC, Loyola DE, Muñoz-Villagrán CM, Quatrini R, Vásquez CC, Pérez-Donoso JM., PLoS One 8(11), 2013
PMID: 24260236
The expression of stlA in Photorhabdus luminescens is controlled by nutrient limitation.
Lango-Scholey L, Brachmann AO, Bode HB, Clarke DJ., PLoS One 8(11), 2013
PMID: 24278476
Lrp of Corynebacterium glutamicum controls expression of the brnFE operon encoding the export system for L-methionine and branched-chain amino acids.
Lange C, Mustafi N, Frunzke J, Kennerknecht N, Wessel M, Bott M, Wendisch VF., J Biotechnol 158(4), 2012
PMID: 21683740
Distinct transcriptional profiles and phenotypes exhibited by Escherichia coli O157:H7 isolates related to the 2006 spinach-associated outbreak.
Parker CT, Kyle JL, Huynh S, Carter MQ, Brandl MT, Mandrell RE., Appl Environ Microbiol 78(2), 2012
PMID: 22081562
Role of general stress-response alternative sigma factors σ(S) (RpoS) and σ(B) (SigB) in bacterial heat resistance as a function of treatment medium pH.
Ait-Ouazzou A, Mañas P, Condón S, Pagán R, García-Gonzalo D., Int J Food Microbiol 153(3), 2012
PMID: 22177853
A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD.
Fröhlich KS, Papenfort K, Berger AA, Vogel J., Nucleic Acids Res 40(8), 2012
PMID: 22180532
Random mutagenesis of global transcription factor cAMP receptor protein for improved osmotolerance.
Zhang H, Chong H, Ching CB, Jiang R., Biotechnol Bioeng 109(5), 2012
PMID: 22179860
Bacterial persistence increases as environmental fitness decreases.
Hong SH, Wang X, O'Connor HF, Benedik MJ, Wood TK., Microb Biotechnol 5(4), 2012
PMID: 22221537
Evolutionary insight from whole-genome sequencing of experimentally evolved microbes.
Dettman JR, Rodrigue N, Melnyk AH, Wong A, Bailey SF, Kassen R., Mol Ecol 21(9), 2012
PMID: 22332770
Understanding physiological responses to pre-treatment inhibitors in ethanologenic fermentations.
Taylor MP, Mulako I, Tuffin M, Cowan D., Biotechnol J 7(9), 2012
PMID: 22331581
A third mode of surface-associated growth: immobilization of Salmonella enterica serovar Typhimurium modulates the RpoS-directed transcriptional programme.
Knudsen GM, Nielsen MB, Grassby T, Danino-Appleton V, Thomsen LE, Colquhoun IJ, Brocklehurst TF, Olsen JE, Hinton JC., Environ Microbiol 14(8), 2012
PMID: 22356617
Targeting of csgD by the small regulatory RNA RprA links stationary phase, biofilm formation and cell envelope stress in Escherichia coli.
Mika F, Busse S, Possling A, Berkholz J, Tschowri N, Sommerfeldt N, Pruteanu M, Hengge R., Mol Microbiol 84(1), 2012
PMID: 22356413
Comparison of the transient responses of Escherichia coli to a glucose pulse of various intensities.
Sunya S, Delvigne F, Uribelarrea JL, Molina-Jouve C, Gorret N., Appl Microbiol Biotechnol 95(4), 2012
PMID: 22370947
RpoS proteolysis is controlled directly by ATP levels in Escherichia coli.
Peterson CN, Levchenko I, Rabinowitz JD, Baker TA, Silhavy TJ., Genes Dev 26(6), 2012
PMID: 22426532
RpoS regulates a novel type of plasmid DNA transfer in Escherichia coli.
Zhang Y, Shi C, Yu J, Ren J, Sun D., PLoS One 7(3), 2012
PMID: 22438941
Polymorphisms in rpoS and stress tolerance heterogeneity in natural isolates of Cronobacter sakazakii.
Alvarez-Ordóñez A, Begley M, Hill C., Appl Environ Microbiol 78(11), 2012
PMID: 22447602
Staying alive: metabolic adaptations to quiescence.
Valcourt JR, Lemons JM, Haley EM, Kojima M, Demuren OO, Coller HA., Cell Cycle 11(9), 2012
PMID: 22510571
Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus.
Khudyakov JI, D'haeseleer P, Borglin SE, Deangelis KM, Woo H, Lindquist EA, Hazen TC, Simmons BA, Thelen MP., Proc Natl Acad Sci U S A 109(32), 2012
PMID: 22586090
Multi-copy genes that enhance the yield of mammalian G protein-coupled receptors in Escherichia coli.
Skretas G, Makino T, Varadarajan N, Pogson M, Georgiou G., Metab Eng 14(5), 2012
PMID: 22609824
Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription.
Kahramanoglou C, Prieto AI, Khedkar S, Haase B, Gupta A, Benes V, Fraser GM, Luscombe NM, Seshasayee AS., Nat Commun 3(), 2012
PMID: 22673913
Resistance to environmental stress requires the RNA chaperones CspC and CspE.
Shenhar Y, Biran D, Ron EZ., Environ Microbiol Rep 4(5), 2012
PMID: 23760898
Characterization of three novel mechanosensitive channel activities in Escherichia coli.
Edwards MD, Black S, Rasmussen T, Rasmussen A, Stokes NR, Stephen TL, Miller S, Booth IR., Channels (Austin) 6(4), 2012
PMID: 22874652
Convergence of the transcriptional responses to heat shock and singlet oxygen stresses.
Dufour YS, Imam S, Koo BM, Green HA, Donohue TJ., PLoS Genet 8(9), 2012
PMID: 23028346
Role of rpoS in Escherichia coli O157:H7 strain H32 biofilm development and survival.
Sheldon JR, Yim MS, Saliba JH, Chung WH, Wong KY, Leung KT., Appl Environ Microbiol 78(23), 2012
PMID: 23001657
Biofilm modifies expression of ribonucleotide reductase genes in Escherichia coli.
Cendra Mdel M, Juárez A, Torrents E., PLoS One 7(9), 2012
PMID: 23050019
Stress-Induced Mutagenesis.
Williams AB, Foster PL., EcoSal Plus 5(1), 2012
PMID: 26442828
Genetic circuit performance under conditions relevant for industrial bioreactors.
Moser F, Broers NJ, Hartmans S, Tamsir A, Kerkman R, Roubos JA, Bovenberg R, Voigt CA., ACS Synth Biol 1(11), 2012
PMID: 23656232
Genome-wide analysis of the Pho regulon in a pstCA mutant of Citrobacter rodentium.
Cheng C, Wakefield MJ, Yang J, Tauschek M, Robins-Browne RM., PLoS One 7(11), 2012
PMID: 23226353
Discretely calibrated regulatory loops controlled by ppGpp partition gene induction across the 'feast to famine' gradient in Escherichia coli.
Traxler MF, Zacharia VM, Marquardt S, Summers SM, Nguyen HT, Stark SE, Conway T., Mol Microbiol 79(4), 2011
PMID: 21299642
The RpoS-mediated general stress response in Escherichia coli.
Battesti A, Majdalani N, Gottesman S., Annu Rev Microbiol 65(), 2011
PMID: 21639793
A comparative genome analysis of the RpoS sigmulon shows a high diversity of responses and origins.
Santos-Zavaleta A, Gama-Castro S, Pérez-Rueda E., Microbiology 157(pt 5), 2011
PMID: 21310789
Stress response regulators identified through genome-wide transcriptome analysis of the (p)ppGpp-dependent response in Rhizobium etli.
Vercruysse M, Fauvart M, Jans A, Beullens S, Braeken K, Cloots L, Engelen K, Marchal K, Michiels J., Genome Biol 12(2), 2011
PMID: 21324192
Prolonged cold stress response of Escherichia coli O157 and the role of rpoS.
Vidovic S, Mangalappalli-Illathu AK, Korber DR., Int J Food Microbiol 146(2), 2011
PMID: 21402428
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
How sulphate-reducing microorganisms cope with stress: lessons from systems biology.
Zhou J, He Q, Hemme CL, Mukhopadhyay A, Hillesland K, Zhou A, He Z, Van Nostrand JD, Hazen TC, Stahl DA, Wall JD, Arkin AP., Nat Rev Microbiol 9(6), 2011
PMID: 21572460
A systems biology approach sheds new light on Escherichia coli acid resistance.
Stincone A, Daudi N, Rahman AS, Antczak P, Henderson I, Cole J, Johnson MD, Lund P, Falciani F., Nucleic Acids Res 39(17), 2011
PMID: 21690099
Microbial laboratory evolution in the era of genome-scale science.
Conrad TM, Lewis NE, Palsson BØ., Mol Syst Biol 7(), 2011
PMID: 21734648
Structural coupling between RNA polymerase composition and DNA supercoiling in coordinating transcription: a global role for the omega subunit?
Geertz M, Travers A, Mehandziska S, Sobetzko P, Chandra-Janga S, Shimamoto N, Muskhelishvili G., MBio 2(4), 2011
PMID: 21810966
Antibacterial mechanism of action of arylamide foldamers.
Mensa B, Kim YH, Choi S, Scott R, Caputo GA, DeGrado WF., Antimicrob Agents Chemother 55(11), 2011
PMID: 21844313
Intergenic sequence comparison of Escherichia coli isolates reveals lifestyle adaptations but not host specificity.
White AP, Sibley KA, Sibley CD, Wasmuth JD, Schaefer R, Surette MG, Edge TA, Neumann NF., Appl Environ Microbiol 77(21), 2011
PMID: 21908635
Phenotypic diversity caused by differential RpoS activity among environmental Escherichia coli isolates.
Chiang SM, Dong T, Edge TA, Schellhorn HE., Appl Environ Microbiol 77(22), 2011
PMID: 21948830
The uncertain consequences of transferring bacterial strains between laboratories - rpoS instability as an example.
Spira B, de Almeida Toledo R, Maharjan RP, Ferenci T., BMC Microbiol 11(), 2011
PMID: 22067413
Inactivation of Escherichia coli by citral.
Somolinos M, García D, Condón S, Mackey B, Pagán R., J Appl Microbiol 108(6), 2010
PMID: 19891710
Differential expression of virulence and stress fitness genes between Escherichia coli O157:H7 strains with clinical or bovine-biased genotypes.
Vanaja SK, Springman AC, Besser TE, Whittam TS, Manning SD., Appl Environ Microbiol 76(1), 2010
PMID: 19880650
Identification of stress-related proteins in Escherichia coli using the pollutant cis-dichloroethylene.
Lee J, Hiibel SR, Reardon KF, Wood TK., J Appl Microbiol 108(6), 2010
PMID: 19919618
Role of RpoS in virulence of pathogens.
Dong T, Schellhorn HE., Infect Immun 78(3), 2010
PMID: 19948835
Adaptation of enteropathogenic Yersinia to low growth temperature.
Palonen E, Lindström M, Korkeala H., Crit Rev Microbiol 36(1), 2010
PMID: 20088683
Delineation of a bacterial starvation stress response network which can mediate antibiotic tolerance development.
Fung DK, Chan EW, Chin ML, Chan RC., Antimicrob Agents Chemother 54(3), 2010
PMID: 20086164
Stationary phase in gram-negative bacteria.
Navarro Llorens JM, Tormo A, Martínez-García E., FEMS Microbiol Rev 34(4), 2010
PMID: 20236330
Involvement of sigmaS accumulation in repression of the flhDC operon in acidic phospholipid-deficient mutants of Escherichia coli.
Uchiyama J, Nobue Y, Zhao H, Matsuzaki H, Nagahama H, Matsuoka S, Matsumoto K, Hara H., Microbiology 156(pt 6), 2010
PMID: 20185506
Dealing with oxidative stress and iron starvation in microorganisms: an overview.
Benjamin JA, Desnoyers G, Morissette A, Salvail H, Massé E., Can J Physiol Pharmacol 88(3), 2010
PMID: 20393591
Metabolomic and transcriptomic stress response of Escherichia coli.
Jozefczuk S, Klie S, Catchpole G, Szymanski J, Cuadros-Inostroza A, Steinhauser D, Selbig J, Willmitzer L., Mol Syst Biol 6(), 2010
PMID: 20461071
Let's stop overlooking bacterial aging.
Książek K, Książek K., Biogerontology 11(6), 2010
PMID: 20440559
Novel aspects of the acid response network of E. coli K-12 are revealed by a study of transcriptional dynamics.
Burton NA, Johnson MD, Antczak P, Robinson A, Lund PA., J Mol Biol 401(5), 2010
PMID: 20603130
Divergence involving global regulatory gene mutations in an Escherichia coli population evolving under phosphate limitation.
Wang L, Spira B, Zhou Z, Feng L, Maharjan RP, Li X, Li F, McKenzie C, Reeves PR, Ferenci T., Genome Biol Evol 2(), 2010
PMID: 20639316
A global metabolic shift is linked to Salmonella multicellular development.
White AP, Weljie AM, Apel D, Zhang P, Shaykhutdinov R, Vogel HJ, Surette MG., PLoS One 5(7), 2010
PMID: 20676398
Crl binds to domain 2 of σ(S) and confers a competitive advantage on a natural rpoS mutant of Salmonella enterica serovar Typhi.
Monteil V, Kolb A, Mayer C, Hoos S, England P, Norel F., J Bacteriol 192(24), 2010
PMID: 20935100
Regulation of glycogen metabolism in yeast and bacteria.
Wilson WA, Roach PJ, Montero M, Baroja-Fernández E, Muñoz FJ, Eydallin G, Viale AM, Pozueta-Romero J., FEMS Microbiol Rev 34(6), 2010
PMID: 20412306
Control of RpoS in global gene expression of Escherichia coli in minimal media.
Dong T, Schellhorn HE., Mol Genet Genomics 281(1), 2009
PMID: 18843507
Death and cannibalism in a seasonal environment facilitate bacterial coexistence.
Rozen DE, Philippe N, Arjan de Visser J, Lenski RE, Schneider D., Ecol Lett 12(1), 2009
PMID: 19019196
Role of RpoS in the virulence of Citrobacter rodentium.
Dong T, Coombes BK, Schellhorn HE., Infect Immun 77(1), 2009
PMID: 18981255
Characterization of the Escherichia coli O157:H7 Sakai GadE regulon.
Kailasan Vanaja S, Bergholz TM, Whittam TS., J Bacteriol 191(6), 2009
PMID: 19114477
Regulation by transcription factors in bacteria: beyond description.
Balleza E, López-Bojorquez LN, Martínez-Antonio A, Resendis-Antonio O, Lozada-Chávez I, Balderas-Martínez YI, Encarnación S, Collado-Vides J., FEMS Microbiol Rev 33(1), 2009
PMID: 19076632
IrrE, a global regulator of extreme radiation resistance in Deinococcus radiodurans, enhances salt tolerance in Escherichia coli and Brassica napus.
Pan J, Wang J, Zhou Z, Yan Y, Zhang W, Lu W, Ping S, Dai Q, Yuan M, Feng B, Hou X, Zhang Y, Ma R, Liu T, Feng L, Wang L, Chen M, Lin M., PLoS One 4(2), 2009
PMID: 19204796
SigmaS controls multiple pathways associated with intracellular multiplication of Legionella pneumophila.
Hovel-Miner G, Pampou S, Faucher SP, Clarke M, Morozova I, Morozov P, Russo JJ, Shuman HA, Kalachikov S., J Bacteriol 191(8), 2009
PMID: 19218380
Borrelia burgdorferi bba74 is expressed exclusively during tick feeding and is regulated by both arthropod- and mammalian host-specific signals.
Mulay VB, Caimano MJ, Iyer R, Dunham-Ems S, Liveris D, Petzke MM, Schwartz I, Radolf JD., J Bacteriol 191(8), 2009
PMID: 19218390
Regulation of c-di-GMP metabolism in biofilms.
Jonas K, Melefors O, Römling U., Future Microbiol 4(3), 2009
PMID: 19327118
Gene expression patterns and differential input into curli fimbriae regulation of all GGDEF/EAL domain proteins in Escherichia coli.
Sommerfeldt N, Possling A, Becker G, Pesavento C, Tschowri N, Hengge R., Microbiology 155(pt 4), 2009
PMID: 19332833
Gene expression induced in Escherichia coli O157:H7 upon exposure to model apple juice.
Bergholz TM, Vanaja SK, Whittam TS., Appl Environ Microbiol 75(11), 2009
PMID: 19346340
Interplay of cellular cAMP levels, {sigma}S activity and oxidative stress resistance in Escherichia coli.
Barth E, Gora KV, Gebendorfer KM, Settele F, Jakob U, Winter J., Microbiology 155(pt 5), 2009
PMID: 19372151
Increased antibiotic resistance of Escherichia coli in mature biofilms.
Ito A, Taniuchi A, May T, Kawata K, Okabe S., Appl Environ Microbiol 75(12), 2009
PMID: 19376922
Polymorphism and selection of rpoS in pathogenic Escherichia coli.
Dong T, Chiang SM, Joyce C, Yu R, Schellhorn HE., BMC Microbiol 9(), 2009
PMID: 19493358
Localized expression profiles of rpoS in Escherichia coli biofilms.
Ito A, May T, Taniuchi A, Kawata K, Okabe S., Biotechnol Bioeng 103(5), 2009
PMID: 19288441
Adapting the machine: adaptor proteins for Hsp100/Clp and AAA+ proteases.
Kirstein J, Molière N, Dougan DA, Turgay K., Nat Rev Microbiol 7(8), 2009
PMID: 19609260
Furfural inhibits growth by limiting sulfur assimilation in ethanologenic Escherichia coli strain LY180.
Miller EN, Jarboe LR, Turner PC, Pharkya P, Yomano LP, York SW, Nunn D, Shanmugam KT, Ingram LO., Appl Environ Microbiol 75(19), 2009
PMID: 19684179
Elevated levels of sigma S inhibit biofilm formation in Escherichia coli: a role for the Rcs phosphorelay.
Ferrières L, Thompson A, Clarke DJ., Microbiology 155(pt 11), 2009
PMID: 19696107
Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA.
Papenfort K, Said N, Welsink T, Lucchini S, Hinton JCD, Vogel J., Mol Microbiol 74(1), 2009
PMID: 19732340
The NlpD lipoprotein is a novel Yersinia pestis virulence factor essential for the development of plague.
Tidhar A, Flashner Y, Cohen S, Levi Y, Zauberman A, Gur D, Aftalion M, Elhanany E, Zvi A, Shafferman A, Mamroud E., PLoS One 4(9), 2009
PMID: 19759820
The response regulator SprE (RssB) modulates polyadenylation and mRNA stability in Escherichia coli.
Carabetta VJ, Mohanty BK, Kushner SR, Silhavy TJ., J Bacteriol 191(22), 2009
PMID: 19767441
Regulation and quality control by Lon-dependent proteolysis.
Van Melderen L, Aertsen A., Res Microbiol 160(9), 2009
PMID: 19772918
Compensatory evolution of gene regulation in response to stress by Escherichia coli lacking RpoS.
Stoebel DM, Hokamp K, Last MS, Dorman CJ., PLoS Genet 5(10), 2009
PMID: 19798444
Growth phase and (p)ppGpp control of IraD, a regulator of RpoS stability, in Escherichia coli.
Merrikh H, Ferrazzoli AE, Lovett ST., J Bacteriol 191(24), 2009
PMID: 19820090
Transcription analysis of central metabolism genes in Escherichia coli. Possible roles of sigma38 in their expression, as a response to carbon limitation.
Olvera L, Mendoza-Vargas A, Flores N, Olvera M, Sigala JC, Gosset G, Morett E, Bolívar F., PLoS One 4(10), 2009
PMID: 19838295
New insights into the role of sigma factor RpoS as revealed in escherichia coli strains lacking the phosphoenolpyruvate:carbohydrate phosphotransferase system.
Flores N, Escalante A, de Anda R, Báez-Viveros JL, Merino E, Franco B, Georgellis D, Gosset G, Bolívar F., J Mol Microbiol Biotechnol 14(4), 2008
PMID: 17938565
Induction of the yjbEFGH operon is regulated by growth rate and oxygen concentration.
Ionescu M, Franchini A, Egli T, Belkin S., Arch Microbiol 189(3), 2008
PMID: 17957352
PhyR is involved in the general stress response of Methylobacterium extorquens AM1.
Gourion B, Francez-Charlot A, Vorholt JA., J Bacteriol 190(3), 2008
PMID: 18024517
Mutations in two global regulators lower individual mortality in Escherichia coli.
Fontaine F, Stewart EJ, Lindner AB, Taddei F., Mol Microbiol 67(1), 2008
PMID: 18036141
RpoS regulation of gene expression during exponential growth of Escherichia coli K12.
Dong T, Kirchhof MG, Schellhorn HE., Mol Genet Genomics 279(3), 2008
PMID: 18158608
Cloning, expression, purification and characterization of the stress kinase YeaG from Escherichia coli.
Tagourti J, Landoulsi A, Richarme G., Protein Expr Purif 59(1), 2008
PMID: 18276156
Signal integration by the two-component signal transduction response regulator CpxR.
Wolfe AJ, Parikh N, Lima BP, Zemaitaitis B., J Bacteriol 190(7), 2008
PMID: 18223085
The phosphate regulon and bacterial virulence: a regulatory network connecting phosphate homeostasis and pathogenesis.
Lamarche MG, Wanner BL, Crépin S, Harel J., FEMS Microbiol Rev 32(3), 2008
PMID: 18248418
Regulation of whole bacterial pathogen transcription within infected hosts.
La MV, Raoult D, Renesto P., FEMS Microbiol Rev 32(3), 2008
PMID: 18266740
Temporal transcriptomic microarray analysis of "Dehalococcoides ethenogenes" strain 195 during the transition into stationary phase.
Johnson DR, Brodie EL, Hubbard AE, Andersen GL, Zinder SH, Alvarez-Cohen L., Appl Environ Microbiol 74(9), 2008
PMID: 18310438
Regulation of transcription by acetate in Escherichia coli: in vivo and in vitro comparisons.
Rosenthal AZ, Kim Y, Gralla JD., Mol Microbiol 68(4), 2008
PMID: 18331469
Significance of rpoS during maturation of Escherichia coli biofilms.
Ito A, May T, Kawata K, Okabe S., Biotechnol Bioeng 99(6), 2008
PMID: 17979199
Cell division in Escherichia coli cultures monitored at single cell resolution.
Roostalu J, Jõers A, Luidalepp H, Kaldalu N, Tenson T., BMC Microbiol 8(), 2008
PMID: 18430255
Construction of a stress-induced system in Escherichia coli for efficient polyhydroxyalkanoates production.
Kang Z, Wang Q, Zhang H, Qi Q., Appl Microbiol Biotechnol 79(2), 2008
PMID: 18347791
Role of the global transcriptional regulator PrrA in Rhodobacter sphaeroides 2.4.1: combined transcriptome and proteome analysis.
Eraso JM, Roh JH, Zeng X, Callister SJ, Lipton MS, Kaplan S., J Bacteriol 190(14), 2008
PMID: 18487335
A role for Lon protease in the control of the acid resistance genes of Escherichia coli.
Heuveling J, Possling A, Hengge R., Mol Microbiol 69(2), 2008
PMID: 18630346
Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli.
Pesavento C, Becker G, Sommerfeldt N, Possling A, Tschowri N, Mehlis A, Hengge R., Genes Dev 22(17), 2008
PMID: 18765794
Regulation of the Salmonella enterica std fimbrial operon by DNA adenine methylation, SeqA, and HdfR.
Jakomin M, Chessa D, Bäumler AJ, Casadesús J., J Bacteriol 190(22), 2008
PMID: 18805972
Global transcription and metabolic flux analysis of Escherichia coli in glucose-limited fed-batch cultivations.
Lemuth K, Hardiman T, Winter S, Pfeiffer D, Keller MA, Lange S, Reuss M, Schmid RD, Siemann-Herzberg M., Appl Environ Microbiol 74(22), 2008
PMID: 18806003
Binding of the unorthodox transcription activator, Crl, to the components of the transcription machinery.
England P, Westblade LF, Karimova G, Robbe-Saule V, Norel F, Kolb A., J Biol Chem 283(48), 2008
PMID: 18818199
Mutation in cyaA in Enterobacter cloacae decreases cucumber root colonization.
Roberts DP, McKenna LF, Hu X, Lohrke SM, Kong HS, de Souza JT, Baker CJ, Lydon J., Arch Microbiol 187(2), 2007
PMID: 17024489
Chaperone Hsp31 contributes to acid resistance in stationary-phase Escherichia coli.
Mujacic M, Baneyx F., Appl Environ Microbiol 73(3), 2007
PMID: 17158627
Transcription factor distribution in Escherichia coli: studies with FNR protein.
Grainger DC, Aiba H, Hurd D, Browning DF, Busby SJ., Nucleic Acids Res 35(1), 2007
PMID: 17164287
The Escherichia coli regulator of sigma 70 protein, Rsd, can up-regulate some stress-dependent promoters by sequestering sigma 70.
Mitchell JE, Oshima T, Piper SE, Webster CL, Westblade LF, Karimova G, Ladant D, Kolb A, Hobman JL, Busby SJ, Lee DJ., J Bacteriol 189(9), 2007
PMID: 17351046
Impact of the rpoS genotype for acid resistance patterns of pathogenic and probiotic Escherichia coli.
Coldewey SM, Hartmann M, Schmidt DS, Engelking U, Ukena SN, Gunzer F., BMC Microbiol 7(), 2007
PMID: 17386106
Decline in ribosomal fidelity contributes to the accumulation and stabilization of the master stress response regulator sigmaS upon carbon starvation.
Fredriksson A, Ballesteros M, Peterson CN, Persson O, Silhavy TJ, Nyström T., Genes Dev 21(7), 2007
PMID: 17403784
Genome-wide expression profiling in Geobacter sulfurreducens: identification of Fur and RpoS transcription regulatory sites in a relGsu mutant.
Krushkal J, Yan B, DiDonato LN, Puljic M, Nevin KP, Woodard TL, Adkins RM, Methé BA, Lovley DR., Funct Integr Genomics 7(3), 2007
PMID: 17406915
Cold-shock-induced de novo transcription and translation of infA and role of IF1 during cold adaptation.
Giangrossi M, Brandi A, Giuliodori AM, Gualerzi CO, Pon CL., Mol Microbiol 64(3), 2007
PMID: 17462025
Thermoregulation of Escherichia coli hchA transcript stability.
Rasouly A, Shenhar Y, Ron EZ., J Bacteriol 189(15), 2007
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Extended -10 promoter in ISAba-1 upstream of blaOXA-23 from Acinetobacter baumannii.
Segal H, Jacobson RK, Garny S, Bamford CM, Elisha BG., Antimicrob Agents Chemother 51(8), 2007
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Causes and consequences of DNA repair activity modulation during stationary phase in Escherichia coli.
Saint-Ruf C, Pesut J, Sopta M, Matic I., Crit Rev Biochem Mol Biol 42(4), 2007
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Adaptive amplification.
Hastings PJ., Crit Rev Biochem Mol Biol 42(4), 2007
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SbcCD regulation and localization in Escherichia coli.
Darmon E, Lopez-Vernaza MA, Helness AC, Borking A, Wilson E, Thacker Z, Wardrope L, Leach DR., J Bacteriol 189(18), 2007
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Analysis of the RpoS regulon in Borrelia burgdorferi in response to mammalian host signals provides insight into RpoS function during the enzootic cycle.
Caimano MJ, Iyer R, Eggers CH, Gonzalez C, Morton EA, Gilbert MA, Schwartz I, Radolf JD., Mol Microbiol 65(5), 2007
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Induction of RpoS degradation by the two-component system regulator RstA in Salmonella enterica.
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6S RNA: a regulator of transcription.
Wassarman KM., Mol Microbiol 65(6), 2007
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Ribosome biogenesis and the translation process in Escherichia coli.
Kaczanowska M, Rydén-Aulin M., Microbiol Mol Biol Rev 71(3), 2007
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Stress-induced mutagenesis in bacteria.
Foster PL., Crit Rev Biochem Mol Biol 42(5), 2007
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Mutation as a stress response and the regulation of evolvability.
Galhardo RS, Hastings PJ, Rosenberg SM., Crit Rev Biochem Mol Biol 42(5), 2007
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Metabolic transcription analysis of engineered Escherichia coli strains that overproduce L-phenylalanine.
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Escherichia coli physiology in Luria-Bertani broth.
Sezonov G, Joseleau-Petit D, D'Ari R., J Bacteriol 189(23), 2007
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Genome-wide screen of Salmonella genes expressed during infection in pigs, using in vivo expression technology.
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YhbO protects cells against multiple stresses.
Abdallah J, Caldas T, Kthiri F, Kern R, Richarme G., J Bacteriol 189(24), 2007
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Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium.
Bergholz TM, Wick LM, Qi W, Riordan JT, Ouellette LM, Whittam TS., BMC Microbiol 7(), 2007
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Monitoring changes in nisin susceptibility of Listeria monocytogenes Scott A as an indicator of growth phase using FACS.
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Cloning, expression, and purification of the general stress protein YhbO from Escherichia coli.
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Expression of the F plasmid ccd toxin-antitoxin system in Escherichia coli cells under nutritional stress.
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Environmental stress and lesion-bypass DNA polymerases.
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The effect of IHF on sigmaS selectivity of the phoA and pst promoters of Escherichia coli.
Taschner NP, Yagil E, Spira B., Arch Microbiol 185(3), 2006
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Osmolyte-induced transcription: -35 region elements and recognition by sigma38 (rpoS).
Rosenthal AZ, Hu M, Gralla JD., Mol Microbiol 59(3), 2006
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Environmental tuning of mutation rates.
Saint-Ruf C, Matic I., Environ Microbiol 8(2), 2006
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Specific growth rate determines the sensitivity of Escherichia coli to thermal, UVA, and solar disinfection.
Berney M, Weilenmann HU, Ihssen J, Bassin C, Egli T., Appl Environ Microbiol 72(4), 2006
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Proteomic profiling of ClpXP substrates after DNA damage reveals extensive instability within SOS regulon.
Neher SB, Villén J, Oakes EC, Bakalarski CE, Sauer RT, Gygi SP, Baker TA., Mol Cell 22(2), 2006
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Regulation of RraA, a protein inhibitor of RNase E-mediated RNA decay.
Zhao M, Zhou L, Kawarasaki Y, Georgiou G., J Bacteriol 188(9), 2006
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Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome.
Blot N, Mavathur R, Geertz M, Travers A, Muskhelishvili G., EMBO Rep 7(7), 2006
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Limited role for the DsrA and RprA regulatory RNAs in rpoS regulation in Salmonella enterica.
Jones AM, Goodwill AG, Elliott T., J Bacteriol 188(14), 2006
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Functional heterogeneity of RpoS in stress tolerance of enterohemorrhagic Escherichia coli strains.
Bhagwat AA, Tan J, Sharma M, Kothary M, Low S, Tall BD, Bhagwat M., Appl Environ Microbiol 72(7), 2006
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Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information.
Yan B, Núñez C, Ueki T, Esteve-Núñez A, Puljic M, Adkins RM, Methé BA, Lovley DR, Krushkal J., Gene 384(), 2006
PMID: 17014972
Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion.
Clark ME, He Q, He Z, Huang KH, Alm EJ, Wan XF, Hazen TC, Arkin AP, Wall JD, Zhou JZ, Fields MW., Appl Environ Microbiol 72(8), 2006
PMID: 16885312
The PhoP/PhoQ two-component system stabilizes the alternative sigma factor RpoS in Salmonella enterica.
Tu X, Latifi T, Bougdour A, Gottesman S, Groisman EA., Proc Natl Acad Sci U S A 103(36), 2006
PMID: 16938894
Gene expression of Escherichia coli in continuous culture during adaptation to artificial sunlight.
Berney M, Weilenmann HU, Egli T., Environ Microbiol 8(9), 2006
PMID: 16913923
Cyclic-di-GMP-mediated signalling within the sigma network of Escherichia coli.
Weber H, Pesavento C, Possling A, Tischendorf G, Hengge R., Mol Microbiol 62(4), 2006
PMID: 17010156
Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12.
Hayes ET, Wilks JC, Sanfilippo P, Yohannes E, Tate DP, Jones BD, Radmacher MD, BonDurant SS, Slonczewski JL., BMC Microbiol 6(), 2006
PMID: 17026754
Nutrient-scavenging stress response in an Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system, as explored by gene expression profile analysis.
Flores S, Flores N, de Anda R, González A, Escalante A, Sigala JC, Gosset G, Bolívar F., J Mol Microbiol Biotechnol 10(1), 2005
PMID: 16491026
Alkaline pH homeostasis in bacteria: new insights.
Padan E, Bibi E, Ito M, Krulwich TA., Biochim Biophys Acta 1717(2), 2005
PMID: 16277975
Stationary-phase regulation of RpoS translation in Escherichia coli.
Hirsch M, Elliott T., J Bacteriol 187(21), 2005
PMID: 16237004
Holoenzyme switching and stochastic release of sigma factors from RNA polymerase in vivo.
Raffaelle M, Kanin EI, Vogt J, Burgess RR, Ansari AZ., Mol Cell 20(3), 2005
PMID: 16285918
The maltodextrin system of Escherichia coli: glycogen-derived endogenous induction and osmoregulation.
Dippel R, Bergmiller T, Böhm A, Boos W., J Bacteriol 187(24), 2005
PMID: 16321937
Alternative sigma factors and their roles in bacterial virulence.
Kazmierczak MJ, Wiedmann M, Boor KJ., Microbiol Mol Biol Rev 69(4), 2005
PMID: 16339734

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