Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015
Metabolic Modeling Tutorial
early discounted registration
ends Feb 21th, 2015

Escherichia coli K-12 substr. MG1655 Polypeptide: RNA polymerase, sigma S (sigma 38) factor

Gene: rpoS Accession Numbers: EG10510 (EcoCyc), b2741, ECK2736

Synonyms: sigS, otsX, abrD, appR, csi2, dpeB, katF, nur, sigma 38 factor, sigma S factor, σS

Regulation Summary Diagram: ?

Component of: RNA polymerase sigma S

rpoS encodes the alternative sigma factor σS, a subunit of RNA polymerase that acts as the master regulator of the general stress response in E. coli.

S efficiently transcribes genes involved in stress responses and secondary metabolism, as well as RNAs from intergenic regions with yet-unknown function(s). In addition, rpoS transcribes a significant fraction of genes related to sugar and to polyamine metabolism in response to cellular stresses and in nucleic acid synthesis, modification, and turnover [Maciag11]. RpoS regulates plasmid transformation by targeting several genes related to DNA uptake, as it is known to encode membrane/periplasmic proteins [Zhang12j]. Most genes belonging to the EσS regulon are also subject to additional forms of gene expression regulation [Maciag11]. Several rpoS-dependent genes are maximally expressed at the transition between the exponential and stationary phases, or even in the mid-exponential phase [Maciag11].

σS is homologous to the housekeeping sigma factor σ70 and recognizes similar consensus promoter sequences [Gaal01, Checroun04a]. Discrimination between σS and σ70 promoters may be achieved by tolerating different levels of deviation from the consensus [Gaal01] and nonoptimal spacing between the -35 and -10 elements [Typas06]. The presence and location of UP elements [Typas05] and -35 region elements [Rosenthal06] may also influence usage of a subset of promoters. Based on promoter sequence comparisons, it was found that selective promoter recognition by either form of RNA polymerase can be affected by the A/T content in the -10/+1 region. Indeed, site-directed mutagenesis experiments confirmed that an A/T bias in the -10/+1 region could improve promoter recognition by EσS [Maciag11]. Genome-wide analyses of RpoS-dependent gene expression showed that up to 10% of the genes in E. coli are under direct or indirect control of σS [Patten04, Weber05]. The effects of σS on E. coli metabolism have been investigated [Rahman06].

A global antagonistic effect on gene expression was perceived between σS, σ54, and σ28, based on transcriptome expression analysis, and this resulted in many physiological traits, including flagellum-mediated motility and utilization of nitrogen sources; as many as 60% of genes in the RpoN regulon are under reciprocal RpoS control [Dong11]. In addition, there is a complex regulatory interaction of the three σ factors: σS, σ54, and σ28 [Dong11].

Polymorphisms in rpoS that affect fitness across different environments are commonly found in E. coli [NotleyMcRobb02, Zinser04, King06].

rpoS responds in a constant way to different environmental stresses in both the planktonic and biofilm phases [Dong11]. The rpoS gene is expressed in response to sudden changes in the environment [Dong11].

σS is itself subject to complex regulation at all levels (transcription, translation, activity, and protein degradation), thereby allowing integration of multiple stress signals in the cell. The regulatory mechanisms and signals are summarized below.

Transcription: Transcription of rpoS is repressed by the phosphorylated response regulator ArcA [Mika05]. During entry into stationary phase in complex medium, transcription of rpoS increases 5- to 10-fold [Mulvey90, Lange94d, Takayanagi94], but this effect is limited in defined medium [Mandel05]. cAMP-CRP negatively controls rpoS transcription [Lange94d]. The BarA regulator is required for exponential-phase induction of rpoS transcription [Mukhopadhyay00a], and ppGpp has a positive effect on the basal level of σS synthesis [Gentry93a, Hirsch02], affecting transcription elongation, but not initiation [Lange95].

mRNA stability and translation: The rpoS mRNA contains a long untranslated 5' region which plays an important role in the regulation of its stability and translation [Cunning98]; a review by Majdalani et al. ([Majdalani05a]) summarized the current knowledge with respect to small RNA regulators. Many factors have been shown to influence formation of secondary structures, translation, and degradation of rpoS mRNA: H-NS binds to rpoS mRNA and enhances its cleavage [Brescia04], while the DsrA small RNA stabilizes it [Lease00a]. rpoS mRNA stability during glucose starvation is diminished in the absence of RNase III function [Freire06]. Hfq is required for translation of the rpoS mRNA [Muffler96a], whereas the OxyS small RNA represses translation of rpoS, possibly by altering Hfq activity [Zhang98d]. HU [Balandina01] and the RprA small RNA [Majdalani02] each stimulate translation of rpoS. Starvation for phosphorus leads to accumulation of σS due to increased translation of rpoS mRNA. The upregulation is dependent on Hfq and may therefore involve an as-yet-unidentified small RNA [Ruiz03]. LrhA represses translation of rpoS in an Hfq-dependent manner, which may also involve an unidentified small RNA [Peterson06]. Twenty-four nucleotides of the ribosome-binding site were shown to be necessary and sufficient for a 10-fold increase in rpoS translation [Hirsch05]. A miaA insertion mutant shows decreased levels of RpoS, consistent with a MiaA requirement for efficient RpoS translation [Thompson14].

Protein activity: 6S RNA activates transcription from several σS-dependent promoters while not affecting the levels of rpoS transcription or σS protein [Trotochaud04]. The alarmone ppGpp enhances the ability of σS to compete with σ70 for binding to core RNA polymerase [Jishage02]; the Rsd protein appears to serve a similar function [Jishage99]. Nitrogen starvation induces σS-dependent gene expression [Gyaneshwar05], although levels of σS are only increased approximately 2-fold [Mandel05], suggesting that nitrogen starvation acts at the level of σS activity [Peterson05]. The RNA polymerase holoenzyme assembly factor Crl enhances σS activity by increasing its ability to compete for the RNA polymerase, core enzyme [Typas07a]. Crl is a cognate enhancer of RpoS activity under different growth conditions [Dudin13]. Subinhibitory concentrations of Eβ-lactam antibiotics induce the RpoS regulon [Gutierrez13].

Under stress, σ38 induces the mutagenic repair of DNA breaks through a network genes that function in the activation of σ38. The genes that appear to be involved in the activation of σ38 are cyoD, mdh, nuoC, sdhD, ubiD, apaH, cspC, cyoA, fre, glnK, hdfR, hemL, hfq, hscB, metJ, nuoG, nuoH, nuoJ, nuoK, nuoL, pgi, rbsK, sdhB, speD, speE, ubiA, ubiE, ubiH, ubiX, and yifE [Al12].

Protein degradation: In exponentially growing cells, the energy-dependent ClpXP protease degrades σS rapidly [Schweder96]. The RssB protein is required for rapid proteolysis of σS; it acts as a direct recognition factor, facilitating degradation of σS by the ClpXP protease [Becker99a]. poly(A) polymerase I [Santos06] as well as IraP [Bougdour06], RNA polymerase holoenzyme assembly factor Crl [Typas07a], and H-NS [Zhou06b] modulate the effect of RssB. rssB transcription is itself controlled by σS [Ruiz01]. Acetyl phosphate is able to transfer a phosphate group to the Asp-58 residue of RssB and activate it [Bouche98], although the phosphorylation level of RssB does not appear to play a role in signaling carbon starvation [Peterson04]. Carbon starvation leads to accumulation of σS due to stabilization of the protein [Zgurskaya97, Mandel05]; the molecular signal has not yet been determined [Peterson05].

Selected reviews: [HenggeAronis02, Repoila03, Venturi03a, Majdalani05a, Magnusson05, Ferenci05, Peterson05, Klauck07, Hengge09, Battesti10]

Crl is a new thermosensor identified in the Escherichia coli RpoS regulon, which interacts directly with σS, promoting the binding of EσS to the csgBp promoter [Bougdour04].

Flores et al. (2007) identified a new role for RpoS as controller of almost all the glycolytic genes in Escherichia coli strains lacking the phosphoenolpyruvate:carbohydrate phosphotransferase system. In addition, they were able to identify genes whose products participate in ppGpp metabolism and are also controlled by RpoS. On the other hand, relA is not transcribed by this factor. Finally, an additional factor to RpoS was found to be involved in the spoT and gpp gene expression [Flores08].

A σ-competition model based on comparative kinetic and thermodynamic properties was developed by Ganguly and Chatterji in 2012 [Ganguly12].

Gene Citations: [Lange94c]

Locations: cytosol

Map Position: [2,864,581 <- 2,865,573] (61.74 centisomes)
Length: 993 bp / 330 aa

Molecular Weight of Polypeptide: 37.972 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009001 , CGSC:18208 , DIP:DIP-10777N , EchoBASE:EB0505 , EcoGene:EG10510 , EcoliWiki:b2741 , Mint:MINT-1228474 , ModBase:P13445 , OU-Microarray:b2741 , PortEco:rpoS , PR:PRO_000023851 , Pride:P13445 , Protein Model Portal:P13445 , RefSeq:NP_417221 , RegulonDB:EG10510 , SMR:P13445 , String:511145.b2741 , Swiss-Model:P13445 , UniProt:P13445

Relationship Links: InterPro:IN-FAMILY:IPR000943 , InterPro:IN-FAMILY:IPR007624 , InterPro:IN-FAMILY:IPR007627 , InterPro:IN-FAMILY:IPR007630 , InterPro:IN-FAMILY:IPR009042 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR012761 , InterPro:IN-FAMILY:IPR013324 , InterPro:IN-FAMILY:IPR013325 , InterPro:IN-FAMILY:IPR014284 , Pfam:IN-FAMILY:PF00140 , Pfam:IN-FAMILY:PF04539 , Pfam:IN-FAMILY:PF04542 , Pfam:IN-FAMILY:PF04545 , Prints:IN-FAMILY:PR00046 , Prosite:IN-FAMILY:PS00715 , Prosite:IN-FAMILY:PS00716

In Paralogous Gene Group: 363 (4 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0001123 - transcription initiation from bacterial-type RNA polymerase promoter Inferred from experiment Inferred by computational analysis [GOA06, Nguyen93]
GO:0006950 - response to stress Inferred from experiment Inferred by computational analysis [GOA06, Maciag11]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006352 - DNA-templated transcription, initiation Inferred by computational analysis [GOA01a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01a]
GO:0010468 - regulation of gene expression Inferred by computational analysis [GOA06]
Molecular Function: GO:0001000 - bacterial-type RNA polymerase core enzyme binding Inferred from experiment [Nguyen93]
GO:0016987 - sigma factor activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, GOA01a, Nguyen93]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01a]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, Mandel05]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: regulation type of regulation transcriptional level sigma factors, anti-sigmafactors

Essentiality data for rpoS knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Reviewed 15-Nov-2005 by Mandel MJ , University of Wisconsin, Madison
Revised 21-Dec-2006 by Keseler I , SRI International

Subunit of: RNA polymerase sigma S

Synonyms: RNA polymerase sigma 38, RNA polymerase sigma 38 holoenzyme

Subunit composition of RNA polymerase sigma S = [(RpoA)2(RpoC)(RpoB)][RpoS]
         RNA polymerase, core enzyme = (RpoA)2(RpoC)(RpoB) (extended summary available)
                 RNA polymerase, α subunit = RpoA (extended summary available)
                 RNA polymerase, β' subunit = RpoC (extended summary available)
                 RNA polymerase, β subunit = RpoB (summary available)
         RNA polymerase, sigma S (sigma 38) factor = RpoS (extended summary available)

Controlled Transcription Units (206 total): ?


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 25
[Ivanova92, UniProt10]
Alternate sequence: F → L; UniProt: (in Ref. 3; CAA78692);
Sequence-Conflict 29
[Mulvey89, UniProt10]
Alternate sequence: A → P; UniProt: (in Ref. 1; CAA34435);
Sequence-Conflict 33
[Tanaka93a, Takayanagi94, UniProt10]
Alternate sequence: Q → L; UniProt: (in Ref. 2 and 6);
Protein-Segment 56 -> 89
UniProt: Sigma-70 factor domain-1; Sequence Annotation Type: region of interest.
Protein-Segment 94 -> 164
UniProt: Sigma-70 factor domain-2; Sequence Annotation Type: region of interest.
Protein-Segment 118 -> 121
UniProt: Interaction with polymerase core subunit RpoC; Sequence Annotation Type: short sequence motif.
Mutagenesis-Variant 173
[Becker99a, UniProt13]
Alternate sequence: K → E; UniProt: Eliminates RpoS proteolysis. Lack of interaction with RssB.
Mutagenesis-Variant 174
[Becker99a, UniProt13]
Alternate sequence: E → T; UniProt: 2-fold increase in RpoS half-life. Does not affect interaction with RssB.
Protein-Segment 174 -> 249
UniProt: Sigma-70 factor domain-3; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 177
[Becker99a, UniProt13]
Alternate sequence: V → K; UniProt: 3-fold increase in RpoS half-life.
Mutagenesis-Variant 178
[Becker99a, UniProt13]
Alternate sequence: Y → L; UniProt: Does not affect RpoS half-life.
Sequence-Conflict 196
[Mulvey89, UniProt10]
Alternate sequence: E → V; UniProt: (in Ref. 1; CAA34435);
Protein-Segment 262 -> 315
UniProt: Sigma-70 factor domain-4; Sequence Annotation Type: region of interest.
DNA-Binding-Region 288 -> 307
UniProt: H-T-H motif; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 328 -> 330
[Mulvey89, UniProt10]
Alternate sequence: FRE → LPRVSKHLSERPVSSEAGFFCAQ; UniProt: (in Ref. 1);

Gene Local Context (not to scale): ?

Transcription Units:


10/20/97 Gene b2741 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10510; confirmed by SwissProt match.


Al12: Al Mamun AA, Lombardo MJ, Shee C, Lisewski AM, Gonzalez C, Lin D, Nehring RB, Saint-Ruf C, Gibson JL, Frisch RL, Lichtarge O, Hastings PJ, Rosenberg SM (2012). "Identity and function of a large gene network underlying mutagenic repair of DNA breaks." Science 338(6112);1344-8. PMID: 23224554

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Balandina01: Balandina A, Claret L, Hengge-Aronis R, Rouviere-Yaniv J (2001). "The Escherichia coli histone-like protein HU regulates rpoS translation." Mol Microbiol 39(4);1069-79. PMID: 11251825

Battesti10: Battesti A, Majdalani N, Gottesman S (2010). "The RpoS-Mediated General Stress Response in Escherichia coli." Annu Rev Microbiol. PMID: 21639793

Becker99a: Becker G, Klauck E, Hengge-Aronis R (1999). "Regulation of RpoS proteolysis in Escherichia coli: the response regulator RssB is a recognition factor that interacts with the turnover element in RpoS." Proc Natl Acad Sci U S A 96(11);6439-44. PMID: 10339606

Bouche98: Bouche S, Klauck E, Fischer D, Lucassen M, Jung K, Hengge-Aronis R (1998). "Regulation of RssB-dependent proteolysis in Escherichia coli: a role for acetyl phosphate in a response regulator-controlled process." Mol Microbiol 27(4);787-95. PMID: 9515704

Bougdour04: Bougdour A, Lelong C, Geiselmann J (2004). "Crl, a low temperature-induced protein in Escherichia coli that binds directly to the stationary phase sigma subunit of RNA polymerase." J Biol Chem 279(19);19540-50. PMID: 14978043

Bougdour06: Bougdour A, Wickner S, Gottesman S (2006). "Modulating RssB activity: IraP, a novel regulator of sigma(S) stability in Escherichia coli." Genes Dev 20(7);884-97. PMID: 16600914

Brescia04: Brescia CC, Kaw MK, Sledjeski DD (2004). "The DNA binding protein H-NS binds to and alters the stability of RNA in vitro and in vivo." J Mol Biol 339(3);505-14. PMID: 15147838

Checroun04a: Checroun C, Bordes P, Leroy O, Kolb A, Gutierrez C (2004). "Interactions between the 2.4 and 4.2 regions of sigmaS, the stress-specific sigma factor of Escherichia coli, and the -10 and -35 promoter elements." Nucleic Acids Res 32(1);45-53. PMID: 14704342

Cunning98: Cunning C, Brown L, Elliott T (1998). "Promoter substitution and deletion analysis of upstream region required for rpoS translational regulation." J Bacteriol 180(17);4564-70. PMID: 9721296

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Dong11: Dong T, Yu R, Schellhorn H (2011). "Antagonistic regulation of motility and transcriptome expression by RpoN and RpoS in Escherichia coli." Mol Microbiol 79(2);375-86. PMID: 21219458

Dudin13: Dudin O, Lacour S, Geiselmann J (2013). "Expression dynamics of RpoS/Crl-dependent genes in Escherichia coli." Res Microbiol 164(8);838-47. PMID: 23867204

Ferenci05: Ferenci T (2005). "Maintaining a healthy SPANC balance through regulatory and mutational adaptation." Mol Microbiol 57(1);1-8. PMID: 15948944

Flores08: Flores N, Escalante A, de Anda R, Baez-Viveros JL, Merino E, Franco B, Georgellis D, Gosset G, Bolivar F (2008). "New Insights into the Role of Sigma Factor RpoS as Revealed in Escherichia coli Strains Lacking the Phosphoenolpyruvate:Carbohydrate Phosphotransferase System." J Mol Microbiol Biotechnol 14(4):176-92. PMID: 17938565

Freire06: Freire P, Amaral JD, Santos JM, Arraiano CM (2006). "Adaptation to carbon starvation: RNase III ensures normal expression levels of bolA1p mRNA and sigma(S)." Biochimie 88(3-4);341-6. PMID: 16309817

Gaal01: Gaal T, Ross W, Estrem ST, Nguyen LH, Burgess RR, Gourse RL (2001). "Promoter recognition and discrimination by EsigmaS RNA polymerase." Mol Microbiol 42(4);939-54. PMID: 11737638

Ganguly12: Ganguly A, Chatterji D (2012). "A comparative kinetic and thermodynamic perspective of the σ-competition model in Escherichia coli." Biophys J 103(6);1325-33. PMID: 22995505

Gentry93a: Gentry DR, Hernandez VJ, Nguyen LH, Jensen DB, Cashel M (1993). "Synthesis of the stationary-phase sigma factor sigma s is positively regulated by ppGpp." J Bacteriol 175(24);7982-9. PMID: 8253685

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Gutierrez13: Gutierrez A, Laureti L, Crussard S, Abida H, Rodriguez-Rojas A, Blazquez J, Baharoglu Z, Mazel D, Darfeuille F, Vogel J, Matic I (2013). "β-lactam antibiotics promote bacterial mutagenesis via an RpoS-mediated reduction in replication fidelity." Nat Commun 4;1610. PMID: 23511474

Gyaneshwar05: Gyaneshwar P, Paliy O, McAuliffe J, Jones A, Jordan MI, Kustu S (2005). "Lessons from Escherichia coli genes similarly regulated in response to nitrogen and sulfur limitation." Proc Natl Acad Sci U S A 102(9);3453-8. PMID: 15716358

Hengge09: Hengge R (2009). "Proteolysis of sigma(S) (RpoS) and the general stress response in Escherichia coli." Res Microbiol. PMID: 19765651

HenggeAronis02: Hengge-Aronis R (2002). "Signal transduction and regulatory mechanisms involved in control of the sigma(S) (RpoS) subunit of RNA polymerase." Microbiol Mol Biol Rev 66(3);373-95, table of contents. PMID: 12208995

Hirsch02: Hirsch M, Elliott T (2002). "Role of ppGpp in rpoS stationary-phase regulation in Escherichia coli." J Bacteriol 184(18);5077-87. PMID: 12193624

Hirsch05: Hirsch M, Elliott T (2005). "Stationary-phase regulation of RpoS translation in Escherichia coli." J Bacteriol 187(21);7204-13. PMID: 16237004

Ivanova92: Ivanova A, Renshaw M, Guntaka RV, Eisenstark A (1992). "DNA base sequence variability in katF (putative sigma factor) gene of Escherichia coli." Nucleic Acids Res 20(20);5479-80. PMID: 1437569

Jishage02: Jishage M, Kvint K, Shingler V, Nystrom T (2002). "Regulation of sigma factor competition by the alarmone ppGpp." Genes Dev 16(10);1260-70. PMID: 12023304

Jishage99: Jishage M, Ishihama A (1999). "Transcriptional organization and in vivo role of the Escherichia coli rsd gene, encoding the regulator of RNA polymerase sigma D." J Bacteriol 181(12);3768-76. PMID: 10368152

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

King06: King T, Seeto S, Ferenci T (2006). "Genotype-by-environment interactions influencing the emergence of rpoS mutations in Escherichia coli populations." Genetics 172(4);2071-9. PMID: 16489226

Klauck07: Klauck E, Typas A, Hengge R (2007). "The sigmaS subunit of RNA polymerase as a signal integrator and network master regulator in the general stress response in Escherichia coli." Sci Prog 90(Pt 2-3);103-27. PMID: 17725229

Lange94c: Lange R, Hengge-Aronis R (1994). "The nlpD gene is located in an operon with rpoS on the Escherichia coli chromosome and encodes a novel lipoprotein with a potential function in cell wall formation." Mol Microbiol 1994;13(4);733-43. PMID: 7997184

Lange94d: Lange R, Hengge-Aronis R (1994). "The cellular concentration of the sigma S subunit of RNA polymerase in Escherichia coli is controlled at the levels of transcription, translation, and protein stability." Genes Dev 8(13);1600-12. PMID: 7525405

Lange95: Lange R, Fischer D, Hengge-Aronis R (1995). "Identification of transcriptional start sites and the role of ppGpp in the expression of rpoS, the structural gene for the sigma S subunit of RNA polymerase in Escherichia coli." J Bacteriol 177(16);4676-80. PMID: 7642494

Lease00a: Lease RA, Belfort M (2000). "A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures." Proc Natl Acad Sci U S A 97(18);9919-24. PMID: 10954740

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

Magnusson05: Magnusson LU, Farewell A, Nystrom T (2005). "ppGpp: a global regulator in Escherichia coli." Trends Microbiol 13(5);236-42. PMID: 15866041

Majdalani02: Majdalani N, Hernandez D, Gottesman S (2002). "Regulation and mode of action of the second small RNA activator of RpoS translation, RprA." Mol Microbiol 46(3);813-26. PMID: 12410838

Majdalani05a: Majdalani N, Vanderpool CK, Gottesman S (2005). "Bacterial small RNA regulators." Crit Rev Biochem Mol Biol 40(2);93-113. PMID: 15814430

Mandel05: Mandel MJ, Silhavy TJ (2005). "Starvation for different nutrients in Escherichia coli results in differential modulation of RpoS levels and stability." J Bacteriol 187(2);434-42. PMID: 15629914

Mika05: Mika F, Hengge R (2005). "A two-component phosphotransfer network involving ArcB, ArcA, and RssB coordinates synthesis and proteolysis of sigmaS (RpoS) in E. coli." Genes Dev 19(22);2770-81. PMID: 16291649

Muffler96a: Muffler A, Fischer D, Hengge-Aronis R (1996). "The RNA-binding protein HF-I, known as a host factor for phage Qbeta RNA replication, is essential for rpoS translation in Escherichia coli." Genes Dev 10(9);1143-51. PMID: 8654929

Mukhopadhyay00a: Mukhopadhyay S, Audia JP, Roy RN, Schellhorn HE (2000). "Transcriptional induction of the conserved alternative sigma factor RpoS in Escherichia coli is dependent on BarA, a probable two-component regulator." Mol Microbiol 37(2);371-81. PMID: 10931332

Mulvey89: Mulvey MR, Loewen PC (1989). "Nucleotide sequence of katF of Escherichia coli suggests KatF protein is a novel sigma transcription factor." Nucleic Acids Res 17(23);9979-91. PMID: 2690013

Mulvey90: Mulvey MR, Switala J, Borys A, Loewen PC (1990). "Regulation of transcription of katE and katF in Escherichia coli." J Bacteriol 172(12);6713-20. PMID: 2254248

Nguyen93: Nguyen LH, Jensen DB, Thompson NE, Gentry DR, Burgess RR (1993). "In vitro functional characterization of overproduced Escherichia coli katF/rpoS gene product." Biochemistry 32(41);11112-7. PMID: 8218173

NotleyMcRobb02: Notley-McRobb L, King T, Ferenci T (2002). "rpoS mutations and loss of general stress resistance in Escherichia coli populations as a consequence of conflict between competing stress responses." J Bacteriol 184(3);806-11. PMID: 11790751

Patten04: Patten CL, Kirchhof MG, Schertzberg MR, Morton RA, Schellhorn HE (2004). "Microarray analysis of RpoS-mediated gene expression in Escherichia coli K-12." Mol Genet Genomics 272(5);580-91. PMID: 15558318

Peterson04: Peterson CN, Ruiz N, Silhavy TJ (2004). "RpoS proteolysis is regulated by a mechanism that does not require the SprE (RssB) response regulator phosphorylation site." J Bacteriol 186(21);7403-10. PMID: 15489452

Peterson05: Peterson CN, Mandel MJ, Silhavy TJ (2005). "Escherichia coli starvation diets: essential nutrients weigh in distinctly." J Bacteriol 187(22);7549-53. PMID: 16267278

Peterson06: Peterson CN, Carabetta VJ, Chowdhury T, Silhavy TJ (2006). "LrhA regulates rpoS translation in response to the Rcs phosphorelay system in Escherichia coli." J Bacteriol 188(9);3175-81. PMID: 16621809

Rahman06: Rahman M, Hasan MR, Oba T, Shimizu K (2006). "Effect of rpoS gene knockout on the metabolism of Escherichia coli during exponential growth phase and early stationary phase based on gene expressions, enzyme activities and intracellular metabolite concentrations." Biotechnol Bioeng 94(3);585-95. PMID: 16511888

Repoila03: Repoila F, Majdalani N, Gottesman S (2003). "Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: the RpoS paradigm." Mol Microbiol 48(4);855-61. PMID: 12753181

Rosenthal06: Rosenthal AZ, Hu M, Gralla JD (2006). "Osmolyte-induced transcription: -35 region elements and recognition by sigma38 (rpoS)." Mol Microbiol 59(3);1052-61. PMID: 16420371

Ruiz01: Ruiz N, Peterson CN, Silhavy TJ (2001). "RpoS-dependent transcriptional control of sprE: regulatory feedback loop." J Bacteriol 183(20);5974-81. PMID: 11566997

Ruiz03: Ruiz N, Silhavy TJ (2003). "Constitutive activation of the Escherichia coli Pho regulon upregulates rpoS translation in an Hfq-dependent fashion." J Bacteriol 185(20);5984-92. PMID: 14526009

Santos06: Santos JM, Freire P, Mesquita FS, Mika F, Hengge R, Arraiano CM (2006). "Poly(A)-polymerase I links transcription with mRNA degradation via sigmaS proteolysis." Mol Microbiol 60(1);177-88. PMID: 16556229

Schweder96: Schweder T, Lee KH, Lomovskaya O, Matin A (1996). "Regulation of Escherichia coli starvation sigma factor (sigma s) by ClpXP protease." J Bacteriol 178(2);470-6. PMID: 8550468

Takayanagi94: Takayanagi Y, Tanaka K, Takahashi H (1994). "Structure of the 5' upstream region and the regulation of the rpoS gene of Escherichia coli." Mol Gen Genet 243(5);525-31. PMID: 8208244

Tanaka93a: Tanaka K, Takayanagi Y, Fujita N, Ishihama A, Takahashi H (1993). "Heterogeneity of the principal sigma factor in Escherichia coli: the rpoS gene product, sigma 38, is a second principal sigma factor of RNA polymerase in stationary-phase Escherichia coli." Proc Natl Acad Sci U S A 90(8);3511-5. PMID: 8475100

Thompson14: Thompson KM, Gottesman S (2014). "The MiaA tRNA modification enzyme is necessary for robust RpoS expression in Escherichia coli." J Bacteriol 196(4);754-61. PMID: 24296670

Trotochaud04: Trotochaud AE, Wassarman KM (2004). "6S RNA function enhances long-term cell survival." J Bacteriol 186(15);4978-85. PMID: 15262935

Typas05: Typas A, Hengge R (2005). "Differential ability of sigma(s) and sigma70 of Escherichia coli to utilize promoters containing half or full UP-element sites." Mol Microbiol 55(1);250-60. PMID: 15612932

Typas06: Typas A, Hengge R (2006). "Role of the spacer between the -35 and -10 regions in sigmas promoter selectivity in Escherichia coli." Mol Microbiol 59(3);1037-51. PMID: 16420370

Typas07a: Typas A, Barembruch C, Possling A, Hengge R (2007). "Stationary phase reorganisation of the Escherichia coli transcription machinery by Crl protein, a fine-tuner of sigma(s) activity and levels." EMBO J 26(6);1569-78. PMID: 17332743

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

Venturi03a: Venturi V (2003). "Control of rpoS transcription in Escherichia coli and Pseudomonas: why so different?." Mol Microbiol 49(1);1-9. PMID: 12823806

Weber05: Weber H, Polen T, Heuveling J, Wendisch VF, Hengge R (2005). "Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity." J Bacteriol 187(5);1591-603. PMID: 15716429

Zgurskaya97: Zgurskaya HI, Keyhan M, Matin A (1997). "The sigma S level in starving Escherichia coli cells increases solely as a result of its increased stability, despite decreased synthesis." Mol Microbiol 24(3);643-51. PMID: 9179856

Zhang12j: Zhang Y, Shi C, Yu J, Ren J, Sun D (2012). "RpoS regulates a novel type of plasmid DNA transfer in Escherichia coli." PLoS One 7(3);e33514. PMID: 22438941

Zhang98d: Zhang A, Altuvia S, Tiwari A, Argaman L, Hengge-Aronis R, Storz G (1998). "The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein." EMBO J 17(20);6061-8. PMID: 9774349

Zhou06b: Zhou Y, Gottesman S (2006). "Modes of regulation of RpoS by H-NS." J Bacteriol 188(19);7022-5. PMID: 16980505

Zinser04: Zinser ER, Kolter R (2004). "Escherichia coli evolution during stationary phase." Res Microbiol 155(5);328-36. PMID: 15207864

Other References Related to Gene Regulation

Hoerter05: Hoerter JD, Arnold AA, Ward CS, Sauer M, Johnson S, Fleming T, Eisenstark A (2005). "Reduced hydroperoxidase (HPI and HPII) activity in the Deltafur mutant contributes to increased sensitivity to UVA radiation in Escherichia coli." J Photochem Photobiol B 79(2);151-7. PMID: 15878120

Hommais04: Hommais F, Krin E, Coppee JY, Lacroix C, Yeramian E, Danchin A, Bertin P (2004). "GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli." Microbiology 150(Pt 1);61-72. PMID: 14702398

Jung03a: Jung IL, Kim IG (2003). "Transcription of ahpC, katG, and katE genes in Escherichia coli is regulated by polyamines: polyamine-deficient mutant sensitive to H2O2-induced oxidative damage." Biochem Biophys Res Commun 301(4);915-22. PMID: 12589799

Kumar11: Kumar R, Shimizu K (2011). "Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures." Microb Cell Fact 10;3. PMID: 21272324

Lange91a: Lange R, Hengge-Aronis R (1991). "Identification of a central regulator of stationary-phase gene expression in Escherichia coli." Mol Microbiol 5(1);49-59. PMID: 1849609

Majdalani01: Majdalani N, Chen S, Murrow J, St John K, Gottesman S (2001). "Regulation of RpoS by a novel small RNA: the characterization of RprA." Mol Microbiol 39(5);1382-94. PMID: 11251852

Mandin10: Mandin P, Gottesman S (2010). "Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA." EMBO J 29(18);3094-107. PMID: 20683441

Marzan13: Marzan LW, Hasan CM, Shimizu K (2013). "Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant." Arch Microbiol 195(3);161-71. PMID: 23274360

McCann93: McCann MP, Fraley CD, Matin A (1993). "The putative sigma factor KatF is regulated posttranscriptionally during carbon starvation." J Bacteriol 175(7);2143-9. PMID: 8458856

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

Moon11: Moon K, Gottesman S (2011). "Competition among Hfq-binding small RNAs in Escherichia coli." Mol Microbiol 82(6);1545-62. PMID: 22040174

Resch10: Resch A, Vecerek B, Palavra K, Blasi U (2010). "Requirement of the CsdA DEAD-box helicase for low temperature riboregulation of rpoS mRNA." RNA Biol 7(6);796-802. PMID: 21045550

Soper08: Soper TJ, Woodson SA (2008). "The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA." RNA 14(9):1907-17. PMID: 18658123

Soper10: Soper T, Mandin P, Majdalani N, Gottesman S, Woodson SA (2010). "Positive regulation by small RNAs and the role of Hfq." Proc Natl Acad Sci U S A 107(21);9602-7. PMID: 20457943

Updegrove11a: Updegrove TB, Wartell RM (2011). "The influence of Escherichia coli Hfq mutations on RNA binding and sRNA-mRNA duplex formation in rpoS riboregulation." Biochim Biophys Acta 1809(10);532-40. PMID: 21889623

Wang11c: Wang X, Kim Y, Hong SH, Ma Q, Brown BL, Pu M, Tarone AM, Benedik MJ, Peti W, Page R, Wood TK (2011). "Antitoxin MqsA helps mediate the bacterial general stress response." Nat Chem Biol 7(6);359-66. PMID: 21516113

Yang06e: Yang S, Lopez CR, Zechiedrich EL (2006). "Quorum sensing and multidrug transporters in Escherichia coli." Proc Natl Acad Sci U S A 103(7);2386-91. PMID: 16467145

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Fri Feb 27, 2015, BIOCYC14A.