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Gene Review

rpoS  -  RNA polymerase, sigma S (sigma 38) factor

Escherichia coli str. K-12 substr. MG1655

Synonyms: ECK2736, JW5437, abrD, appR, csi2, ...
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Disease relevance of rpoS


High impact information on rpoS

  • Using a combination of gene fusion analysis and pulse-chase experiments, we demonstrate that the hfq mutant is specifically impaired in rpoS translation [1].
  • Our analysis also indicates that at least five different signals [cAMP, a growth rate-related signal (ppGpp?), a cell density signal, an osmotic signal, and a starvation signal] are involved in the control of all these processes that regulate rpoS/sigma S expression [5].
  • The Escherichia coli host factor I, Hfq, binds to many small regulatory RNAs and is required for OxyS RNA repression of fhlA and rpoS mRNA translation [6].
  • The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein [7].
  • The katF gene product, a stationary phase-specific sigma factor, was not required for the expression of rmf [8].

Chemical compound and disease context of rpoS

  • For E. coli CFT073, introduction of an rpoS deletion impaired trehalose accumulation, osmotolerance and stationary-phase thermotolerance [9].
  • Mutation of the phoP gene rendered Salmonella as sensitive to hydrogen peroxide as an rpoS mutant after growth in low Mg(2+) [10].
  • We compared the viabilities (direct viable counts) and culturabilities (colony counts) in seawater of Escherichia coli and Salmonella typhimurium strains and those in which rpoS was deleted or which were deficient in guanosine 3',5'-bispyrophosphate (ppGpp) synthesis (relA spoT) [11].
  • The E. coli parental strains reached the non-culturable state in 33 days when the plate counts were evaluated on Luria-Bertani agar containing sodium pyruvate, whereas cells of the rpoS mutants lost their culturability in only 21 days [12].
  • When tetracycline was present, tetA(C) reduced acid tolerance, suppressed rpoS expression, and increased the concentration of total soluble proteins in stationary-phase Escherichia coli [13].

Biological context of rpoS


Anatomical context of rpoS


Associations of rpoS with chemical compounds

  • Inasmuch as this inhibition by poly(P)ase did not affect the levels of the stringent-response guanosine nucleotides (pppGpp and ppGpp) and in view of the capacity of additional rpoS expression to suppress the poly(P)ase inhibition of katE expression, a role is proposed for poly(P) in inducing the expression of rpoS [18].
  • In stark contrast, the inactivation of both oxyR and rpoS genes dramatically decreased the viability of glucose-starved cells [19].
  • Indeed, the rpoS mutant strain shows severely impaired growth on some sugars such as fructose and N-acetylglucosamine [20].
  • The rpoS gene controls the production of indole, which acts as a signal molecule in stationary-phase cells, via regulation of the tnaA-encoded tryptophanase enzyme [20].
  • The rpoS gene product (sigma 38) was rapidly degraded after addition of chloramphenicol to cultures in the exponential, but not the stationary phase [21].

Regulatory relationships of rpoS

  • We found that a crl null allele influences expression of RpoS-regulated genes in a fashion similar to an rpoS null allele [22].

Other interactions of rpoS

  • Mutations in rprA and compensating mutations in the rpoS leader demonstrate that RprA interacts with the same region of the RpoS leader as DsrA [23].
  • However, a mutation in rpoS did not prevent an increase in hmp expression by paraquat in exponentially growing cells [24].
  • With the exception of the dksA mutant, which had a modest defect in Luria-Bertani medium, none of these mutants was defective for rpoS stationary-phase induction [25].
  • Evolution of multi-gene segments in the mutS-rpoS intergenic region of Salmonella enterica serovar Typhimurium LT2 [26].
  • However, the genetic elimination of the rpoS, whose product is an alternative sigma factor (RpoS), derepressed the tktA gene expression in the stationary growth phase, indicating that the RpoS sigma factor negatively regulates the tktA gene expression in the stationary growth phase [27].

Analytical, diagnostic and therapeutic context of rpoS

  • Co-immunoprecipitation and gel mobility shift experiments revealed that the OxyS RNA binds Hfq, suggesting that OxyS represses rpoS translation by altering Hfq activity [7].
  • As demonstrated by two dimensional gel electrophoresis, this induction of the RelA protein resulted in global alterations in gene expression including increased synthesis of some rpoS-dependent proteins [28].
  • Transcription levels of the two divergently transcribed agf operons required for biogenesis of thin aggregative fimbriae by Northern blot analysis with gene probes for agfA and agfD as well as expression levels of AgfA by Western blotting were compared in the wild type, the constitutive mutants and their respective ompR and rpoS- derivatives [29].
  • Gel mobility shift assays show that HU is able to bind specifically an RNA fragment containing the translational initiation region of rpoS mRNA 1000-fold more strongly than double-stranded DNA [30].
  • Sequence analysis of the complementing clone revealed an 1.008-bp open reading frame which is predicted to encode a 336-amino-acid protein with 71 to 63% overall identity to other reported rpoS gene products [31].


  1. The RNA-binding protein HF-I, known as a host factor for phage Qbeta RNA replication, is essential for rpoS translation in Escherichia coli. Muffler, A., Fischer, D., Hengge-Aronis, R. Genes Dev. (1996) [Pubmed]
  2. Mutations that increase expression of the rpoS gene and decrease its dependence on hfq function in Salmonella typhimurium. Brown, L., Elliott, T. J. Bacteriol. (1997) [Pubmed]
  3. Control of rpoS transcription in Escherichia coli and Pseudomonas: why so different? Venturi, V. Mol. Microbiol. (2003) [Pubmed]
  4. The rpoS gene from Yersinia enterocolitica and its influence on expression of virulence factors. Iriarte, M., Stainier, I., Cornelis, G.R. Infect. Immun. (1995) [Pubmed]
  5. 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. Lange, R., Hengge-Aronis, R. Genes Dev. (1994) [Pubmed]
  6. The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Zhang, A., Wassarman, K.M., Ortega, J., Steven, A.C., Storz, G. Mol. Cell (2002) [Pubmed]
  7. The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein. Zhang, A., Altuvia, S., Tiwari, A., Argaman, L., Hengge-Aronis, R., Storz, G. EMBO J. (1998) [Pubmed]
  8. Regulation of the Escherichia coli rmf gene encoding the ribosome modulation factor: growth phase- and growth rate-dependent control. Yamagishi, M., Matsushima, H., Wada, A., Sakagami, M., Fujita, N., Ishihama, A. EMBO J. (1993) [Pubmed]
  9. The osmotic stress response and virulence in pyelonephritis isolates of Escherichia coli: contributions of RpoS, ProP, ProU and other systems. Culham, D.E., Lu, A., Jishage, M., Krogfelt, K.A., Ishihama, A., Wood, J.M. Microbiology (Reading, Engl.) (2001) [Pubmed]
  10. The PhoP/PhoQ two-component system stabilizes the alternative sigma factor RpoS in Salmonella enterica. Tu, X., Latifi, T., Bougdour, A., Gottesman, S., Groisman, E.A. Proc. Natl. Acad. Sci. U.S.A. (2006) [Pubmed]
  11. Influence of the RpoS (KatF) sigma factor on maintenance of viability and culturability of Escherichia coli and Salmonella typhimurium in seawater. Munro, P.M., Flatau, G.N., Clément, R.L., Gauthier, M.J. Appl. Environ. Microbiol. (1995) [Pubmed]
  12. Involvement of rpoS in the survival of Escherichia coli in the viable but non-culturable state. Boaretti, M., Lleò, M.M., Bonato, B., Signoretto, C., Canepari, P. Environ. Microbiol. (2003) [Pubmed]
  13. Reduction of acid tolerance by tetracycline in Escherichia coli expressing tetA(C) is reversed by cations. Hung, K.F., Byrd, J.J., Bose, J.L., Kaspar, C.W. Appl. Environ. Microbiol. (2006) [Pubmed]
  14. 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. Tanaka, K., Takayanagi, Y., Fujita, N., Ishihama, A., Takahashi, H. Proc. Natl. Acad. Sci. U.S.A. (1993) [Pubmed]
  15. Hypochlorous acid stress in Escherichia coli: resistance, DNA damage, and comparison with hydrogen peroxide stress. Dukan, S., Touati, D. J. Bacteriol. (1996) [Pubmed]
  16. Decrease in cell viability in an RMF, sigma(38), and OmpC triple mutant of Escherichia coli. Samuel Raj, V., Füll, C., Yoshida, M., Sakata, K., Kashiwagi, K., Ishihama, A., Igarashi, K. Biochem. Biophys. Res. Commun. (2002) [Pubmed]
  17. Functional heterogeneity of RpoS in stress tolerance of enterohemorrhagic Escherichia coli strains. Bhagwat, A.A., Tan, J., Sharma, M., Kothary, M., Low, S., Tall, B.D., Bhagwat, M. Appl. Environ. Microbiol. (2006) [Pubmed]
  18. Inorganic polyphosphate and the induction of rpoS expression. Shiba, T., Tsutsumi, K., Yano, H., Ihara, Y., Kameda, A., Tanaka, K., Takahashi, H., Munekata, M., Rao, N.N., Kornberg, A. Proc. Natl. Acad. Sci. U.S.A. (1997) [Pubmed]
  19. Non-growing Escherichia coli cells starved for glucose or phosphate use different mechanisms to survive oxidative stress. Moreau, P.L., Gérard, F., Lutz, N.W., Cozzone, P. Mol. Microbiol. (2001) [Pubmed]
  20. SigmaS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of sigmaS-dependent genes and identification of their promoter sequences. Lacour, S., Landini, P. J. Bacteriol. (2004) [Pubmed]
  21. Structure of the 5' upstream region and the regulation of the rpoS gene of Escherichia coli. Takayanagi, Y., Tanaka, K., Takahashi, H. Mol. Gen. Genet. (1994) [Pubmed]
  22. Crl stimulates RpoS activity during stationary phase. Pratt, L.A., Silhavy, T.J. Mol. Microbiol. (1998) [Pubmed]
  23. Regulation and mode of action of the second small RNA activator of RpoS translation, RprA. Majdalani, N., Hernandez, D., Gottesman, S. Mol. Microbiol. (2002) [Pubmed]
  24. Paraquat regulation of hmp (flavohemoglobin) gene expression in Escherichia coli K-12 is SoxRS independent but modulated by sigma S. Membrillo-Hernández, J., Kim, S.O., Cook, G.M., Poole, R.K. J. Bacteriol. (1997) [Pubmed]
  25. Role of ppGpp in rpoS stationary-phase regulation in Escherichia coli. Hirsch, M., Elliott, T. J. Bacteriol. (2002) [Pubmed]
  26. Evolution of multi-gene segments in the mutS-rpoS intergenic region of Salmonella enterica serovar Typhimurium LT2. Kotewicz, M.L., Li, B., Levy, D.D., LeClerc, J.E., Shifflet, A.W., Cebula, T.A. Microbiology (Reading, Engl.) (2002) [Pubmed]
  27. RpoS-mediated growth-dependent expression of the Escherichia coli tkt genes encoding transketolases isoenzymes. Jung, I.L., Phyo, K.H., Kim, I.G. Curr. Microbiol. (2005) [Pubmed]
  28. Role of guanosine tetraphosphate in gene expression and the survival of glucose or seryl-tRNA starved cells of Escherichia coli K12. Nystöm, T. Mol. Gen. Genet. (1994) [Pubmed]
  29. Multicellular and aggregative behaviour of Salmonella typhimurium strains is controlled by mutations in the agfD promoter. Römling, U., Sierralta, W.D., Eriksson, K., Normark, S. Mol. Microbiol. (1998) [Pubmed]
  30. The Escherichia coli histone-like protein HU regulates rpoS translation. Balandina, A., Claret, L., Hengge-Aronis, R., Rouviere-Yaniv, J. Mol. Microbiol. (2001) [Pubmed]
  31. Role of rpoS in stress survival and virulence of Vibrio cholerae. Yildiz, F.H., Schoolnik, G.K. J. Bacteriol. (1998) [Pubmed]
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