Abstract
The sigma S subunit of RNA polymerase (encoded by the rpoS gene) is the master regulator in a complex regulatory network that controls stationary-phase induction and osmotic regulation of many genes in Escherichia coli. Here we demonstrate that the histone-like protein H-NS is also a component of this network, in which it functions as a global inhibitor of gene expression during the exponential phase of growth. On two-dimensional gels, at least 22 sigma S-controlled proteins show increased expression in an hns mutant. H-NS also inhibits the expression of sigma S itself by a mechanism that acts at the posttranscriptional level. Our results indicate that relief of repression by H-NS plays a role in stationary-phase induction as well as in hyperosmotic induction of rpoS translation. Whereas certain sigma S-dependent genes (e.g., osmY) are only indirectly regulated by H-NS via its role in the control of sigma S expression, others are also H-NS-regulated in a sigma S-independent manner. (For this latter class of genes, rpoS hns double mutants show higher levels of expression than mutants deficient in rpoS alone.) In addition, we demonstrate that the slow-growth phenotype of hns mutants is suppressed in hns rpoS double mutants and that many second-site suppressor mutants that spontaneously arise from hns strains carry lesions that affect the expression of sigma S.
Full Text
The Full Text of this article is available as a PDF (565.7 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Altuvia S., Almirón M., Huisman G., Kolter R., Storz G. The dps promoter is activated by OxyR during growth and by IHF and sigma S in stationary phase. Mol Microbiol. 1994 Jul;13(2):265–272. doi: 10.1111/j.1365-2958.1994.tb00421.x. [DOI] [PubMed] [Google Scholar]
- Arnqvist A., Olsén A., Normark S. Sigma S-dependent growth-phase induction of the csgBA promoter in Escherichia coli can be achieved in vivo by sigma 70 in the absence of the nucleoid-associated protein H-NS. Mol Microbiol. 1994 Sep;13(6):1021–1032. doi: 10.1111/j.1365-2958.1994.tb00493.x. [DOI] [PubMed] [Google Scholar]
- Atlung T., Brøndsted L. Role of the transcriptional activator AppY in regulation of the cyx appA operon of Escherichia coli by anaerobiosis, phosphate starvation, and growth phase. J Bacteriol. 1994 Sep;176(17):5414–5422. doi: 10.1128/jb.176.17.5414-5422.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bertin P., Lejeune P., Laurent-Winter C., Danchin A. Mutations in bglY, the structural gene for the DNA-binding protein H1, affect expression of several Escherichia coli genes. Biochimie. 1990 Dec;72(12):889–891. doi: 10.1016/0300-9084(90)90008-5. [DOI] [PubMed] [Google Scholar]
- Brøndsted L., Atlung T. Anaerobic regulation of the hydrogenase 1 (hya) operon of Escherichia coli. J Bacteriol. 1994 Sep;176(17):5423–5428. doi: 10.1128/jb.176.17.5423-5428.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Dassa J., Fsihi H., Marck C., Dion M., Kieffer-Bontemps M., Boquet P. L. A new oxygen-regulated operon in Escherichia coli comprises the genes for a putative third cytochrome oxidase and for pH 2.5 acid phosphatase (appA) Mol Gen Genet. 1991 Oct;229(3):341–352. doi: 10.1007/BF00267454. [DOI] [PubMed] [Google Scholar]
- Dersch P., Kneip S., Bremer E. The nucleoid-associated DNA-binding protein H-NS is required for the efficient adaptation of Escherichia coli K-12 to a cold environment. Mol Gen Genet. 1994 Oct 28;245(2):255–259. doi: 10.1007/BF00283274. [DOI] [PubMed] [Google Scholar]
- Dersch P., Schmidt K., Bremer E. Synthesis of the Escherichia coli K-12 nucleoid-associated DNA-binding protein H-NS is subjected to growth-phase control and autoregulation. Mol Microbiol. 1993 May;8(5):875–889. doi: 10.1111/j.1365-2958.1993.tb01634.x. [DOI] [PubMed] [Google Scholar]
- Giaever H. M., Styrvold O. B., Kaasen I., Strøm A. R. Biochemical and genetic characterization of osmoregulatory trehalose synthesis in Escherichia coli. J Bacteriol. 1988 Jun;170(6):2841–2849. doi: 10.1128/jb.170.6.2841-2849.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Harrison J. A., Pickard D., Higgins C. F., Khan A., Chatfield S. N., Ali T., Dorman C. J., Hormaeche C. E., Dougan G. Role of hns in the virulence phenotype of pathogenic salmonellae. Mol Microbiol. 1994 Jul;13(1):133–140. doi: 10.1111/j.1365-2958.1994.tb00408.x. [DOI] [PubMed] [Google Scholar]
- Hengge-Aronis R., Fischer D. Identification and molecular analysis of glgS, a novel growth-phase-regulated and rpoS-dependent gene involved in glycogen synthesis in Escherichia coli. Mol Microbiol. 1992 Jul;6(14):1877–1886. doi: 10.1111/j.1365-2958.1992.tb01360.x. [DOI] [PubMed] [Google Scholar]
- Hengge-Aronis R., Klein W., Lange R., Rimmele M., Boos W. Trehalose synthesis genes are controlled by the putative sigma factor encoded by rpoS and are involved in stationary-phase thermotolerance in Escherichia coli. J Bacteriol. 1991 Dec;173(24):7918–7924. doi: 10.1128/jb.173.24.7918-7924.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hengge-Aronis R., Lange R., Henneberg N., Fischer D. Osmotic regulation of rpoS-dependent genes in Escherichia coli. J Bacteriol. 1993 Jan;175(1):259–265. doi: 10.1128/jb.175.1.259-265.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hengge-Aronis R. Survival of hunger and stress: the role of rpoS in early stationary phase gene regulation in E. coli. Cell. 1993 Jan 29;72(2):165–168. doi: 10.1016/0092-8674(93)90655-a. [DOI] [PubMed] [Google Scholar]
- Higgins C. F., Dorman C. J., Stirling D. A., Waddell L., Booth I. R., May G., Bremer E. A physiological role for DNA supercoiling in the osmotic regulation of gene expression in S. typhimurium and E. coli. Cell. 1988 Feb 26;52(4):569–584. doi: 10.1016/0092-8674(88)90470-9. [DOI] [PubMed] [Google Scholar]
- Higgins C. F., Hinton J. C., Hulton C. S., Owen-Hughes T., Pavitt G. D., Seirafi A. Protein H1: a role for chromatin structure in the regulation of bacterial gene expression and virulence? Mol Microbiol. 1990 Dec;4(12):2007–2012. doi: 10.1111/j.1365-2958.1990.tb00559.x. [DOI] [PubMed] [Google Scholar]
- Kaasen I., Falkenberg P., Styrvold O. B., Strøm A. R. Molecular cloning and physical mapping of the otsBA genes, which encode the osmoregulatory trehalose pathway of Escherichia coli: evidence that transcription is activated by katF (AppR) J Bacteriol. 1992 Feb;174(3):889–898. doi: 10.1128/jb.174.3.889-898.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lange R., Barth M., Hengge-Aronis R. Complex transcriptional control of the sigma s-dependent stationary-phase-induced and osmotically regulated osmY (csi-5) gene suggests novel roles for Lrp, cyclic AMP (cAMP) receptor protein-cAMP complex, and integration host factor in the stationary-phase response of Escherichia coli. J Bacteriol. 1993 Dec;175(24):7910–7917. doi: 10.1128/jb.175.24.7910-7917.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lange R., Hengge-Aronis R. Growth phase-regulated expression of bolA and morphology of stationary-phase Escherichia coli cells are controlled by the novel sigma factor sigma S. J Bacteriol. 1991 Jul;173(14):4474–4481. doi: 10.1128/jb.173.14.4474-4481.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lange R., Hengge-Aronis R. Identification of a central regulator of stationary-phase gene expression in Escherichia coli. Mol Microbiol. 1991 Jan;5(1):49–59. doi: 10.1111/j.1365-2958.1991.tb01825.x. [DOI] [PubMed] [Google Scholar]
- Lange R., Hengge-Aronis R. 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. 1994 Jul 1;8(13):1600–1612. doi: 10.1101/gad.8.13.1600. [DOI] [PubMed] [Google Scholar]
- Lejeune P., Danchin A. Mutations in the bglY gene increase the frequency of spontaneous deletions in Escherichia coli K-12. Proc Natl Acad Sci U S A. 1990 Jan;87(1):360–363. doi: 10.1073/pnas.87.1.360. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Loewen P. C., von Ossowski I., Switala J., Mulvey M. R. KatF (sigma S) synthesis in Escherichia coli is subject to posttranscriptional regulation. J Bacteriol. 1993 Apr;175(7):2150–2153. doi: 10.1128/jb.175.7.2150-2153.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lomovskaya O. L., Kidwell J. P., Matin A. Characterization of the sigma 38-dependent expression of a core Escherichia coli starvation gene, pexB. J Bacteriol. 1994 Jul;176(13):3928–3935. doi: 10.1128/jb.176.13.3928-3935.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lucht J. M., Dersch P., Kempf B., Bremer E. Interactions of the nucleoid-associated DNA-binding protein H-NS with the regulatory region of the osmotically controlled proU operon of Escherichia coli. J Biol Chem. 1994 Mar 4;269(9):6578–6578. [PubMed] [Google Scholar]
- Matin A. The molecular basis of carbon-starvation-induced general resistance in Escherichia coli. Mol Microbiol. 1991 Jan;5(1):3–10. doi: 10.1111/j.1365-2958.1991.tb01819.x. [DOI] [PubMed] [Google Scholar]
- McCann M. P., Fraley C. D., Matin A. The putative sigma factor KatF is regulated posttranscriptionally during carbon starvation. J Bacteriol. 1993 Apr;175(7):2143–2149. doi: 10.1128/jb.175.7.2143-2149.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Mellies J., Brems R., Villarejo M. The Escherichia coli proU promoter element and its contribution to osmotically signaled transcription activation. J Bacteriol. 1994 Jun;176(12):3638–3645. doi: 10.1128/jb.176.12.3638-3645.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Mulvey M. R., Switala J., Borys A., Loewen P. C. Regulation of transcription of katE and katF in Escherichia coli. J Bacteriol. 1990 Dec;172(12):6713–6720. doi: 10.1128/jb.172.12.6713-6720.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Nguyen L. H., Jensen D. B., Thompson N. E., Gentry D. R., Burgess R. R. In vitro functional characterization of overproduced Escherichia coli katF/rpoS gene product. Biochemistry. 1993 Oct 19;32(41):11112–11117. doi: 10.1021/bi00092a021. [DOI] [PubMed] [Google Scholar]
- O'Farrell P. H. High resolution two-dimensional electrophoresis of proteins. J Biol Chem. 1975 May 25;250(10):4007–4021. [PMC free article] [PubMed] [Google Scholar]
- Olsén A., Arnqvist A., Hammar M., Sukupolvi S., Normark S. The RpoS sigma factor relieves H-NS-mediated transcriptional repression of csgA, the subunit gene of fibronectin-binding curli in Escherichia coli. Mol Microbiol. 1993 Feb;7(4):523–536. doi: 10.1111/j.1365-2958.1993.tb01143.x. [DOI] [PubMed] [Google Scholar]
- Owen-Hughes T. A., Pavitt G. D., Santos D. S., Sidebotham J. M., Hulton C. S., Hinton J. C., Higgins C. F. The chromatin-associated protein H-NS interacts with curved DNA to influence DNA topology and gene expression. Cell. 1992 Oct 16;71(2):255–265. doi: 10.1016/0092-8674(92)90354-f. [DOI] [PubMed] [Google Scholar]
- Schellhorn H. E., Stones V. L. Regulation of katF and katE in Escherichia coli K-12 by weak acids. J Bacteriol. 1992 Jul;174(14):4769–4776. doi: 10.1128/jb.174.14.4769-4776.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Spassky A., Rimsky S., Garreau H., Buc H. H1a, an E. coli DNA-binding protein which accumulates in stationary phase, strongly compacts DNA in vitro. Nucleic Acids Res. 1984 Jul 11;12(13):5321–5340. doi: 10.1093/nar/12.13.5321. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Styrvold O. B., Strøm A. R. Synthesis, accumulation, and excretion of trehalose in osmotically stressed Escherichia coli K-12 strains: influence of amber suppressors and function of the periplasmic trehalase. J Bacteriol. 1991 Feb;173(3):1187–1192. doi: 10.1128/jb.173.3.1187-1192.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Takayanagi Y., Tanaka K., Takahashi H. Structure of the 5' upstream region and the regulation of the rpoS gene of Escherichia coli. Mol Gen Genet. 1994 Jun 3;243(5):525–531. doi: 10.1007/BF00284200. [DOI] [PubMed] [Google Scholar]
- Tanaka K., Takayanagi Y., Fujita N., Ishihama A., Takahashi H. 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. 1993 Apr 15;90(8):3511–3515. doi: 10.1073/pnas.90.8.3511. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tupper A. E., Owen-Hughes T. A., Ussery D. W., Santos D. S., Ferguson D. J., Sidebotham J. M., Hinton J. C., Higgins C. F. The chromatin-associated protein H-NS alters DNA topology in vitro. EMBO J. 1994 Jan 1;13(1):258–268. doi: 10.1002/j.1460-2075.1994.tb06256.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ueguchi C., Mizuno T. The Escherichia coli nucleoid protein H-NS functions directly as a transcriptional repressor. EMBO J. 1993 Mar;12(3):1039–1046. doi: 10.1002/j.1460-2075.1993.tb05745.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Weichart D., Lange R., Henneberg N., Hengge-Aronis R. Identification and characterization of stationary phase-inducible genes in Escherichia coli. Mol Microbiol. 1993 Oct;10(2):407–420. [PubMed] [Google Scholar]
- Yamada H., Yoshida T., Tanaka K., Sasakawa C., Mizuno T. Molecular analysis of the Escherichia coli hns gene encoding a DNA-binding protein, which preferentially recognizes curved DNA sequences. Mol Gen Genet. 1991 Nov;230(1-2):332–336. doi: 10.1007/BF00290685. [DOI] [PubMed] [Google Scholar]
- Yamashino T., Ueguchi C., Mizuno T. Quantitative control of the stationary phase-specific sigma factor, sigma S, in Escherichia coli: involvement of the nucleoid protein H-NS. EMBO J. 1995 Feb 1;14(3):594–602. doi: 10.1002/j.1460-2075.1995.tb07035.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Yim H. H., Brems R. L., Villarejo M. Molecular characterization of the promoter of osmY, an rpoS-dependent gene. J Bacteriol. 1994 Jan;176(1):100–107. doi: 10.1128/jb.176.1.100-107.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Yoshida T., Ueguchi C., Yamada H., Mizuno T. Function of the Escherichia coli nucleoid protein, H-NS: molecular analysis of a subset of proteins whose expression is enhanced in a hns deletion mutant. Mol Gen Genet. 1993 Feb;237(1-2):113–122. doi: 10.1007/BF00282791. [DOI] [PubMed] [Google Scholar]
- Zuber F., Kotlarz D., Rimsky S., Buc H. Modulated expression of promoters containing upstream curved DNA sequences by the Escherichia coli nucleoid protein H-NS. Mol Microbiol. 1994 Apr;12(2):231–240. doi: 10.1111/j.1365-2958.1994.tb01012.x. [DOI] [PubMed] [Google Scholar]