Sequences in the -35 region of Escherichia coli rpoS-dependent genes promote transcription by EσS

Journal of Bacteriology

Volumn 178, Issue 10, 1996, Pages 2785-2793

  Wise, Arlene ^a   Brems, Rory ^a   Ramakrishnan, Vidhya ^a   Villarejo, Merna ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

ARTICLE; BACTERIAL GENE; ESCHERICHIA COLI; GENE SEQUENCE; MOLECULAR RECOGNITION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; PROMOTER REGION; SITE DIRECTED MUTAGENESIS; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

AMINO ACID TRANSPORT SYSTEMS; BACTERIAL PROTEINS; BASE SEQUENCE; BINDING SITES; CARRIER PROTEINS; COENZYMES; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENES, BACTERIAL; GENES, REPORTER; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PERIPLASMIC BINDING PROTEINS; PROMOTER REGIONS (GENETICS); SIGMA FACTOR; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0029935116     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.178.10.2785-2793.1996     Document Type: Article

References (67)

1. Aldea, M., T. Garrido, C. Hernandez-Chico, M. Vicente, and S. R. Kushner. 1989. Induction of a growth-phase-dependent promoter triggers transcription of bolA, an Escherichia coli morphogene. EMBO J. 8:3923-3931.
2. S in stationary phase. Mol. Microbiol. 13:265-272.
3. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (ed). 1992. Short protocols in molecular biology, 2nd ed. John Wiley and Sons, Inc., New York.
4. S-dependent genes in Escherichia coli. J. Bacteriol. 177:3455-3464.
5. S-dependent genes in Escherichia coli. J. Bacteriol. 177:413-422.
6. Cairney, J., I. R. Booth, and C. F. Higgins. 1985. Osmoregulation of gene expression in Salmonella typhimurium: proU encodes an osmotically induced betaine transport system. J. Bacteriol. 164:1224-1232.
7. Casadaban, M. 1976. Transposition and fusion of the lac genes to selected promoters in Escherichia coli using bacteriophage, lambda and Mu. J. Mol. Biol. 104:541-555.
8. Chan, B., and S. Busby. 1989. Recognition of nucleotide sequences at the Escherichia coli galactose operon P1 promoter by RNA polymerase. Gene 84:227-236.
9. Chang, Y.-Y., A.-Y. Wang, and J. E. Cronan, Jr. 1994. Expression of Escherichia coli pyruvate oxidase (poxB) depends on the sigma factor encoded by the rpoS (katF) gene. Mol. Microbiol. 11:1019-1028.
10. Cowing, D. W., J. C. A. Bardwell, E. A. Craig, C. Woolford, R. W. Hendrix, and C. A. Gross. 1985. Consensus sequences for Escherichia coli heat shock gene promoters. Proc. Natl. Acad. Sci. USA 82:2679-2683.
11. Culham, D. E., B. Lasby, A. G. Marangoni, J. L. Milner, B. A. Steer, R. W. van Nues, and J. M. Woods. 1993. Isolation and sequencing of Escherichia coli gene proP reveals unusual structural features of the osmoregulatory proline/betaine transporter, ProP. J. Mol. Biol. 229:268-276.
12. Dattananda, C. S., K. Rajkumari, and J. Gowrishankar. 1991. Multiple mechanisms contribute to osmotic inducibility of prof operon expression in Escherichia coli: demonstration of two osmoresponsive promoters and of a negative regulatory element within the first structural gene. J. Bacteriol. 173:7481-7490.
13. S holoenzymes. Mol. Microbiol. 16:649-656.
14. Elliott, T. 1992. A method for constructing single-copy lac fusions in Salmonella typhimurium and its application to the hemA-prfA operon. J. Bacteriol. 174:245-253.
15. Gardella, T., H. Moyle, and M. M. Susskind. 1989. A mutant Escherichia coli sigma-70 subunit of RNA polymerase with altered promoter specificity. J. Mol. Biol. 206:579-590.
16. S is positively regulated by ppGpp. J. Bacteriol. 175:7982-7989.
17. Gowrishankar, J. 1985. Identification of osmoresponsive genes in Escherichia coli: evidence of participation of potassium and proline transport systems in osmoregulation. J. Bacteriol. 164:434-445.
18. Gowrishankar, J. 1989. Nucleotide sequence of the osmoregulatory genes of Escherichia coli. J. Bacteriol. 171:1923-1931.
19. Harley, C. B., and R. P. Reynolds. 1987. Analysis of E. coli promoter sequences. Nucleic Acids Res. 15:2343-2358.
20. Hawley, D. K., and W. R. McClure. 1983. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 11:2237-2255.
21. Helmann, J. D., and M. J. Chamberlin. 1988. Structure and function of bacterial sigma factors. Annu. Rev. Biochem. 57:839-872.
22. Hengge-Aronis, R. 1993. Survival of hunger and stress: the role of rpoS in early stationary phase gene regulation in Escherichia coli. Cell 72:165-168.
23. Hengge-Aronis, R., and D. Fisher. 1992. Identification and molecular analysis of glgS, a novel growth-phase regulated and rpoS-dependent gene involved in glycogen synthesis in Escherichia coli. Mol. Microbiol. 6:1877-1886.
24. Hengge-Aronis, R., W. Klein, R. Lange, M. Rimmele, and W. Boos. 1991. 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. 173:7918-7924.
25. Hengge-Aronis, R., R. Lange, N. Hennenberg, and D. Fischer. 1993. Osmotic regulation of rpoS-dependent genes in Escherichia coli. J. Bacteriol. 175:259-265.
26. Holmes, D. S., and M. Quigley. 1981. A rapid boiling method for the preparation of bacterial plasmids. Anal. Biochem. 114:193-197.
27. Huisman, G., and R. Kolter. 1994. Sensing starvation: a homoserine lactone dependent signaling pathway in Escherichia coli. Science 265:537-539.
28. Innes, M. A., D. H. Gelfand, J. J. Sninsky, and T. J. White. 1990. PCR protocols: a guide to methods and applications. Academic Press, New York.
29. Jovanovich, S. B., M. T. Record, Jr., and R. R. Burgess. 1989. In an Escherichia coli coupled transcription-translation system, expression of the osmoregulated gene proU is stimulated at elevated potassium concentrations and by an extract from cells grown at high osmolality. J. Biol. Chem. 264:7821-7825.
30. Jung, J. U., C. Gutierrez, F. Martin, M. Ardourel, and M. Villarejo. 1990. Transcription of osmB, a gene encoding an Escherichia coli lipoprotein, is regulated by dual signals: osmotic stress and stationary phase. J. Biol. Chem. 262:10574-10581.
31. Keilty, S., and M. Rosenberg. 1987. Constitutive function of a positively regulated promoter reveals new sequences essential for activity. J. Biol. Chem. 262:6389-6395.
32. Kobayashi, M., K. Nagata, and A. Ishihama. 1990. Promoter selectivity of Escherichia coli RNA polymerase: effect of base substitutions in the promoter -35 region on promoter strength. Nucleic Acids Res. 18:7367-7372.
33. Kunkel, T. A. 1985. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc. Natl. Acad. Sci. USA 82:488-492.
34. 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. 175:7910-7917.
35. S. J. Bacteriol. 173:4474-4481.
36. Lange, R., and R. Hengge-Aronis. 1991. Identification of a central regulator of stationary-phase gene expression in Escherichia coli. Mol. Microbiol. 5:49-59.
37. Lange, R., and R. Hengge-Aronis. 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. 8:1600-1612.
38. Lomovskaya, O. L., J. P. Kidwell, and A. Matin. 1994. Characterization of the sigma-38 dependent expression of a core Escherichia coli starvation gene, pexB. J. Bacteriol. 176:3928-3935.
39. Lonetto, M., M. Gribakov, and C. A. Gross. 1992. The sigma-70 family: sequence conservation and evolutionary relationships. J. Bacteriol. 174: 3843-3849.
40. Lowry, O. H., N. J. Rosebrough, A. L. Farr, and R. J. Randall. 1951. Protein measurement with the Folin phenol reagent. J. Biol. Chem. 193:265-275.
41. Manna, D., and J. Gowrishankar. 1994. Evidence for involvement of proteins HU and RpoS in transcription of the osmoresponsive proU operon in Escherichia coli. J. Bacteriol. 176:5378-5384.
42. May, G., E. Faatz, J. M. Lucht, M. Haardt, M. Bollinger, and E. Bremmer. 1989. Characterization of the osmoregulated Escherichia coli proU promoter and identification of ProV as a membrane-associated protein. Mol. Microbiol. 3:1521-1531.
43. May, G., E. Faatz, M. Villarejo, and E. Bremer. 1986. Binding protein-dependent transport of glycine betaine and its osmotic regulation in Escherichia coli K-12. Mol. Gen. Genet. 205:225-233.
44. Melies, J., R. Brems, and M. Villarejo. 1994. The Escherichia coli proU promoter element and its contribution to osmotically-signaled transcription activation. J. Bacteriol. 176:3638-3645.
45. Melies, J., A. Wise, and M. Villarejo. 1995. Two different Escherichia coli proP promoters respond to osmotic and growth phase signals. J. Bacteriol. 177:144-151,
46. Miller, J. H. 1972. Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
47. Mulvej, M. R., and P. C. Loewen. 1989. Nucleotide sequence of katF of Escherichia coli suggests katF protein is a novel transcription factor. Nucleic Acids Res. 17:9979-9991.
48. Nguyen, L., D. Jensen, N. Thompson, D. Gentry, and R. Burgess. 1993. In vitro functional characterization of overproduced Escherichia coli katF/rpoS gene product. Biochemistry 32:11112-11117.
49. Prince, B. 1991. Osmoregulated transcription of the proU operon of Escherichia coli. Ph.D. thesis. University of California, Davis.
50. Saporito, S. M., B. J. Smith-White, and R. P. Cunningham. 1988. Nucleotide sequence of the ah gene of Escherichia coli K-12. J. Bacteriol. 170:4542-4547.
51. Shaw, W. V. 1975. Chloramphenicol acetyltransferase from chloramphenicol-resistant bacteria. Methods Enzymol. 43:737-755.
52. Siegele, D. A., J. C. Hu, W. A. Walter, and C. A. Gross. 1989. Altered promoter recognition by mutant forms of the sigma-70 subunit of Escherichia coli RNA polymerase. J. Mol. Biol. 206:591-603.
53. Silhavy, T. J., M. L. Berman, and L. W. Enquist. 1984. Experiments with gene fusions. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
54. Simons, R. W., F. Houman, and N. Kleckner. 1987. Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene 53:85-96.
55. Szoke, P. A., T. L. Allen, and P. L. DeHaseth. 1987. Promoter recognition by Escherichia coli RNA polymerase: effects of base substitutions in the -10 and -35 regions. Biochemistry 26:6188-6194.
56. Tanaka, K., S. Kusano, N. Fujita, A. Ishihama, and H. Takahashi. 1995. Promoter determinants for Escherichia coli RNA polymerase containing sigma-38 (the rpoS gene product). Nucleic Acids Res. 23:827-834.
57. 38, is a second principal a factor of RNA polymerase in stationary-phase Escherichia coli. Proc. Natl. Acad. Sci. USA 90:3511-3515.
58. Utsami, R., S. Kusafuka, T. Nakayama, K. Tanaka, Y. Takayanagi, H. Takahashi, M. Noda, and M. Kawamukai. 1993. Stationary-phase-specific expression of the fic gene in Escherichia coli K-12 is controlled by the rpoS gene product (sigma-38). FEMS Microbiol. Lett. 113:273-278.
59. Waldburger, C., T. Gardella, R. Wong, and M. M. Susskind. 1990. Changes in conserved region 2 of Escherichia coli sigma-70 affecting promoter recognition. J. Mol. Biol. 215:267-276.
60. Wang, A.-Y., and J. E. Cronan. 1994. The growth phase-dependent synthesis of cyclopropane fatty acids in Escherichia coli is the result of an RpoS (KatF)-dependent promoter plus enzyme instability. Mol. Microbiol. 11: 1009-1017.
61. Weichart, D., R. Lange, N. Henneberg, and R. Hengge-Aronis. 1993. Identification and characterization of stationary phase-inducible genes in Escherichia coli. Mol. Microbiol. 10:407-420.
62. Xu, J., and R. C. Johnson. 1995. aldB, an RpoS-dependent gene in Escherichia coli encoding an aldehyde dehydrogenase that is repressed by Fis and activated by Crp. J. Bacteriol. 177:3166-3175.
63. S, in Escherichia coli: involvement of the nucleoid protein H-NS. EMBO J. 14:594-602.
64. Yim, H. H., R. L. Brems, and M. Villarejo. 1994. Molecular characterization of the promoter of osmY, an rpoS-dependent gene. J. Bacteriol. 176:100-107.
65. Yim, H. H., and M. Villarejo. 1992. osmY, a new hyperosmotically inducible gene, encodes a periplasmic protein of Escherichia coli. J. Bacteriol. 174: 3637-3644.
66. Youderian, P., S. Bouvier, and M. M. Susskind. 1982. Sequence determinants of promoter activity. Cell 30:843-853.
67. E and Pseudomonas aeruginosa AlgU: E. coli rpoE restores mucoidy and reduces sensitivity to reactive oxygen intermediates in algU mutants of P. aeruginosa. J. Bacteriol. 177:3259-3268.