• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of jbacterPermissionsJournals.ASM.orgJournalJB ArticleJournal InfoAuthorsReviewers
J Bacteriol. Sep 1994; 176(17): 5560–5564.
PMCID: PMC196750

Growth rate-dependent control of the rrnB P1 core promoter in Escherichia coli.

Abstract

We have extended our previous studies of the DNA sequences required for growth rate-dependent control of rRNA transcription in Escherichia coli. Utilizing a reporter system suitable for evaluation of promoters with low activities, we have found that the core promoter region of rrnB P1 (-41 to +1 with respect to the transcription initiation site) is sufficient for growth rate-dependent control of transcription, both in the presence and in the absence of guanosine 3'-diphosphate 5'-diphosphate (ppGpp). The core promoter contains the -10 and -35 hexamers for recognition by the sigma 70 subunit of RNA polymerase but lacks the upstream (UP) element, which increases transcription by interacting with the alpha subunit of RNA polymerase. It also lacks the binding sites for the positive transcription factor FIS. Thus, the UP element, FIS, and ppGpp are not needed for growth rate-dependent regulation of rRNA transcription. In addition, we find that several core promoter mutations, including -10 and -35 hexamer substitutions, severely reduce rrnB P1 activity without affecting growth rate-dependent control. Thus, a high activity is not a determinant of growth rate regulation of rRNA transcription.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (955K), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Ball CA, Osuna R, Ferguson KC, Johnson RC. Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J Bacteriol. 1992 Dec;174(24):8043–8056. [PMC free article] [PubMed]
  • Baracchini E, Bremer H. Stringent and growth control of rRNA synthesis in Escherichia coli are both mediated by ppGpp. J Biol Chem. 1988 Feb 25;263(6):2597–2602. [PubMed]
  • Baracchini E, Bremer H. Control of rRNA synthesis in Escherichia coli at increased rrn gene dosage. Role of guanosine tetraphosphate and ribosome feedback. J Biol Chem. 1991 Jun 25;266(18):11753–11760. [PubMed]
  • Cole JR, Olsson CL, Hershey JW, Grunberg-Manago M, Nomura M. Feedback regulation of rRNA synthesis in Escherichia coli. Requirement for initiation factor IF2. J Mol Biol. 1987 Dec 5;198(3):383–392. [PubMed]
  • Condon C, French S, Squires C, Squires CL. Depletion of functional ribosomal RNA operons in Escherichia coli causes increased expression of the remaining intact copies. EMBO J. 1993 Nov;12(11):4305–4315. [PMC free article] [PubMed]
  • Dickson RR, Gaal T, deBoer HA, deHaseth PL, Gourse RL. Identification of promoter mutants defective in growth-rate-dependent regulation of rRNA transcription in Escherichia coli. J Bacteriol. 1989 Sep;171(9):4862–4870. [PMC free article] [PubMed]
  • Dombroski AJ, Walter WA, Record MT, Jr, Siegele DA, Gross CA. Polypeptides containing highly conserved regions of transcription initiation factor sigma 70 exhibit specificity of binding to promoter DNA. Cell. 1992 Aug 7;70(3):501–512. [PubMed]
  • Gaal T, Barkei J, Dickson RR, deBoer HA, deHaseth PL, Alavi H, Gourse RL. Saturation mutagenesis of an Escherichia coli rRNA promoter and initial characterization of promoter variants. J Bacteriol. 1989 Sep;171(9):4852–4861. [PMC free article] [PubMed]
  • Gaal T, Gourse RL. Guanosine 3'-diphosphate 5'-diphosphate is not required for growth rate-dependent control of rRNA synthesis in Escherichia coli. Proc Natl Acad Sci U S A. 1990 Jul;87(14):5533–5537. [PMC free article] [PubMed]
  • Gaal T, Rao L, Estrem ST, Yang J, Wartell RM, Gourse RL. Localization of the intrinsically bent DNA region upstream of the E.coli rrnB P1 promoter. Nucleic Acids Res. 1994 Jun 25;22(12):2344–2350. [PMC free article] [PubMed]
  • Gosink KK, Ross W, Leirmo S, Osuna R, Finkel SE, Johnson RC, Gourse RL. DNA binding and bending are necessary but not sufficient for Fis-dependent activation of rrnB P1. J Bacteriol. 1993 Mar;175(6):1580–1589. [PMC free article] [PubMed]
  • Gourse RL, de Boer HA, Nomura M. DNA determinants of rRNA synthesis in E. coli: growth rate dependent regulation, feedback inhibition, upstream activation, antitermination. Cell. 1986 Jan 17;44(1):197–205. [PubMed]
  • Gourse RL, Stark MJ, Dahlberg AE. Regions of DNA involved in the stringent control of plasmid-encoded rRNA in vivo. Cell. 1983 Apr;32(4):1347–1354. [PubMed]
  • Gourse RL, Takebe Y, Sharrock RA, Nomura M. Feedback regulation of rRNA and tRNA synthesis and accumulation of free ribosomes after conditional expression of rRNA genes. Proc Natl Acad Sci U S A. 1985 Feb;82(4):1069–1073. [PMC free article] [PubMed]
  • Hernandez VJ, Bremer H. Guanosine tetraphosphate (ppGpp) dependence of the growth rate control of rrnB P1 promoter activity in Escherichia coli. J Biol Chem. 1990 Jul 15;265(20):11605–11614. [PubMed]
  • Hernandez VJ, Bremer H. Characterization of RNA and DNA synthesis in Escherichia coli strains devoid of ppGpp. J Biol Chem. 1993 May 25;268(15):10851–10862. [PubMed]
  • Jensen KF, Pedersen S. Metabolic growth rate control in Escherichia coli may be a consequence of subsaturation of the macromolecular biosynthetic apparatus with substrates and catalytic components. Microbiol Rev. 1990 Jun;54(2):89–100. [PMC free article] [PubMed]
  • Jinks-Robertson S, Gourse RL, Nomura M. Expression of rRNA and tRNA genes in Escherichia coli: evidence for feedback regulation by products of rRNA operons. Cell. 1983 Jul;33(3):865–876. [PubMed]
  • Josaitis CA, Gaal T, Ross W, Gourse RL. Sequences upstream of the-35 hexamer of rrnB P1 affect promoter strength and upstream activation. Biochim Biophys Acta. 1990 Aug 27;1050(1-3):307–311. [PubMed]
  • Newlands JT, Josaitis CA, Ross W, Gourse RL. Both fis-dependent and factor-independent upstream activation of the rrnB P1 promoter are face of the helix dependent. Nucleic Acids Res. 1992 Feb 25;20(4):719–726. [PMC free article] [PubMed]
  • Nilsson L, Verbeek H, Vijgenboom E, van Drunen C, Vanet A, Bosch L. FIS-dependent trans activation of stable RNA operons of Escherichia coli under various growth conditions. J Bacteriol. 1992 Feb;174(3):921–929. [PMC free article] [PubMed]
  • Nomura M, Gourse R, Baughman G. Regulation of the synthesis of ribosomes and ribosomal components. Annu Rev Biochem. 1984;53:75–117. [PubMed]
  • Rao L, Ross W, Appleman JA, Gaal T, Leirmo S, Schlax PJ, Record MT, Jr, Gourse RL. Factor independent activation of rrnB P1. An "extended" promoter with an upstream element that dramatically increases promoter strength. J Mol Biol. 1994 Feb 4;235(5):1421–1435. [PubMed]
  • Ross W, Gosink KK, Salomon J, Igarashi K, Zou C, Ishihama A, Severinov K, Gourse RL. A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science. 1993 Nov 26;262(5138):1407–1413. [PubMed]
  • Ross W, Thompson JF, Newlands JT, Gourse RL. E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivo. EMBO J. 1990 Nov;9(11):3733–3742. [PMC free article] [PubMed]
  • Ryals J, Little R, Bremer H. Control of rRNA and tRNA syntheses in Escherichia coli by guanosine tetraphosphate. J Bacteriol. 1982 Sep;151(3):1261–1268. [PMC free article] [PubMed]
  • Sarmientos P, Cashel M. Carbon starvation and growth rate-dependent regulation of the Escherichia coli ribosomal RNA promoters: differential control of dual promoters. Proc Natl Acad Sci U S A. 1983 Nov;80(22):7010–7013. [PMC free article] [PubMed]
  • Sarmientos P, Sylvester JE, Contente S, Cashel M. Differential stringent control of the tandem E. coli ribosomal RNA promoters from the rrnA operon expressed in vivo in multicopy plasmids. Cell. 1983 Apr;32(4):1337–1346. [PubMed]
  • Schreiber G, Metzger S, Aizenman E, Roza S, Cashel M, Glaser G. Overexpression of the relA gene in Escherichia coli. J Biol Chem. 1991 Feb 25;266(6):3760–3767. [PubMed]
  • Simons RW, Houman F, Kleckner N. Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene. 1987;53(1):85–96. [PubMed]
  • Xiao H, Kalman M, Ikehara K, Zemel S, Glaser G, Cashel M. Residual guanosine 3',5'-bispyrophosphate synthetic activity of relA null mutants can be eliminated by spoT null mutations. J Biol Chem. 1991 Mar 25;266(9):5980–5990. [PubMed]
  • Yamagishi M, de Boer HA, Nomura M. Feedback regulation of rRNA synthesis. A mutational alteration in the anti-Shine-Dalgarno region of the 16 S rRNA gene abolishes regulation. J Mol Biol. 1987 Dec 5;198(3):547–550. [PubMed]
  • Zacharias M, Göringer HU, Wagner R. Analysis of the Fis-dependent and Fis-independent transcription activation mechanisms of the Escherichia coli ribosomal RNA P1 promoter. Biochemistry. 1992 Mar 10;31(9):2621–2628. [PubMed]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...