Maximum rrn promoter activity in Escherichia coli at saturating concentrations of free RNA polymerase

Biochimie

Volumn 92, Issue 1, 2010, Pages 12-20

  Ehrenberg, M ^a   Dennis, P P ^b   Bremer, H ^c  

^a UPPSALA UNIVERSITY   (Sweden)

^b NATIONAL SCIENCE FOUNDATION   (United States)

^c UNIVERSITY OF TEXAS AT DALLAS   (United States)

Author keywords

E. coli; Free RNA polymerase; rrn P1 promoter activity; Transcriptional pausing

Indexed keywords

RIBOSOME RNA; RNA 16S; RNA 23S; RNA POLYMERASE;

ARTICLE; BACTERIAL STRAIN; CELL CYCLE; ELECTRON MICROSCOPY; ESCHERICHIA COLI; GENE DELETION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; NONHUMAN; OPERON; PROMOTER REGION; PROTEIN EXPRESSION; PROTEIN FUNCTION; RIBOSOME; RNA BINDING; RNA SYNTHESIS; RNA TRANSCRIPTION;

DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; KINETICS; PROMOTER REGIONS, GENETIC; RNA, BACTERIAL; RNA, MESSENGER; RNA, RIBOSOMAL; SEQUENCE DELETION;

ESCHERICHIA COLI;

EID: 72049099609     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2009.10.002     Document Type: Article

References (29)

1. Condon C., French S., and Squires C.L. Depletion of functional ribosomal RNA operons in Escherichia coli causes increased expression of the remaining intact copies. EMBO J. 12 (1993) 4305-4315
2. Liang S., Bipatnath M., Xu Y., Chen S., Dennis P., Ehrenberg M., and Bremer H. Activities of constitutive promoters in Escherichia coli. J. Mol. Biol. 292 (1999) 19-37
3. Dennis P.P., Ehrenberg M., and Bremer H. Control of rRNA synthesis in Escherichia coli: a systems biology approach. Microbiol. Mol. Biol. Rev. 68 (2004) 639-668
4. Zhang X., and Bremer H. Effects of Fis on ribosome synthesis and activity and on rRNA promoter activities in Escherichia coli. J. Mol. Biol. 259 (1996) 27-40
5. Quan S., Zhang N., French S., and Squires C.L. Transcriptional polarity in rRNA operons of Escherichia coli nusA and nusB mutant strains. J. Bacteriol. 187 (2005) 1632-1638
6. Dennis P.P., Ehrenberg M., Fange D., and Bremer H. Varying rate of RNA chain elongation during rrn transcription in Escherichia coli. J. Bacteriol. 191 (2009) 3740-3746
7. Klumpp S., and Hwa T. Stochasticity and traffic jams in the transcription of ribosomal RNA: intriguing role of termination and antitermination. Proc. Natl. Acad. Sci. U.S.A. 105 (2008) 18159-18164
8. Epshtein V., and Nudler E. Cooperation between RNA polymerase molecules in transcription elongation. Science 300 (2003) 801-805
9. Bremer H., Dennis P., and Ehrenberg M. Free RNA polymerase and modeling global transcription in Escherichia coli. Biochimie 85 (2003) 597-609
10. H. Bremer, P.P. Dennis, Modulation of chemical composition and other parameters of the cell at different exponential growth rates, in: A. Böck, R. Curtiss III, J.B. Kaper, P.D. Karp, F.C. Neidhardt, T. Nyström, J.M. Slauch, C.L. Squires, D. Ussery (Eds.), EcoSal-Escherichia coli and Salmonella: Cellular and Molecular Biology, http://www.ecosal.org. ASM Press, Washington, DC (posting date 10.07.2008) (Chapter 5.2.3).
11. Record M.T., Reznikoff W.S., Craig M.L., McQuade K.L., and Schlax P. Escherichia coli RNA polymerase Eσ70, promoters, and the kinetics of the steps of transcription initiation. In: Neidhardt F.C. (Ed). Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. second ed. (1996), American Society for Microbiology, Washington, DC 792-821
12. Krummel B., and Chamberlin M.J. RNA chain initiation by Escherichia coli RNA polymerase. Structural transitions of the enzyme in early ternary complexes. Biochemistry 28 (1989) 7829-7842
13. Kubori T., and Shimamoto N. Physical interference between Escherichia coli RNA polymerase molecules transcribing in tandem enhances abortive synthesis and misincorporation. Nucleic Acids Res. 25 (1997) 2640-2647
14. Farnham P.J., and Platt T. Rho-independent termination: dyad symmetry in DNA causes RNA polymerase to pause during transcription in vitro. Nucleic Acids Res. 9 (1981) 563-577
15. Bai L., Shundrovsky A., and Wang M.D. Sequence-dependent kinetic model for transcription elongation by RNA polymerase. J. Mol. Biol. 344 (2004) 335-349
16. Kingston R.E., and Chamberlin M.J. Pausing and attenuation of in vitro transcription in the rrnB operon of E. coli. Cell 27 (1981) 523-531
17. Bai L., Santangelo T.J., and Wang M.D. Single-molecule analysis of RNA polymerase transcription. Annu. Rev. Biophys. Biomol. Struct. 35 (2006) 343-360
18. Dennis P.P. Regulation of stable RNA synthesis in Escherichia coli. Nat. New Biol. 232 (1971) 43-47
19. Dennis P.P. Stable ribonucleic acid synthesis during the cell division cycle in slowly growing Escherichia coli B-r. J. Biol. Chem. 247 (1972) 204-208
20. Shen V., and Bremer H. Rate of ribosomal ribonucleic acid chain elongation in Escherichia coli B/r during chloramphenicol treatment. J. Bacteriol. 130 (1977) 1109-1116
21. Klumpp S., and Hwa T. Growth-rate-dependent partitioning of RNA polymerases in bacteria. Proc. Natl. Acad. Sci. USA 105 (2008) 20245-20250
22. Zhang X., Dennis P., Ehrenberg M., and Bremer H. Kinetic properties of rrn promoters in Escherichia coli. Biochimie 84 (2002) 981-996
23. Nomura M., Bedwell D.M., Yamagishi M., Cole J., and Colb J.M. RNA polymerase regulation of RNA synthesis in Escherichia coli: stringent control and ribosome feedback regulation. In: Reznikoff W.S. (Ed). RNA Polymerase and the Regulation of Transcription: Proceedings of the Sixteenth Steenbock Symposium Held July 13th Through July 17th, 1986, at the University of Wisconsin - Madison, U.S.A. (1987), Elsevier, New York 137-149
24. Gummesson B., Magnusson L., Lovmar M., Persson O., Kvint K., Ballesteros M., Farewell A., and Nyström T. Increased RNA polymerase availability directs resources towards growth at the expense of maintenance. EMBO J. 28 (2009) 2209-2219
25. Vogel U., and Jensen K.F. Effects of the antiterminator boxA on transcription elongation kinetics and ppGpp inhibition of transcription elongation in Escherichia coli. J. Biol. Chem. 270 (1995) 18335-18340
26. Bipatnath M., Dennis P.P., and Bremer H. Initiation and velocity of chromosome replication in Escherichia coli B/r and K-12. J. Bacteriol. 180 (1998) 265-273
27. Michelsen O., Teixeira de Mattos M.J., Jensen P.R., and Hansen F.G. Precise determinations of C and D periods by flow cytometry in Escherichia coli K-12 and B/r. Microbiology (Reading, England) 149 (2003) 1001-1010
28. Liang S.T., Ehrenberg M., Dennis P., and Bremer H. Decay of rplN and lacZ mRNA in Escherichia coli. J. Mol. Biol. 288 (1999) 521-538
29. Bremer H., and Churchward G. An examination of the Cooper-Helmstetter theory of DNA replication in bacteria and its underlying assumptions. J. Theor. Biol. 69 (1977) 645-654