Free RNA polymerase and modeling global transcription in Escherichia coli

Biochimie

Volumn 85, Issue 6, 2003, Pages 597-609

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

^a UPPSALA UNIVERSITY   (Sweden)

^b UNIVERSITY OF TEXAS AT DALLAS   (United States)

^c NATIONAL SCIENCE FOUNDATION   (United States)

Author keywords

E. coli; ppGpp; Promoters; RNA polymerase; rrn

Indexed keywords

RNA POLYMERASE;

ACCURACY; BACTERIAL GENE; CONCENTRATION (PARAMETERS); CYTOPLASM; DNA BINDING; ESCHERICHIA COLI; GENE ACTIVITY; GENE DOSAGE; GENE INTERACTION; GROWTH RATE; KINETICS; MATHEMATICAL MODEL; MICHAELIS MENTEN KINETICS; NONHUMAN; PREDICTION; PROMOTER REGION; QUANTITATIVE ANALYSIS; REVIEW; RNA SYNTHESIS; RNA TRANSCRIPTION;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0038760038     PISSN: 03009084     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0300-9084(03)00105-6     Document Type: Article

References (43)

1. 70), promoters, and the kinetics of the steps of transcription initiation, Second ed, Escherichia Coli and Salmonella Typhimurium: Cellular and Molecular Biology, American Society for Microbiology, Washington, DC, 1996, pp. 792-821.
2. F. Jacob, J. Monod, Genetic regulatory mechanism in the synthesis of proteins, J. Mol. Biol. 3 (1961) 318-356.
3. N.S. Shepherd, P.P. Dennis, H. Bremer, Cytoplasmic RNA polymerase in Escherichia coli, J. Bacteriol. 183 (2001) 2527-2534.
4. S. Liang, M. Bipatnath, Y.-C. Xu, S.-L. Chen, P.P. Dennis, M. Ehrenberg, H. Bremer, Activities of constitutive promoters in Escherichia coli, J. Mol. Biol. 292 (1999) 19-37.
5. X. Zhang, P. Dennis, M. Ehrenberg, H. Bremer, Kinetic properties of rrn promoters in E. coli, Biochimie 84 (2002) 981-996.
6. S. Cooper, C. Helmstetter, Chromosome replication and the division cycle of Escherichia coli B/r, J. Mol. Biol. 31 (1968) 519-540.
7. M. Bipatnath, P.P. Dennis, H. Bremer, Initiation and velocity of chromosome replication in Escherichia coli B/r and K-12, J. Bacteriol. 180 (1998) 265-173.
8. G. Churchward, H. Bremer, R. Young, Transcription in bacteria at different DNA concentrations, J. Bacteriol. 150 (1982) 572-581.
9. S. Jinks-Robertson, R. Gourse, M. Nomura, Expression of rRNA and tRNA genes in Escherichia coli: Evidence for feedback regulation by products of rRNA operons, Cell 33 (1983) 865-876.
10. C. Condon, S. French, C. Squires, C.L. Squires, Depletion of functional ribosomal RNA operons in Escherichia coli causes increased expression of the remaining intact copies, EMBO J. 12 (1993) 4305-4315.
11. J.R. Cole, C.L. Olsson, J.W.B. Hershey, M. Grunberg-Manago, M. Nomura, Feed-back regulation of rRNA synthesis in Escherichia coli: Requirement for initiation factor IF2, J. Mol. Biol. 198 (1987) 383-392.
12. E. Baracchini, H. Bremer, Control of rRNA synthesis in Escherichia coli at increased rrn gene dosage, J. Biol. Chem. 266 (1991) 11753-11760.
13. P.P. Dennis, Stable ribonucleic acid synthesis during the cell division cycle in slowly growing Escherichia coli B/r, J. Biol. Chem. 247 (1972) 204-208.
14. J. Ryals, R. Little, H. Bremer, Control of rRNA and tRNA syntheses in Escherichia coli by guanosine tetraphosphate, J. Bacteriol. 151 (1982) 1261-1268.
15. H. Bremer, P.P. Dennis, Modulation of chemical composition and other parameters of the cell by growth rate, second ed, in: F.C. Neidhardt, R. Curtiss III, J.L. Ingraham, E.C.C. Lin, K.B. Low, B. Magasanik, W.S. Reznikoff, M. Riley, M. Schaechter, H.E. Umbarger (Eds.), Escherichia Coli and Salmonella Typhimurium: Cellular and Molecular Biology, ASM Press, Washington, DC, 1996, pp. 1553-1569.
16. R.E. Kingston, M. Chamberlin, Pausing and attenuation of in vitro transcription in the rrnB operon of E. coli, Cell 27 (1981) 523-531.
17. R.E. Kingston, R.R. Gutell, R.A. Taylor, M. Chamberlin, Transcriptional mapping of plasmid pKK3535. Quantitation of the effect of guanosine tetraphosphate on binding to the rrnB promoter and a λ promoter with sequence homologies to the cII binding region, J. Mol. Biol. 146 (1981) 433-449.
18. V.J. Hernandez, H. Bremer, Characterization of RNA and DNA synthesis in Escherichia coli strains devoid of ppGpp, J. Biol. Chem. 268 (1993) 10851-10862.
19. H. Bremer, M. Ehrenberg, Guanosine tetraphosphate as a global regulator of bacterial RNA synthesis: A model involving RNA polymerase pausing and queuing, Biochim. Biophys. Acta 1262 (1995) 15-36.
20. G. Churchward, E. Estiva, H. Bremer, Growth rate-dependent control of chromosome replication initiation in Escherichia coli, J. Bacteriol. 145 (1981) 1232-1238.
21. H. Bremer, A stochastic process determines the time at which cell division begins in Escherichia coli, J. Theor. Biol. 118 (1986) 351-365.
22. X. Zhang, H. Bremer, Effects of Fis on ribosome synthesis and activity and on rRNA promoter activities in E. coli, J. Mol. Biol. 259 (1996) 27-40.
23. F. Neidhardt, H.E. Umbarger, second ed, in: F.C. Neidhardt, R. Curtiss III, J.L. Ingraham, E.C.C. Lin, K.B. Low, B. Magasani, W.S. Reznikoff, M. Riley, M. Schaechter, H.E. Umbarger (Eds.), Escherichia Coli and Salmo Nella Typhimurium: Cellular and Molecular Biology, ASM Press, Washington, DC, 1996, pp. 13-16.
24. H. Bremer, D. Yuan, RNA chain growth rate in Escherichia coli, J. Mol. Biol. (1968) 163-180.
25. W.R. McClure, Mechanism and control of transcription initiation in prokaryotes. Ann. Rev. Biochem. 54 (1985) 171-204.
26. D. Murray, H. Brener, Control of spoT-dependent ppGpp synthesis and degradation in Escherichia coli, J. Mol. Biol. 259 (1996) 41-57.
27. N.S. Shepherd, G. Churchward, H. Bremer, Synthesis and activity of ribonucleic acid polymerase in Escherichia coli, J. Bacteriol. 141 (1980) 1098-1108.
28. T. Gaal, R. Gourse, Guanosine 3′-diphosphate 5′-diphosphate is not required for growth rate-dependent control of rRNA synthesis in Escherichia coli, Proc. Natl. Acad. Sci. USA 87 (1990) 5533-5537.
29. T. Gaal, M.S. Bartlett, W. Ross, C.L. Turnbough, R.L. Gourse, Transcription regulation by initiating NTP concentration: RNA synthesis in bacteria, Science 278 (1997) 2092-2097.
30. B. Barker, T. Gaal, C.A. Josaitis, R. Gourse, Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro, J. Mol. Biol. 305 (2001) 673-688.
31. M. Barker, T. Gaal, R. Gourse, Mechanism of regulation of transcription initiation by ppGpp. II. Models for positive control based on properties of RNAP mutants and competition for RNAP, J. Mol. Biol. 305 (2001) 689-702.
32. T. Saitoh, A. Ishihama, Biosynthesis of RNA polymerase in Escherichia coli. VI. Distribution of RNA polymerase subunits between nucleoid and cytoplasm, J. Mol. Biol. 115 (1977) 403-416.
33. M.J. Chamberlin, RNA polymerase - An overview, RNA Polymerase, 1976, pp. 17-67.
34. Y. Iwakura, A. Ishihama, Biosynthesis of RNA polymerase in Escherichia coli. II. Control of RNA polymerase synthesis during nutritional shift up and down, Mol. Gen. Genet. 142 (1975) 67-84.
35. Y. Iwakura, K. Ito, A. Ishihama, Biosynthesis of RNA polymerase in Escherichia coli. I. Control of RNA polymerase content at various growth rates, Mol. Gen. Genet. 133 (1974) 1-23.
36. P.P. Dennis, The regulation of the synthesis and the activity of a mutant RNA polymerase in the bacterium Escherichia coli, Proc. Natl. Acad. Sci. USA 74 (1977) 5416-5420.
37. P.P. Dennis, Transcription patterns of adjacent segments on the chromosome of Escherichia coli containing genes coding for four 50S ribosomal proteins and the β and β′ subunits of RNA polymerase, J. Mol. Biol. 115 (1977) 603-625.
38. W.L. Downing, P.P. Dennis, Transcription products from the rplKA-JL-rpoBC gene cluster, J. Mol. Biol. 194 (1987) 609-620.
39. W. Downing, P.P. Dennis, RNA polymerase activity may regulate transcription initiation and attenuation in the rplKAJLrpoBC operon in Escherichia coli, J. Biol. Chem. 266 (1991) 1304-1311.
40. R.M. Blumenthal, P.P. Dennis, Gene expression in E. coli during partial rifampicin-mediated restrictions in transcription initiation, Mol. Gen. Genet. 165 (1978) 79-86.
41. R. Little, P.P. Dennis, Expression of RNA polymerase and ribosome component genes in Escherichia coli mutants having conditionally defective RNA polymerases, J. Bacteriol. 137 (1979) 115-123.
42. R. Little, P.P. Dennis, Regulation of RNA polymerase synthesis. Condition lethal mutations in the β subunit gene, J. Biol. Chem. 255 (1979) 3536-3541.
43. L.E. Post, G.D. Strycharty, M. Nomura, H. Lewis, P.P. Dennis, Nucleotide sequence of the ribosomal protein gene cluster adjacent to the gene for the RNA polymerase sub-unit β in Escherichia coli, Proc. Natl. Acad. Sci. 76 (1979) 1697-1701.