Guanosine 3',5'-bis(diphosphate) (PPGpp)-dependent inhibition of transcription from stringelatly controlled Escherichia coli promoters can be explained by an altered initiation pathway that traps RNA polymerase

European Journal of Biochemistry

Volumn 247, Issue 3, 1997, Pages 990-999

  Heinemann, Marianne ^a   Wagner, Rolf ^a  

^a HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

Escherichia coli RNA polymerase; Guanosine 3',5' bis(diphosphate); Ribosomal RNA promoter; Stringent control; Transcription regulation

Indexed keywords

GUANOSINE 3' DIPHOSPHATE 5' DIPHOSPHATE; GUANOSINE 3' DIPHOSPHATE 5' TRIPHOSPHATE; RNA POLYMERASE;

ARTICLE; ENZYME ACTIVITY; ESCHERICHIA COLI; GROWTH RATE; IN VITRO STUDY; PRIORITY JOURNAL; PROMOTER REGION; REACTION ANALYSIS; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

ESCHERICHIA COLI;

EID: 0030805716     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1432-1033.1997.00990.x     Document Type: Article

References (44)

1. Lukacsovich, T., Boros, I. & Venetianer, P. (1987) New regulatory features of the promoters of an Escherichia coli rRNA gene, J. Bacteriol. 169, 272-277.
2. Kingston, R. E. (1983) Effects of deletions near Escherichia coli rrnB promoter P2 on inhibition of in vitro transcription by guanosine tetraphosphate, Biochemistry 22, 5249-5254.
3. Sarmientos, P., Sylvester, J. E., Contente, S. & Cashel, M. (1983) Differential stringent control of the tandem E. coli ribosomal RNA promoters from the rrnA operon expressed in vivo in multicopy plasmids, Cell 32, 1337-1346.
4. Glaser, G., Sarmientos, P. & Cashel, M. (1983) Functional interrelationship between two tandem E. coli ribosomal RNA promoters, Nature 302, 74-76.
5. Liebig, B. & Wagner, R. (1995) Effects of different growth conditions on the in vivo activity of the tandem Escherichia coli ribosomal RNA promoters P1 and P2, Mol. & Gen. Genet. 249, 328-335.
6. Gafny, R., Cohen, S., Nachaliel, N. & Glaser, G. (1994) Isolated P2 rRNA promoters of Escherichia coli are strong promoters that are subject to stringent control, J. Mol. Biol. 243, 152-156.
7. Condon, C., Liveris, D., Squires, C., Schwartz, I. & Squires, C. L. (1995) rRNA operon multiplicity in Escherichia coli and the physiological implications of rrn inactivation, J. Bacteriol. 177, 4152-4156.
8. Josaitis, C. A., Gaal, T. & Gourse, R. L. (1995) Stringent control and growth-rate-dependent control have nonidentical promoter sequence requirements, Proc. Natl Acad. Sci. USA 92, 1117-1121.
9. Zacharias, M., Göringer, H. U. & Wagner, R. (1989) Influence of the GCGC discriminator motif introduced into the ribosomal RNA P2- and tac promoter on growth rate control and stringent sensitivity, EMBO J. 11, 3357-3363.
10. Cashel, M. & Rudd, K. E. (1987) The stringent response, in Escherichia coli and Salmonella typhimurium: cellular and molecular biology (Neidhardt, F. C., Ingraham, J. L., Low, K. B., Magasanik, B., Schaechter, M. & Umbarger, H. E., eds) pp. 1410-1438, American Society for Microbiology, Washington D.C.
11. Krohn, M. & Wagner, R. (1995) A procedure for the rapid preparation of guanosine tetraphosphate (ppGpp) from Escherichia coli ribosomes, Anal. Biochem. 225, 188-190.
12. Gonzales, N., Wiggs, J. & Chamberlin, M. J. (1977) A simple procedure for resolution of E. coli RNA polymerase holoenzyme from core polymerase, Arch. Biochem. Biophys. 182, 404-408.
13. Burgess, R. R. & Jendrisak, J. J. (1975) A procedure for the rapid, large scale purification of E. coli DNA-dependent RNA polymerase involving polymin P precipitation and DNA cellulose chromatography, Biochemistry 14, 4636-4638.
14. Chamherlin, M. J., Nierman, W. C., Wiggs, J. & Neff, N. (1979) A quantitative assay for bacterial RNA polymerases, J. Biol. Chem. 254, 10061-10069.
15. Igarashi, K. & Ishihama, A. (1991) Bipartite functional map of the E. coli RNA polymerase α subunit: involvement of the C-terminal region in transcription activation by cAMP-CRP, Cell 65, 1015-1022.
16. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989) Molecular cloning: a laboratory manual, Cold Spring Harbor Laboratory, Cold Spring Harbor NY.
17. Tippner, D., Afflerbach, H., Bradaczek, C. & Wagner, R. (1994) Evidence for a regulatory function of the histone-like E. coli protein H-NS in ribosomal RNA synthesis, Mol. Microbiol. 11, 589-604.
18. Pardon, B. & Wagner, R. (1995) The Escherichia coli ribosomal RNA leader nut region interacts specifically with mature 16S RNA, Nucleic Acids Res. 23, 932-941.
19. Gourse, R. L. (1988) Visualization and quantitative analysis of complex formation between E. coli RNA polymerase and an rRNA promoter in vitro, Nucleic Acids Res. 16, 9789-9809.
20. Roe, J. H., Burgess, R. R. & Record, M. T. (1984) Kinetics and mechanism of the interaction of Escherichia coli RNA polymerase with the lambda PR promoter, J. Mol. Biol. 176, 495-522.
21. Wellington, S. R. & Spiegelman, G. B. (1993) The kinetics of formation of complexes between Escherichia coli RNA polymerase and the rrnB P1 and P2 promoters of Bacillus subtilis, J. Biol. Chem. 268, 7205-7214.
22. Leirmo, S., Harrison, C., Cayley, D. S., Burgess, R. R. & Record, T. (1987) Replacement of potassium chloride by potassium glutamate dramatically enhances protein-DNA interactions in vitro, Biochemistry 26, 2095-2101.
23. McClure, W. R. (1985) Mechanism of control of transcription initiation in prokaryotes, Ann. Rev. Biochem. 54, 171-204.
24. Kovacic, R. T. (1987) The 0°C closed complexes between Escherichia coli RNA polymerase and two promoters, T7-A3 and lac UV5, J. Biol. Chem. 262, 13654-13661.
25. McClure, W. R. (1980) Rate-limiting steps in RNA chain initiation, Proc. Natl Acad. Sci. USA 77, 5634-5638.
26. Leirmo, S. & Gourse, R. L. (1991). Factor-independent activation of Escherichia coli rRNA transcription. I. Kinetic analysis of the roles of the upstream activator region and supercoiling on transcription of the rrnB promoter in vitro, J. Mol. Biol. 220, 555-568.
27. Cech, C. L. & McClure, W. R. (1980) Characterization of RNA polymerase-T7 promoter binary complexes. Biochemistry 19, 2440-2447.
28. Miller, D. L. & Weissbach, H. (1977) The interactions of elongation factor Tu, in Nucleic acid-protein recognition (Vogel, H. J., ed.) pp. 409-440, Academic Press, NY.
29. Garner, M. M. & Revzin, A. (1981) A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the E. coli lactose operon regulatory system, Nucleic Acids Res. 9, 3047-3060.
30. Adhya, S. & Gottesman, M. (1982) Promoter occlusion: transcription through a promoter may inhibit its activity. Cell 29, 939-944.
31. Lukacsovich, T. Gaal, T. & Venetianer, P. (1989) The structural basis of the high in vivo strength of the rRNA P2 promoter of Escherichia coli, Gene (Amst.) 78, 189-194.
32. Langert, W., Meuthen, M. & Müller, K. (1991) Functional characteristics of the rrnD promoters of Escherichia coli. J. Biol. Chem. 266, 21608-21615.
33. Kassavetis, G. A. & Geiduschek, E. P. (1993) RNA polymerase marching backward, Science 259, 944-945.
34. Orlova, M., Newlands, J., Das, A., Goldfarb, A. & Borukhov, S. (1995) Intrinsic transcript cleavage activity of RNA polymerase, Proc. Natl Acad. Sci. USA 92, 4596-4600.
35. Munson, L. M. & Reznikoff, W. S. (1981) Abortive initiation and long RNA synthesis. Biochemistry 20, 2081-2085.
36. Stefano, J. E. & Gralla, J. (1979) Lac UV5 transcription in vitro. Rate limitation subsequent to formation of an RNA polymerase-DNA complex, Biochemistry 18, 1063-1067.
37. Ohlsen, K. L. & Gralla, J. D. (1992) DNA melting within stable closed complexes at the Escherichia coli rrnB P1 promoter, J. Biol. Chem. 267, 19813-19818.
38. Hamming, J., Geert, A. B. & Gruber, M. (1980) E. coli RNA polymerase-rRNA promoter interaction and the effect of ppGpp, Nucleic Acids Res. 8, 3947-3963.
39. Travers, A. A., Buckland, R. & Debenham, P. G. (1980) Functional heterogeneity of Escherichia coli RNA polymerase holoenzyme, Biochemistry 19, 1656-1662.
40. Ryals, J., Little, R. & Bremer, H. (1982) Control of rRNA and tRNA syntheses in Escherichia coli by guanosine tetraphosphate, J. Bacteriol. 151, 1261-1268.
41. Ozaki, M., Fujita, N., Wada, A. & Ishihama, A. (1992) Promoter selectivity of the stationary-phase forms of Escherichia coli RNA polymerase and conversion in vitro of the S1 form enzyme into a log-phase enzyme-like form, Nucleic Acids Res. 20, 257-261.
42. Krohn, M. & Wagner, R. (1996) Transcriptional pausing of RNA polymerase in the presence of guanosine tetraphosphate depends on the promoter and gene sequence, J. Biol. Chem. 271, 23884-23894.
43. Lamond, A. I. & Travers, A. A. (1985) Stringent control of bacterial transcription, Cell 41, 6-8.
44. Travers, A. A. (1976) Modulation of RNA polymerase specificity by ppGpp, Mol. & Gen. Genet. 147, 225-232.