The TRTGn motif stabilizes the transcription initiation open complex

Journal of Molecular Biology

Volumn 322, Issue 3, 2002, Pages 521-532

  Voskuil, Martin I ^a   Chambliss, Glenn H ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

16 region; Extended 10; Promoter; RNA polymerase; Transcription

Indexed keywords

AMYLASE; DNA; NUCLEOTIDE; RNA POLYMERASE;

ARTICLE; DNA STRAND; ESCHERICHIA COLI; GENE MUTATION; GRAM POSITIVE BACTERIUM; HALF LIFE TIME; MELTING POINT; MUTAGENESIS; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN MOTIF; TEMPERATURE; TRANSCRIPTION INITIATION; WILD TYPE;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; POSIBACTERIA;

EID: 0036384435     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00802-1     Document Type: Article

References (31)

1. Moran, C. P., Jr, Lang, N., Le Grice, S. F. J., Lee, G., Stephens, M., Sonenshein, A. L. et al. (1982). Nucleotide sequences that signal the initiation of transcription and translation in Bacillus subtilis. Mol. Gen. Genet. 186, 339-346.
2. Henkin, T. M. & Sonenshein, A. L. (1987). Mutations of the Escherichia coli lacUV5 promoter resulting in increased expression in Bacillus subtilis. Mol. Gen. Genet. 209, 467-474.
3. A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA. Nucl. Acids Res. 23, 2351-2360.
4. Voskuil, M. I. & Chambliss, G. H. (1998). The -16 region of Bacillus subtilis and other Gram-positive bacterial promoters. Nucl. Acids Res. 26, 3584-3590.
5. Voskuil, M. I., Voepel, K. & Chambliss, G. H. (1995). The -16 region, a vital sequence for the utilization of a promoter in Bacillus subtilis and Escherichia coli. Mol. Microbiol. 17, 271-279.
6. Bown, J. A., Barne, K. A., Minchin, S. D. & Busby, S. J. W. (1997). Extended -10 promoters. In Nucleic Acids and Molecular Biology (Eckstein, F. & Lilley, D. M. J., eds), Springer, Berlin.
7. Keilty, S. & Rosenberg, M. (1987). Constitutive function of a positively regulated promoter reveals new sequences essential for activity. J. Biol. Chem. 262, 6395-6398.
8. Chan, B. & Busby, S. (1989). Recognition of nucleotide sequences at the Escherichia coli galactose operon P1 promoter by RNA polymerase. Gene, 84, 227-236.
9. Belyaeva, T., Griffiths, L., Minchin, S., Cole, J. & Busby, S. (1993). The Escherichia coli cysG promoter belongs to the "extended -10 class" of bacterial promoters. J. Biochem. 296, 851-857.
10. Burr, T., Mitchell, J., Kolb, A., Minchin, S. & Busby, S. (2000). DNA sequence elements located immediately upstream of the -10 hexamer in Escherichia coli promoters: a systematic study. Nucl. Acids Res. 28, 1864-1870.
11. DeHaseth, P. L., Zupancic, M. L. & Record, M. T., Jr (1998). RNA polymerase-promoter interactions: the comings and goings of RNA polymerase. J. Bacteriol. 180, 3019-3025.
12. A-RNA polymerase-dependent promoters. J. Mol. Biol. 286, 683-693.
13. Burns, H. & Minchin, S. (1994). Thermal energy requirement for strand separation during contacts. Nucl. Acids Res. 22, 3840-3845.
14. Barne, K., Bown, J., Busby, S. & Minchin, S. (1997). Region 2.5 of the RNA polymerase σ70 subunit is responsible for the recognition of the "extended -10 motif" at promoters. EMBO J. 16, 4034-4040.
15. Bown, J. A., Owens, J. T., Meares, C. F., Fujita, N., Ishihama, A., Busby, S. J. W. & Minchin, S. D. (1999). Organization of open complexes at Escherichia coli promoters. J. Biol. Chem. 274, 2263-2270.
16. Juang, Y.-L. & Helmann, J. D. (1994). The delta subunit of Bacillus RNA polymerase. An allosteric effector of the initiation and core-recycling phases of transcription. J. Mol. Biol. 239, 1-14.
17. Le Grice, S. F. J., Shih, C.-C., Wipple, F. & Sonenshein, A. L. (1986). Seperation and analysis of the RNA polymerase binding sites of a complex Bacillus subtilis promoter. Mol. Gen. Genet. 204, 229-236.
18. 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 rrn B P1 promoter in vitro. J. Mol. Biol. 220, 555-568.
19. Morita, M. & Oka, A. (1979). The structure of a transcriptional unit on colicin E1 plasmid. Eur. J. Biochem. 97, 435-443.
20. Whipple, F. W. & Sonenshein, A. L. (1992). Mechanism of initiation of transcription by Bacillus subtilis RNA polymerase at several promoters. J. Mol. Biol. 223, 399-414.
21. Dobinson, K. F. & Spiegelman, G. B. (1987). Effect of the δ subunit of Bacillus subtilis RNA polymerase on initiation of RNA synthesis at two bacteriophage φ29 promoters. Biochemistry, 26, 8206-8213.
22. A-RNA polymerase that are stabilzed by DNA supercoiling. Nucl. Acids Res. 21, 935-940.
23. Ling, M. L., Risman, S. S., Klement, J. F., McGraw, N. & McAllister, W. T. (1989). Abortive initiation by bactetiophage T3 and T7 RNA polymerases under conditions of limiting substrate. Nucl. Acids Res. 17, 1605-1618.
24. Diaz, G. A., Rong, M., McAllister, W. T. & Durbin, R. K. (1996). The stability of abortively cycling T7 RNA polymerase complexes depends upon template conformation. Biochemistry, 35, 10837-10843.
25. Ujvari, A. & Martin, C. T. (1996). Thermodynamic and kinetic measurements of promoter binding by T7 RNA polymerase. Biochemistry, 35, 14574-14582.
26. Jia, Y. & Patel, S. S. (1997). Kinetic mechanism of transcription initiation by bacteriophage T7 RNA polymerase. Biochemistry, 36, 4223-4232.
27. Whipple, F. W. & Sonenshein, A. L. (1990). Initial interaction of Bacillus subtilis RNA polymerase with promoter sites. In Genetics and Biotechnology of Bacilli (Ganesan, A. T. & Hoch, J. A., eds), pp. 109-114, Academic Press, New York.
28. Pfeffer, S. R., Stahl, S. & Chamberlin, M. J. (1977). Binding of Escherichia coli RNA polymerase to T7 DNA: displacement of holoenzyme from promoter complexes by heparin. J. Biol. Chem. 252, 5403-5407.
29. Glasel, J. A. (1995). Validity of nucleic acid purities monitored by 260 nm/280 nm absorbance ratios. Biotechniques, 18, 62-63.
30. Barik, S. (1995). Site-directed mutagenesis by double polymerase chain reaction. Mol. Biotech. 3, 1-7.
31. Ross, W., Thompson, J. F., Newlands, J. T. & Gourse, R. L. (1990). Escherichia coli Fis protein activates ribosomal RNA transcription in vitro and in vivo. EMBO J. 9, 3733-3742.