Mechanism and Regulation of E. coli RNA Polymerase

McClure, William R.

Abstract

The research proposed will be a systematic biochemical investigation of the mechanism and regulation of E. coli. RNA Polymerase. Several gene regulatory systems will be investigated in vitro. The focus throughout will be to understand how DNA sequences in the control regions of genes contribute to the regulation of transcription initiation. The mechanism of action of several transcriptional activators and repressors will be examined. The effects of DNA supercoiling on selected systems will also be investigated. In two bacteriophage systems, the effects of convergent transcription between two (or more) opposing promoters will be studied. The experiments proposed rely on standard biochemical assays for determining in vitro promoter strength. These results will be complemented in some cases with direct measurements of in vivo RNA chain initiation frequency and in other cases with direct measurements of in vitro binding of RNA polymerase and other regulatory proteins. The answers to the questions we have posed will contribute to the biochemical description of the control of gene expression.

Funding Agency

• Agency: National Institute of Health (NIH)
• Institute: National Institute of General Medical Sciences (NIGMS)
• Type: Research Project (R01)
• Project #: 5R01GM030375-08
• Application #: 3278119
• Study Section: Microbial Physiology and Genetics Subcommittee 2 (MBC)
• Project Start: 1981-07-01
• Project End: 1990-06-30
• Budget Start: 1988-07-01
• Budget End: 1989-06-30
• Support Year: 8
• Fiscal Year: 1988

Institution

• Name: Carnegie-Mellon University
• Type: Schools of Arts and Sciences
• DUNS #: 052184116
• City: Pittsburgh
• State: PA
• Country: United States
• Zip Code: 15213

Publications

Li, X Y; McClure, W R (1998) Stimulation of open complex formation by nicks and apurinic sites suggests a role for nucleation of DNA melting in Escherichia coli promoter function. J Biol Chem 273:23558-66

Li, X Y; McClure, W R (1998) Characterization of the closed complex intermediate formed during transcription initiation by Escherichia coli RNA polymerase. J Biol Chem 273:23549-57

Schaefer, K L; McClure, W R (1997) Antisense RNA control of gene expression in bacteriophage P22. II. Kinetic mechanism and cation specificity of the pairing reaction. RNA 3:157-74

Schaefer, K L; McClure, W R (1997) Antisense RNA control of gene expression in bacteriophage P22. I. Structures of sar RNA and its target, ant mRNA. RNA 3:141-56

Li, M; McClure, W R; Susskind, M M (1997) Changing the mechanism of transcriptional activation by phage lambda repressor. Proc Natl Acad Sci U S A 94:3691-6

Yee, Y C; Kisslinger, B; Yu, V L et al. (1996) A mechanism of rifamycin inhibition and resistance in Pseudomonas aeruginosa. J Antimicrob Chemother 38:133-7

Su, T T; McClure, W R (1994) Selective binding of Escherichia coli RNA polymerase to topoisomers of minicircles carrying the TAC16 and TAC17 promoters. J Biol Chem 269:13511-21

Goodrich, J A; McClure, W R (1992) Regulation of open complex formation at the Escherichia coli galactose operon promoters. Simultaneous interaction of RNA polymerase, gal repressor and CAP/cAMP. J Mol Biol 224:15-29

Goodrich, J A; McClure, W R (1991) Competing promoters in prokaryotic transcription. Trends Biochem Sci 16:394-7

Goodrich, J A; Schwartz, M L; McClure, W R (1990) Searching for and predicting the activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF). Nucleic Acids Res 18:4993-5000