The -11A of promoter DNA and two conserved amino acids in the melting region of 70 both directly affect the rate limiting step in formation of the stable RNA polymerase-promoter complex, but they do not necessarily interact
Open Access
- 6 June 2007
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 35 (12) , 4141-4153
- https://doi.org/10.1093/nar/gkm431
Abstract
Formation of the stable, strand separated, ‘open’ complex between RNA polymerase and a promoter involves DNA melting of approximately 14 base pairs. The likely nucleation site is the highly conserved −11A base in the non-template strand of the −10 promoter region. Amino acid residues Y430 and W433 on the σ70 subunit of the RNA polymerase participate in the strand separation. The roles of −11A and of the Y430 and W433 were addressed by employing synthetic consensus promoters containing base analog and other substitutions at −11 in the non-template strand, and σ70 variants bearing amino acid substitutions at positions 430 and 433. Substitutions for −11A and for Y430 and W433 in σ70 have small or no effects on formation of the initial RNA polymerase-promoter complex, but exert their effects on subsequent steps on the way to formation of the open complex. As substitutions for Y430 and W433 also affect open complex formation on promoter DNA lacking the −11A base, it is concluded that these amino acid residues have other (or additional) roles, not involving the −11A. The effects of the substitutions at −11A of the promoter and Y430 and W433 of σ70 are cumulative.Keywords
This publication has 46 references indexed in Scilit:
- An Unsubstituted C2 Hydrogen of Adenine Is Critical and Sufficient at the –11 Position of a Promoter to Signal Base Pair DeformationJournal of Biological Chemistry, 2004
- Structural Basis of Transcription Initiation: RNA Polymerase Holoenzyme at 4 Å ResolutionScience, 2002
- Interaction of RNA polymerase with forked DNA: Evidence for two kinetically significant intermediates on the pathway to the final complexProceedings of the National Academy of Sciences, 2002
- Structure of the Bacterial RNA Polymerase Promoter Specificity σ SubunitMolecular Cell, 2002
- A “master” in base unpairing during isomerization of a promoter upon RNA polymerase bindingProceedings of the National Academy of Sciences, 2001
- Different Roles for Basic and Aromatic Amino Acids in Conserved Region 2 of Escherichia coli ς70 in the Nucleation and Maintenance of the Single-stranded DNA Bubble in Open RNA Polymerase-Promoter ComplexesJournal of Biological Chemistry, 2001
- Function of the bacterial TATAAT −10 element as single-stranded DNA during RNA polymerase isomerizationProceedings of the National Academy of Sciences, 2001
- Sequence Determinants for the Recognition of the Fork Junction DNA Containing the −10 Region of Promoter DNA by E. coli RNA PolymeraseBiochemistry, 2000
- Aromatic amino acids in region 2.3 of Escherichia coli sigma 70 participate collectively in the formation of an RNA polymerase-promoter open complexJournal of Molecular Biology, 2000
- Escherichia coli promoter opening and −10 recognition: mutational analysis of σ70The EMBO Journal, 2000