A consensus adenine at position -11 of the nontemplate strand of bacterial promoter is important for nucleation of promoter melting

The Journal of Biological Chemistry
E HeydukT Heyduk

Abstract

Numerous studies have suggested an important role of adenine at position -11 of the nontemplate strand of bacterial promoters for sequence-specific recognition of the -10 promoter element in single-stranded form. In this work, we attempted to identify a specific step in transcription initiation reaction that is most critically dependent on specific recognition of -11A. Mutating -11A in the context of a model promoter resulted in a profound decrease of the rate of heparin-resistant promoter complex formation and in a modest increase of the rate of heparin-resistant complex dissociation. The identity of nontemplate base at position -11 became relatively unimportant when the duplex in the vicinity of this position was destabilized by base pair mismatches. For promoters with a nonnative thymine at nontemplate position -11, we observed a remarkable correlation between the rate of heparin-resistant complex formation (or transcription activity) and the free energy of duplex stability in the vicinity of this residue, indicating that the replacement of -11A with a T affected a step in the reaction that involves local melting of DNA duplex. These data show that a promoter melting defect caused by a loss of RNA polymerase contact with -11...Continue Reading

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Citations

Jun 4, 2008·Nature Reviews. Microbiology·Shanil P HaugenRichard L Gourse
Sep 6, 2011·Nucleosides, Nucleotides & Nucleic Acids·Olga Nikolaevna KorolevaValeriy Lvovich Drutsa
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Mar 31, 2011·Nucleic Acids Research·Teresa Del Peso-SantosVictoria Shingler
Oct 16, 2012·Nucleic Acids Research·Teresa Del Peso-SantosVictoria Shingler
Dec 29, 2012·PLoS Computational Biology·Robert C BrewsterRob Phillips
Jul 9, 2014·Annual Review of Microbiology·Andrey FeklístovCarol A Gross
May 1, 2015·Biomolecules·Mary E Karpen, Pieter L deHaseth
Oct 7, 2008·Biophysical Chemistry·Jayanthi Ramprakash, Frederick P Schwarz
Dec 25, 2007·Journal of Molecular Biology·Lisa A SchroederPieter L deHaseth
Nov 17, 2007·Journal of Molecular Biology·Patricia C BurrowsMartin Buck
Feb 19, 2008·Biophysical Journal·Marko Djordjevic, Ralf Bundschuh
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Jul 17, 2016·Nucleic Acids Research·Teresa Del Peso Santos, Victoria Shingler
Mar 13, 2019·Nature Communications·Lingting LiYu Zhang
Nov 11, 2020·Proceedings of the National Academy of Sciences of the United States of America·Kemardo K HenryRichard L Gourse
Mar 12, 2020·Molecular Cell·James ChenSeth A Darst
Jan 11, 2018·Synthetic and Systems Biotechnology·Michael D Engstrom, Brian F Pfleger

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