An intersubunit contact stimulating transcription initiation by E coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4

Genes & Development
Wilma RossRichard L Gourse

Abstract

The C-terminal domain of the Escherichia coli RNA polymerase (RNAP) alpha subunit (alphaCTD) stimulates transcription initiation by interacting with upstream (UP) element DNA and a variety of transcription activators. Here we identify specific substitutions in region 4.2 of sigma 70 (sigma(70)) and in alphaCTD that decrease transcription initiation from promoters containing some, but not all, UP elements. This decrease in transcription derives from a decrease in the initial equilibrium constant for RNAP binding (K(B)). The open complexes formed by the mutant and wild-type RNAPs differ in DNAse I sensitivity at the junction of the alphaCTD and sigma DNA binding sites, correlating with the differences in transcription. A model of the DNA-alphaCTD-sigma region 4.2 ternary complex, constructed from the previously determined X-ray structures of the Thermus aquaticus sigma region 4.2-DNA complex and the E. coli alphaCTD-DNA complex, indicates that the residues identified by mutation in sigma region 4.2 and in alphaCTD are in very close proximity. Our results strongly suggest that alphaCTD, when bound to an UP element proximal subsite, contacts the RNAP sigma(70) subunit, increasing transcription. Previous data from the literature sug...Continue Reading

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Citations

Apr 23, 2004·Current Opinion in Structural Biology·Catherine L LawsonRichard H Ebright
Jun 4, 2008·Nature Reviews. Microbiology·Shanil P HaugenRichard L Gourse
Feb 22, 2008·Proceedings of the National Academy of Sciences of the United States of America·Shanil P HaugenRichard L Gourse
Nov 12, 2009·Proceedings of the National Academy of Sciences of the United States of America·Brian P HudsonCatherine L Lawson
Jun 25, 2008·The Journal of Biological Chemistry·Nataliya BarinovaAndrey Kulbachinskiy
Dec 14, 2011·Nucleic Acids Research·Virgil A RhodiusCarol A Gross
May 8, 2007·Journal of Bacteriology·Shicheng ChenEdward D Walker
Aug 29, 2006·Journal of Bacteriology·Li ShenYou-Xun Zhang
Mar 2, 2005·Proceedings of the National Academy of Sciences of the United States of America·Bianca SclaviHermann Heumann
Oct 27, 2005·Proceedings of the National Academy of Sciences of the United States of America·Kate J NewberryRichard G Brennan
Mar 12, 2005·Proceedings of the National Academy of Sciences of the United States of America·Bryce E NickelsAnn Hochschild
Jan 1, 2005·Proceedings of the National Academy of Sciences of the United States of America·Caroline A DavisRuth M Saecker
Jan 1, 2005·Proceedings of the National Academy of Sciences of the United States of America·Wilma Ross, Richard L Gourse
Jun 26, 2012·Annual Review of Microbiology·David J LeeStephen J W Busby
Feb 8, 2013·The Journal of Biological Chemistry·Katsuhiko S Murakami
May 30, 2015·Biomolecules·Emily F RuffIrina Artsimovitch
Nov 28, 2015·Biochemistry·Monica ChanderLilian Ming-Te Hsu
Jun 23, 2009·Molecular Microbiology·Kimberly B Decker, Deborah M Hinton
May 8, 2004·Molecular Microbiology·Gilbert OrsiniAnnie Kolb
Jul 2, 2015·Annual Review of Microbiology·Georgiy A Belogurov, Irina Artsimovitch
Aug 29, 2012·Molecular Microbiology·Minsang ShinHyon E Choy
Dec 1, 2004·Annual Review of Genetics·Brian J PaulRichard L Gourse
Jan 21, 2004·Molecular Cell·Deepti JainSeth A Darst
Feb 13, 2007·Metabolic Engineering·Hal Alper, Gregory Stephanopoulos
Jul 26, 2005·Molecular Cell·Deepti JainSeth A Darst
Nov 18, 2017·Science·Bin LiuThomas A Steitz
Jun 23, 2009·Molecular Microbiology·Andrew D Klocko, Karen M Wassarman
Jul 8, 2010·Acta Crystallographica. Section D, Biological Crystallography·Samuel Lara-GonzálezCatherine L Lawson
Mar 16, 2016·Proceedings of the National Academy of Sciences of the United States of America·Jared T WinkelmanRichard L Gourse
Jul 15, 2020·The Biochemical Journal·Patcharawarin RuantoDouglas F Browning

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