The strong efficiency of the Escherichia coli gapA P1 promoter depends on a complex combination of functional determinants

The Biochemical Journal
Benoit ThouvenotChristiane Branlant

Abstract

The Escherichia coli multi-promoter region of the gapA gene ensures a high level of GAPDH (glyceraldehyde-3-phosphate dehydrogenase) production under various growth conditions. In the exponential phase of growth, gapA mRNAs are mainly initiated at the highly efficient gapA P1 promoter. In the present study, by using site-directed mutagenesis and chemical probing of the RPo (open complex) formed by Esigma70 (holoenzyme associated with sigma70) RNAP (RNA polymerase) at promoter gapA P1, we show that this promoter is an extended -10 promoter that needs a -35 sequence for activity. The -35 sequence compensates for the presence of a suboptimal -10 hexamer. A tract of thymine residues in the spacer region, which is responsible for a DNA distortion, is also required for efficient activity. We present the first chemical probing of an RPo formed at a promoter needing both a -10 extension and a -35 sequence. It reveals a complex array of RNAP-DNA interactions. In agreement with the fact that residue A-11 in the non-template strand is flipped out in a protein pocket in previously studied RPos, the corresponding A residue in gapA P1 promoter is protected in RPo and is essential for activity. However, in contrast with some of the previous f...Continue Reading

References

Jul 5, 1987·Journal of Molecular Biology·J A BorowiecJ D Gralla
Apr 10, 1986·Nature·H S KooD M Crothers
Apr 1, 1968·Journal of Bacteriology·M G Sargent
Apr 25, 1983·Nucleic Acids Research·D K Hawley, W R McClure
Apr 11, 1993·Nucleic Acids Research·S Lisser, H Margalit
Oct 27, 1998·Trends in Biochemical Sciences·M G MunteanuS Pongor
Jul 27, 2001·Proceedings of the National Academy of Sciences of the United States of America·M S Fenton, J D Gralla
Apr 5, 2002·Molecular Cell·Elizabeth A CampbellSeth A Darst
Jun 28, 2002·Cell·Brian A YoungCarol A Gross
Sep 13, 2002·Journal of Molecular Biology·Martin I Voskuil, Glenn H Chambliss
Feb 13, 2003·Current Opinion in Structural Biology·Katsuhiko S Murakami, Seth A Darst
Aug 9, 2003·Nucleic Acids Research·Jennie E MitchellStephen D Minchin

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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
Mar 15, 2011·Nucleic Acids Research·Shivani S SinghDavid C Grainger
Oct 16, 2012·Nucleic Acids Research·Teresa Del Peso-SantosVictoria Shingler
Jul 23, 2014·Proceedings of the National Academy of Sciences of the United States of America·Peng XuMattheos Koffas
Jan 14, 2009·Proceedings of the National Academy of Sciences of the United States of America·India G Hook-Barnard, Deborah M Hinton
Apr 25, 2012·Biotechnology and Bioengineering·Han-Saem ChoJong Moon Park
Dec 6, 2011·Journal of Theoretical Biology·Valentina BaldazziHidde de Jong
Mar 21, 2013·Integrative Biology : Quantitative Biosciences From Nano to Macro·Marko Djordjevic
Mar 3, 2017·BMC Evolutionary Biology·Jelena Guzina, Marko Djordjevic
Sep 20, 2018·Nature Communications·Douglas McCloskeyBernhard O Palsson
Apr 1, 2021·EcoSal Plus·Angela TramontiRoberto Contestabile

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