Insights into the architecture and stoichiometry of Escherichia coli PepA*DNA complexes involved in transcriptional control and site-specific DNA recombination by atomic force microscopy.

Nucleic Acids Research
Phu Nguyen Le MinhD Charlier

Abstract

Multifunctional Aminopeptidase A (PepA) from Escherichia coli is involved in the control of two distinct DNA transaction processes: transcriptional repression of the carAB operon, encoding carbamoyl phosphate synthase and site-specific resolution of ColE1-type plasmid multimers. Both processes require communication at a distance along a DNA molecule and PepA is the major structural component of the nucleoprotein complexes that underlie this communication. Atomic Force Microscopy was used to analyze the architecture of PepA.carAB and PepA.cer site complexes. Contour length measurements, bending angle analyses and volume determinations demonstrate that the carP1 operator is foreshortened by approximately 235 bp through wrapping around one PepA hexamer. The highly deformed part of the operator extends from slightly upstream of the -35 hexamer of the carP1 promoter to just downstream of the IHF-binding site, and comprises the binding sites for the PurR and RutR transcriptional regulators. This extreme remodeling of the carP1 control region provides a straightforward explanation for the strict requirement of PepA in the establishment of pyrimidine and purine-specific repression of carAB transcription. We further provide a direct phy...Continue Reading

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Citations

Jun 5, 2012·The Journal of Biological Chemistry·Cordula BöhmH Ulrich Göringer
May 18, 2010·Nucleic Acids Research·Phu Le Minh NguyenDaniel Charlier
Dec 3, 2014·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Gabriel N AugheyJi-Long Liu
Jun 22, 2015·Computational Biology and Chemistry·Ernesto Pérez-RuedaGabriel Moreno-Hagelsieb
Feb 19, 2011·Microbiology·Herfita AgustiandariArnold J M Driessen
Mar 5, 2013·Methods : a Companion to Methods in Enzymology·Maria Eugenia Fuentes-PerezFernando Moreno-Herrero
Mar 22, 2013·Biochemical Society Transactions·Sean D Colloms
Mar 6, 2012·Biophysical Journal·M E Fuentes-PerezF Moreno-Herrero
Sep 19, 2016·Biochimica Et Biophysica Acta. General Subjects·Davide AmidaniClaudio Rivetti
Jul 4, 2019·Amino Acids·Daniel Charlier, Indra Bervoets
Jul 5, 2017·Seminars in Cell & Developmental Biology·Emily C BeckwittBennett Van Houten
Jun 25, 2015·Microbiology Spectrum·Caroline Midonet, Francois-Xavier Barre
Sep 10, 2015·Microbiology Spectrum·Fabian M Commichau, Jörg Stülke
Jul 6, 2021·Frontiers in Microbiology·Tomohiro ShimadaAkira Ishihama
Jul 22, 2021·APL Bioengineering·Kavit H S MainAlice L B Pyne

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Methods Mentioned

BETA
AFM
atomic force microscopy
PCR
X-ray
footprinting
in vitro transcription

Software Mentioned

Bending Analysis Program
WSxM
NanoScope
Bending Analysis
Statistical Package for the Social Sciences
ImageJ

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