The arginine repressor of Escherichia coli K-12 makes direct contacts to minor and major groove determinants of the operators

Journal of Molecular Biology
H WangDaniel Charlier

Abstract

In order to gain further insight into the molecular mechanism of arginine-dependent operator recognition by the hexameric Escherichia coli arginine repressor we have probed protein-DNA interactions in vitro and in vivo. We have extensively applied the chemical modification-protection and premodification-interference approach to two operators, the natural operator overlapping the P2 promoter of the carAB operon and a fully symmetrical consensus sequence. Backbone contacts were revealed by hydroxyl radical footprinting and phosphate ethylation interference. Base-specific contacts to purines and pyrimidines were revealed by methylation protection and premodification interference, KMnO4 and NH2OH.HCl-specific modification of thymine and cytosine residues, base-removal (depurination and depyrimidation), and base substitution (uracil and inosine). Additional information on the groove specificity of repressor binding was obtained by small ligand binding interference (distamycin and methyl green). In vivo, we measured the effects on the repressibility of 24 single base-pair substitutions obtained by saturation mutagenesis of half an Arg box in the carAB operator. The results of these experiments point to the conclusion that a hexameric...Continue Reading

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Citations

May 18, 2010·Nucleic Acids Research·Phu Le Minh NguyenDaniel Charlier
Jan 29, 2013·Nucleic Acids Research·Ningning SongDaniel Charlier
Mar 3, 2006·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Jan MassantDominique Maes
Jul 14, 2010·Journal of Bacteriology·Galadriel Hovel-MinerHoward A Shuman
Jun 7, 2008·Microbiology and Molecular Biology Reviews : MMBR·Charles L Turnbough, Robert L Switzer
Sep 6, 2000·Journal of Molecular Biology·D CharlierN Glansdorff
Sep 1, 2015·Applied and Environmental Microbiology·Jin-Sook KimHyeon-Cheol Lee
Apr 8, 2015·Journal of Bacteriology·Amit Pathania, Abhijit A Sardesai
Jul 4, 2019·Amino Acids·Daniel Charlier, Indra Bervoets
Mar 12, 2020·Biochimica Et Biophysica Acta. General Subjects·Ricardo B MariuttiRaghuvir K Arni
Dec 1, 2004·EcoSal Plus·Daniel Charlier, Nicolas Glansdorff
Sep 14, 2007·Journal of Molecular Biology·Marina CaldaraDaniel Charlier

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