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Nucleic Acids Research Advance Access published online on September 18, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm712
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genomics

High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes

Benjamin Lang1, Nicolas Blot2, Emeline Bouffartigues3, Malcolm Buckle3, Marcel Geertz2, Claudio O. Gualerzi4, Ramesh Mavathur2, Georgi Muskhelishvili2, Cynthia L. Pon4, Sylvie Rimsky3, Stefano Stella4, M. Madan Babu1,* and Andrew Travers1

1MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK, 2School of Engineering and Science, Research II-112, Jacobs University, Campus Ring 1, 28759 Bremen, Germany, 3Enzymologie et cinétique structurale UMR 8113, Laboratoire de Biotechnologie et Pharmacologie Génétique Appliquée (LBPA), CNRS, ENS de Cachan, 61 Avenue du Président Wilson, 94235 Cachan, France and 4Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032 Camerino (MC), Italy

*To whom correspondence should be addressed. Tel: +44 1223 402208; Fax: +44 1223 213556; Email: madanm{at}mrc-lmb.cam.ac.uk Correspondence may also be addressed to Andrew Travers. Tel: +44 1223 402419; Fax: +44 1223 412142; Email: aat{at}mrc-lmb.cam.ac.uk

Received June 11, 2007. Revised August 22, 2007. Accepted August 24, 2007.

The global transcriptional regulator H-NS selectively silences bacterial genes associated with pathogenicity and responses to environmental insults. Although there is ample evidence that H-NS binds preferentially to DNA containing curved regions, we show here that a major basis for this selectivity is the presence of a conserved sequence motif in H-NS target transcriptons. We further show that there is a strong tendency for the H-NS binding sites to be clustered, both within operons and in genes contained in the pathogenicity-associated islands. In accordance with previously published findings, we show that these motifs occur in AT-rich regions of DNA. On the basis of these observations, we propose that H-NS silences extensive regions of the bacterial chromosome by binding first to nucleating high-affinity sites and then spreading along AT-rich DNA. This spreading would be reinforced by the frequent occurrence of the motif in such regions. Our findings suggest that such an organization enables the silencing of extensive regions of the genetic material, thereby providing a coherent framework that unifies studies on the H-NS protein and a concrete molecular basis for the genetic control of H-NS transcriptional silencing.


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