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

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

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

Benjamin Lang,¹ Nicolas Blot,² Emeline Bouffartigues,³ Malcolm Buckle,³ Marcel Geertz,² Claudio O Gualerzi,⁴ Ramesh Mavathur,² Georgi Muskhelshvili,² Cynthia Pon,⁴ Sylvie Rimsky,³ Stefano Stella,⁴
M. Madan Babu,^1* Andrew Travers^1*

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 cinetique structurale UMR 8113, Laboratoire de Biotechnologie et Pharmacologie Genetique Appliquee (LBPA), CNRS, Ecole Normale Superieure, 61 Avenue du President Wilson, 94235 Cachan France.
⁴Laboratory of Genetics, Dept. of Biology MCA, University of Camerino, 62032 Camerino (MC), Italy.

*To whom correspondence should be addressed. Emails: madanm@mrc-lmb.cam.ac.uk, aat@mrc-lmb.cam.ac.uk

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1. Analysis of the ChIP-chip dataset for H-NS by Grainger et al, NAR 2006; 34:4642-52

2. Analysis of differentially expressed genes in E. coli K12 (hns knockout mutants)

3. Analysis of differentially expressed genes in E. coli K12 (conditional DNA gyrase ^_ and topoisomerase IV ^_)

4. Analysis of the composite set of genes

5. Analysis of E. coli virulence plasmid pO157

6. Analysis of Salmonella typhi plasmid R27

7. Analysis of genes on pathogenicity islands in uropathogenic E. coli (Strain 536)

8. AT content analysis for the differentially expressed genes in all three data sets

9. AT content analysis for both plasmids

10. Statistical analysis and results of Wilcoxon signed-rank tests

11. Motif content of sequences known to be bound by H-NS

12. AT rich blocks in genes repressed by H-NS PDF, Doc, HTML