High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes.
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.
Lang
Benjamin
B
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
Blot
Nicolas
N
Bouffartigues
Emeline
E
Buckle
Malcolm
M
Geertz
Marcel
M
Gualerzi
Claudio O
CO
Mavathur
Ramesh
R
Muskhelishvili
Georgi
G
Pon
Cynthia L
CL
Rimsky
Sylvie
S
Stella
Stefano
S
Babu
M Madan
MM
Travers
Andrew
A
D020856:AT Rich Sequence; D001426:Bacterial Proteins / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D018983:DNA Footprinting; D004269:DNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D020868:Gene Silencing; D016680:Genome, Bacterial; D044404:Genomic Islands; D023281:Genomics; D009876:Operon; D020560:Proteobacteria / Q000235:genetics
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; C031908:H-NS protein, bacteria