title: Genome-wide identification of Bacillus subtilis Zur-binding sites associated with a Zur box expands its known regulatory network.
abstract: BACKGROUND
  The Bacillus subtilis Zur transcription factor recognizes a specific DNA motif, the Zur box, to repress expression of genes in response to zinc availability. Although several Zur-regulated genes are well characterized, a genome-wide mapping of Zur-binding sites is needed to define further the set of genes directly regulated by this protein.
  
  
  RESULTS
  Using chromatin immunoprecipitation coupled with hybridization to DNA tiling arrays (ChIP-on-chip), we reported the identification of 80 inter- and intragenic chromosomal sites bound by Zur. Seven Zur-binding regions constitute the Zur primary regulon while 35 newly identified targets were associated with a predicted Zur box. Using transcriptional fusions an intragenic Zur box was showed to promote a full Zur-mediated repression when placed within a promoter region. In addition, intragenic Zur boxes appeared to mediate a transcriptional cis-repressive effect (4- to 9-fold) but the function of Zur at these sites remains unclear. Zur binding to intragenic Zur boxes could prime an intricate mechanisms of regulation of the transcription elongation, possibly with other transcriptional factors. However, the disruption of zinc homeostasis in Δzur cells likely affects many cellular processes masking direct Zur-dependent effects. Finally, most Zur-binding sites were located near or within genes responsive to disulfide stress. These findings expand the potential Zur regulon and reveal unknown interconnections between zinc and redox homeostasis regulatory networks.
  
  
  CONCLUSIONS
  Our findings considerably expand the potential Zur regulon, and reveal a new level of complexity in Zur binding to its targets via a Zur box motif and via a yet unknown mechanism that remains to be characterized.
authors: INRA, UMR1319 Micalis, F-78352, Jouy-en-Josas, France. eric.prestel@jouy.inra.fr.|AgroParisTech, UMR Micalis, F-78352, Jouy-en-Josas, France. eric.prestel@jouy.inra.fr.
authors: Eric
authors: E
authors: Prestel
authors: INRA, UMR1319 Micalis, F-78352, Jouy-en-Josas, France. philippe.noirot@jouy.inra.fr.|AgroParisTech, UMR Micalis, F-78352, Jouy-en-Josas, France. philippe.noirot@jouy.inra.fr.
authors: Philippe
authors: P
authors: Noirot
authors: INRA, UMR1319 Micalis, F-78352, Jouy-en-Josas, France. sandrine.auger@jouy.inra.fr.|AgroParisTech, UMR Micalis, F-78352, Jouy-en-Josas, France. sandrine.auger@jouy.inra.fr.
authors: Sandrine
authors: S
authors: Auger
mesh_terms: D019677:Artificial Gene Fusion; D001412:Bacillus subtilis / Q000235:genetics* / Q000378:metabolism*; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D004269:DNA, Bacterial / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D017930:Genes, Reporter; D006706:Homeostasis; D009693:Nucleic Acid Hybridization; D011485:Protein Binding; D018085:Regulon; D014157:Transcription Factors / Q000378:metabolism*; D015032:Zinc / Q000378:metabolism*
chemical_list: D004269:DNA, Bacterial; D014157:Transcription Factors; D015032:Zinc
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