title: Genome-wide mapping of TnrA-binding sites provides new insights into the TnrA regulon in Bacillus subtilis.
abstract: Under nitrogen limitation conditions, Bacillus subtilis induces a sophisticated network of adaptation responses. More precisely, the B. subtilis TnrA regulator represses or activates directly or indirectly the expression of a hundred genes in response to nitrogen availability. The global TnrA regulon have already been identified among which some directly TnrA-regulated genes have been characterized. However, a genome-wide mapping of in vivo TnrA-binding sites was still needed to clearly define the set of genes directly regulated by TnrA. Using chromatin immunoprecipitation coupled with hybridization to DNA tiling arrays (ChIP-on-chip), we now provide in vivo evidence that TnrA reproducibly binds to 42 regions on the chromosome. Further analysis with real-time in vivo transcriptional profiling, combined with results from previous reports, allowed us to define the TnrA primary regulon. We identified 35 promoter regions fulfilling three criteria necessary to be part of this primary regulon: (i) TnrA binding in ChIP-on-chip experiments and/or in previous in vitro studies; (ii) the presence of a TnrA box; (iii) TnrA-dependent expression regulation. In addition, the TnrA primary regulon delimitation allowed us to improve the TnrA box consensus. Finally, our results reveal new interconnections between the nitrogen regulatory network and other cellular processes.
authors.affiliation: UMR1319 Micalis, INRA, F-78352, Jouy-en-Josas, France.|UMR Micalis, AgroParisTech, F-78352, Jouy-en-Josas, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Mirouze
authors.affiliation: UMR1319 Micalis, INRA, F-78352, Jouy-en-Josas, France.|UMR Micalis, AgroParisTech, F-78352, Jouy-en-Josas, France.
authors.forename: Elena
authors.initials: E
authors.lastname: Bidnenko
authors.affiliation: UMR1319 Micalis, INRA, F-78352, Jouy-en-Josas, France.|UMR Micalis, AgroParisTech, F-78352, Jouy-en-Josas, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Noirot
authors.affiliation: UMR1319 Micalis, INRA, F-78352, Jouy-en-Josas, France.|UMR Micalis, AgroParisTech, F-78352, Jouy-en-Josas, France.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Auger
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics* / Q000378:metabolism*; D001426:Bacterial Proteins / Q000378:metabolism*; D001665:Binding Sites; D002874:Chromosome Mapping; D016384:Consensus Sequence; D017353:Gene Deletion; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D005973:Glutamine / Q000378:metabolism; D009584:Nitrogen / Q000378:metabolism; D011485:Protein Binding; D018085:Regulon; D012097:Repressor Proteins / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D012097:Repressor Proteins; C101458:ScgR protein, Bacillus subtilis; D005973:Glutamine; D009584:Nitrogen
keywords: Bacillus subtilis; ChIP-on-chip; TnrA regulator; nitrogen metabolism; oxidative stress