Genome‐wide mapping of TnrA‐binding sites provides new insights into the TnrA regulon in Bacillus subtilis

• Published in: MicrobiologyOpen (Weinheim) Vol. 4; no. 3; pp. 423 - 435
• Main Authors: Mirouze, Nicolas, Bidnenko, Elena, Noirot, Philippe, Auger, Sandrine
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01.06.2015; Wiley; BlackWell Publishing Ltd
• Subjects: Amino acids; Bacillus subtilis; Bacillus subtilis - genetics; Bacillus subtilis - metabolism; Bacterial Proteins - metabolism; Binding Sites; Biosynthesis; Cellular communication; ChIP‐on‐chip; Chromatin; Chromosome Mapping; Chromosomes; Consensus Sequence; Deoxyribonucleic acid; DNA; E coli; Enzymes; Gene Deletion; Gene expression; Gene Expression Regulation, Bacterial; Gene mapping; Genes; Genes, Bacterial; Genome, Bacterial; Genomes; Glutamine - metabolism; Hybridization; Immunoprecipitation; Life Sciences; Mapping; Metabolism; Nitrogen; Nitrogen - metabolism; Original Research; Oxidative stress; Protein Binding; Proteins; Regulation; Regulon; Repressor Proteins - metabolism; Stress response; Tiling; TnrA regulator; Transcription; Transcription, Genetic; ChIP-on-chip; TnrA regulator; Bacillus subtilis; oxidative stress; nitrogen metabolism; bacillus subtilis; ChIP on chip
• ISSN: 2045-8827; 2045-8827
• DOI: 10.1002/mbo3.249

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. In this study, we focused on mapping the DNA‐binding sites of the Bacillus subtilis TnrA regulator at the genomic scale. Further analysis with real‐time in vivo transcriptional profiling allowed to define the TnrA primary regulon and to improve the TnrA box consensus. New connections were revealed between the control of nitrogen availability and other cellular processes.