Analyses of competent and non-competent subpopulations of Bacillus subtilis reveal yhfW, yhxC and ncRNAs as novel players in competence.

Upon competence-inducing nutrient-limited conditions only part of the B. subtilis population becomes competent. Here, we separated the two sub-populations by Fluorescence Assisted Cell Sorting (FACS). Using RNA-seq we confirmed the previously described ComK regulon. We also found for the first time significantly down-regulated genes in the competent sub-population. The down-regulated genes are not under direct control by ComK, but have higher levels of corresponding antisense RNAs in the competent subpopulation. During competence, cell-division and replication are halted. By investigating the proteome during competence we found higher levels of the regulators of cell division, MinD and Noc. The exonucleases SbcC and SbcD were also primarily regulated at the post-transcriptional level. In the competent sub-population yhfW was newly identified as being highly up-regulated. Its absence reduces the expression of comG, and has a modest, but statistically significant effect on the expression of comK. Although expression of yhfW is higher in the competent subpopulation, no ComK-binding site is present in its promoter region. Mutants of yhfW have a small but significant defect in transformation. Metabolomic analyses revealed significant reductions in tricarboxylic acid (TCA) cycle metabolites and several amino acids in a DeltayhfW mutant. RNA-seq analysis of DeltayhfW revealed higher expression of the NAD synthesis genes nadA, nadB and nadC. This article is protected by copyright. All rights reserved.