Transcriptome analysis of antibiotic-producing Bacillus subtilis SC-8 using RNA-seq provoked by small peptides from wild type and PapR mutant of Bacillus cereus strains

Bacillus subtilis SC-8 is known to show a narrow antimicrobial activity against foodborne pathogen Bacillus cereus group, representatively including B. cereus and B. anthracis. Peptide-activating PlcR (PapR) plays a significant role as a pleiotropic regulator of extracellular virulence factor. Previously we reported that PapR is assumed to stimulate antibiotic production of B. subtilis SC-8 when co-cultivated with B. cereus. Therefore, to understand effect of PapR on interspecies interactions, we investigated a global transcriptome of B. subtilis SC-8 using RNA-seq in response to small peptides from wild type (WT) and PapR mutant (MT) of B. cereus strains. Compared to MT strain, total 376 genes were significantly regulated in effect of small peptides from WT strain. In this case, genes related to carbohydrate transport and metabolism (9.6%), transcription (8.6%), signal transduction mechanisms (8.6%), and energy production and conversion (7.9%) were noticeably down-regulated in WT strain. Additionally, the expression of biosynthetic genes encoding several antibiotics in B. subtilis SC-8 genome was significantly decreased. Furthermore, there were almost the half number of up- or down-regulated genes (42.9%) involved in glycolysis and the majority of genes related to TCA cycle (80%) showed altered expression level when compared between in presence of small peptides from WT and MT strains. Using expression profiles, the molecular mechanisms for changes in antibiotic production and other related factors were examined in presence of WT and MT B. cereus strains. This study provides a reference for the further study of antibiotic production of B. subtilis SC-8 against B. cereus group.