In Bacillus subtilis LutR is part of the global complex regulatory network governing the adaptation to the transition from exponential growth to stationary phase

• Published in: Microbiology (Society for General Microbiology) 2014-02, Vol.160 (Pt 2), p.243-260
• Main Authors: İrigül-Sönmez, Öykü, Köroğlu, Türkan E, Öztürk, Büşra, Kovács, Ákos T, Kuipers, Oscar P, Yazgan-Karataş, Ayten
• Format: Article
• Language: English
• Subjects: Artificial Gene Fusion; Bacillus subtilis - genetics; Bacillus subtilis - growth & development; Bacillus subtilis - metabolism; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; beta-Galactosidase - analysis; beta-Galactosidase - genetics; Electrophoretic Mobility Shift Assay; Gene Deletion; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Gene Regulatory Networks; Genes, Reporter - genetics; Microarray Analysis; Real-Time Polymerase Chain Reaction; Regulon; Transcription Factors - genetics; Transcription Factors - metabolism
• ISSN: 1350-0872; 1465-2080
• DOI: 10.1099/mic.0.064675-0

The lutR gene, encoding a product resembling a GntR-family transcriptional regulator, has previously been identified as a gene required for the production of the dipeptide antibiotic bacilysin in Bacillus subtilis. To understand the broader regulatory roles of LutR in B. subtilis, we studied the genome-wide effects of a lutR null mutation by combining transcriptional profiling studies using DNA microarrays, reverse transcription quantitative PCR, lacZ fusion analyses and gel mobility shift assays. We report that 65 transcriptional units corresponding to 23 mono-cistronic units and 42 operons show altered expression levels in lutR mutant cells, as compared with lutR(+) wild-type cells in early stationary phase. Among these, 11 single genes and 25 operons are likely to be under direct control of LutR. The products of these genes are involved in a variety of physiological processes associated with the onset of stationary phase in B. subtilis, including degradative enzyme production, antibiotic production and resistance, carbohydrate utilization and transport, nitrogen metabolism, phosphate uptake, fatty acid and phospholipid biosynthesis, protein synthesis and translocation, cell-wall metabolism, energy production, transfer of mobile genetic elements, induction of phage-related genes, sporulation, delay of sporulation and cannibalism, and biofilm formation. Furthermore, an electrophoretic mobility shift assay performed in the presence of both SinR and LutR revealed a close overlap between the LutR and SinR targets. Our data also revealed a significant overlap with the AbrB regulon. Together, these findings reveal that LutR is part of the global complex, interconnected regulatory systems governing adaptation of bacteria to the transition from exponential growth to stationary phase.