Genome-wide analysis of the stationary-phase sigma factor (sigma-H) regulon of Bacillus subtilis.
Sigma-H is an alternative RNA polymerase sigma factor that directs the transcription of many genes that function at the transition from exponential growth to stationary phase in Bacillus subtilis. Twenty-three promoters, which drive transcription of 33 genes, are known to be recognized by sigma-H-containing RNA polymerase. To identify additional genes under the control of sigma-H on a genome-wide basis, we carried out transcriptional profiling experiments using a DNA microarray containing >99% of the annotated B. subtilis open reading frames. In addition, we used a bioinformatics-based approach aimed at the identification of promoters recognized by RNA polymerase containing sigma-H. This combination of approaches was successful in confirming most of the previously described sigma-H-controlled genes. In addition, we identified 26 putative promoters that drive expression of 54 genes not previously known to be under the direct control of sigma-H. Based on the known or inferred function of most of these genes, we conclude that, in addition to its previously known roles in sporulation and competence, sigma-H controls genes involved in many physiological processes associated with the transition to stationary phase, including cytochrome biogenesis, generation of potential nutrient sources, transport, and cell wall metabolism.
Britton
Robert A
RA
Department of Biology, Building 68-530, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Eichenberger
Patrick
P
Gonzalez-Pastor
Jose Eduardo
JE
Fawcett
Paul
P
Monson
Rita
R
Losick
Richard
R
Grossman
Alan D
AD
D001412:Bacillus subtilis / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics*; D001665:Binding Sites; D016680:Genome, Bacterial; D020411:Oligonucleotide Array Sequence Analysis; D018085:Regulon; D014157:Transcription Factors / Q000235:genetics*; D014158:Transcription, Genetic
D001426:Bacterial Proteins; C087737:Spo0H protein, Bacillus subtilis; D014157:Transcription Factors