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Journal of Bacteriology, September 2002, p. 4881-4890, Vol. 184, No. 17
0021-9193/02/$04.00+0     DOI: 10.1128/JB.184.17.4881-4890.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Genome-Wide Analysis of the Stationary-Phase Sigma Factor (Sigma-H) Regulon of Bacillus subtilis

Robert A. Britton,1 Patrick Eichenberger,2 Jose Eduardo Gonzalez-Pastor,2 Paul Fawcett,2,{dagger} Rita Monson,1 Richard Losick,2 and Alan D. Grossman1*

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 ,1 Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 021382

Received 5 April 2002/ Accepted 11 June 2002

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.

* Corresponding author. Mailing address: Department of Biology, Building 68-530, Massachusetts Institute of Technology, Cambridge, MA 02139. Phone: (617) 253-1515. Fax: (617) 253-2643. E-mail: adg{at}mit.edu.

{dagger} Present address: Department of Biochemistry, Stanford University, Stanford, CA 94035.

Journal of Bacteriology, September 2002, p. 4881-4890, Vol. 184, No. 17
0021-9193/02/$04.00+0     DOI: 10.1128/JB.184.17.4881-4890.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



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