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

Abstract

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.Bacterial sigma factors are positive regulators of gene expression that interact with core RNA polymerase and direct the initiation of transcription from defined promoter sequences (22, 25). The major sigma factor in most bacteria, sigma-A, is required for expression of many of the so-called housekeeping functions and the bulk of the RNA during growth. Many bacteria have multiple alternative sigma factors, which are responsible for directing transcription of specialized gene sets. Bacillus subtilis has at least 17 alternative sigma factors which are involved in a variety of processes, including certain stress responses, chemotaxis, and motility (25,30). One of the more dramatic examples of gene regulation by alternative sigma factors is the process of endospore formation (sporulation) in B. subtilis. The sporulation program of gene expression in B. subtilis is carried out under the direction of five alternative sigma factors whose activities are subject to spatial and temporal control (14, 51). Here we report the results of transcriptional profiling experiments aimed at identifying, on a genome-wide basis, genes under the control of one of these sigma factors, sigma-H.Sigma-H, the sigH (spo0H) gene product, directs the transcription of several genes that function in the transition from exponential growth to stationary phase, including the initiation of spore formation and entry into the state of genetic competence (1,7,12,20). Sigma-H is required at an early stage of sporulation and directly activates transcription of several sporulation genes including spo0A, spo0F, kinA, spo0M, spoVG, and spoVS and the spoIIA operon (2,4,28,41,42,46,54,59,61). Sigma-H also directs the transcription of several mem...

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