The Spo0A regulon of Bacillus subtilis

Abstract

SummaryThe master regulator for entry into sporulation in Bacillus subtilis is the DNA-binding protein Spo0A, which has been found to influence, directly or indirectly, the expression of over 500 genes during the early stages of development. To search on a genomewide basis for genes under the direct control of Spo0A, we used chromatin immunoprecipitation in combination with gene microarray analysis to identify regions of the chromosome at which an activated form of Spo0A binds in vivo . This information in combination with transcriptional profiling using gene microarrays, gel electrophoretic mobility shift assays, using the DNA-binding domain of Spo0A, and bioinformatics enabled us to assign 103 genes to the Spo0A regulon in addition to 18 previously known members. Thus, in total, 121 genes, which are organized as 30 single-gene units and 24 operons, are likely to be under the direct control of Spo0A. Forty of these genes are under the positive control of Spo0A, and 81 are under its negative control. Among newly identified members of the regulon with transcription that was stimulated by Spo0A are genes for metabolic enzymes and genes for efflux pumps. Among members with transcription that was inhibited by Spo0A are genes encoding components of the DNA replication machinery and genes that govern flagellum biosynthesis and chemotaxis. Also included in the regulon are many (25) genes with products that are direct or indirect regulators of gene transcription. Spo0A is a master regulator for sporulation, but many of its effects on the global pattern of gene transcription are likely to be mediated indirectly by regulatory genes under its control.

kinA mRNA is missing a stop codon in the undomesticated Bacillus subtilis strain ATCC 6051

“…Spo0A~P directly regulates about 120 genes required for various stationary-phase phenomena including sporulation, competence development, production of degradative enzymes, cannibalism and biofilm formation (Molle et al, 2003). Spo0A-regulated genes can be classified into two groups based on Spo0A dose dependency: low-threshold genes require a low level of Spo0A~P for activation or repression of transcription, whereas high-threshold genes require a high level of Spo0A~P for transcription (Fujita et al, 2005).…”

“…In response to nutrient depletion, a histidine kinase phosphorylates itself, and then this phosphate residue is sequentially transferred to Spo0F, Spo0B and finally Spo0A. Spo0A is a member of a response-regulator family of transcriptional regulators, and phosphorylated Spo0A (Spo0A~P) activates transcription of early sporulation genes.Spo0A~P directly regulates about 120 genes required for various stationary-phase phenomena including sporulation, competence development, production of degradative enzymes, cannibalism and biofilm formation (Molle et al, 2003). Spo0A-regulated genes can be classified into two groups based on Spo0A dose dependency: low-threshold genes require a low level of Spo0A~P for activation or repression of transcription, whereas high-threshold genes require a high level of Spo0A~P for transcription (Fujita et al, 2005).…”

Phosphorylation of Spo0A by the Histidine Kinase KinD Requires the Lipoprotein Med in Bacillus subtilis

“…Colonies of cells that are mutant for sdp or skf are mutant for cannibalism and exhibit accelerated sporulation. A previous survey of members of the Spo0A regulon for genes involved in cannibalism revealed that a mutation in the gene med caused accelerated sporulation (25). Here we show that Med acts by stimulating phosphorylation of Spo0A and that the target of Med is KinD.…”

“…Med acts by stimulating phosphorylation (and under some conditions, dephosphorylation) of Spo0A indirectly through KinD. Previous work has shown that Spo0AϳP directly represses transcription of med (13,25). The negative regulation of med by Spo0A thus constitutes a negative feedback loop wherein the activity of KinD is curtailed as Spo0AϳP levels rise.…”

“…Spo0A is a member of the response regulator family of transcription factors and is active in its phosphorylated state (Spo0AϳP) (14,22). When phosphorylated, Spo0A can act as both an activator and repressor and is known to directly regulate about 120 genes (13,25) and indirectly over 500 genes (12,25).…”