Genome-wide analysis of temporally regulated and compartment-specific gene expression in sporulating cells of Bacillus subtilis

Abstract

Temporal and compartment-specific control of gene expression during sporulation in Bacillus subtilis is governed by a cascade of four RNA polymerase subunits. s F in the prespore and s E in the mother cell control early stages of development, and are replaced at later stages by s G and s K , respectively. Ultimately, a comprehensive description of the molecular mechanisms underlying spore morphogenesis requires the knowledge of all the intervening genes and their assignment to specific regulons. Here, in an extension of earlier work, DNA macroarrays have been used, and members of the four compartment-specific sporulation regulons have been identified. Genes were identified and grouped based on: i) their temporal expression profile and ii) the use of mutants for each of the four sigma factors and a bofA allele, which allows s K activation in the absence of s G . As a further test, artificial production of active alleles of the sigma factors in non-sporulating cells was employed. A total of 439 genes were found, including previously characterized genes whose transcription is induced during sporulation: 55 in the s F regulon, 154 s E -governed genes, 113 s G -dependent genes, and 132 genes under s K control. The results strengthen the view that the activities of s F , s E , s G and s K are largely compartmentalized, both temporally as well as spatially, and that the major vegetative sigma factor (s A ) is active throughout sporulation. The results provide a dynamic picture of the changes in the overall pattern of gene expression in the two compartments of the sporulating cell, and offer insight into the roles of the prespore and the mother cell at different times of spore morphogenesis.

Cardiolipin Enrichment in Spore Membranes and Its Involvement in Germination of Bacillus subtilis Marburg

“…Transcriptional profiling showing that the mRNA level of clsA and ywjE exhibits a s E -dependent increase by 2.1 and 11.7, respectively (Eichenberger et al, 2003), provides supporting evidence. Recent temporal profiling (Steil et al, 2005) also indicates a s G -dependent increase of ywjE. The hypothesis that the gene product of pssA is involved in CL production in spore membranes is consistent with the observation that pssA is apparently activated upon entry into the sporulation phase by s X and s W (Cao and Helmann, 2004).…”

Small acid-soluble spore proteins of Clostridium acetobutylicum are able to protect DNA in vitro and are specifically cleaved by germination protease GPR and spore protease YyaC

“…Microarray data confirmed a similar expression pattern in B. subtilis (Steil et al, 2005;Wang et al, 2006) and in C. acetobutylicum (Jones et al, 2008). Accordingly, C. acetobutylicum mRNA transcripts of ssp genes could be verified only in total RNA samples of sporulating cells (Fig.…”

“…The existence of a second GPR-like activity was suggested after the observation that B. subtilis spores lacking GPR are still able, albeit more slowly, to degrade a/b-type SASPs and to form colonies (Postemsky et al, 1978;Sanchez-Salas et al, 1992). GPR was classified as an atypical aspartic acid protease (Carroll & Setlow, 2005) and recently the yyaC gene product, which belongs to the s F regulon of B. subtilis (Steil et al, 2005;Wang et al, 2006), was suggested as a putative GPR-like enzyme based on conserved aspartic acid residues similar to GPR (Carroll, 2008). However, enzyme activity and substrate specificity of GPR were analysed only in B. megaterium and B. subtilis (Sanchez-Salas et al, 1992;Carroll & Setlow, 2005;Traag et al, 2013).…”

FisB mediates membrane fission during sporulation in Bacillus subtilis

“…The first mother cell-specific transcription factor that is induced during sporulation is the alternative s factor s E (Stragier and Losick 1996;Piggot and Losick 2002). The s E regulon has been defined by transcriptional profiling (Eichenberger et al 2003;Feucht et al 2003;Steil et al 2005), and strains harboring deletions in most of the genes in the regulon have been generated (Eichenberger et al 2003). Using the criteria described above, we examined a subset of this ordered library of mutants using the fluorescent membrane fission assay of Sharp and Pogliano (1999).…”