We report the identification and characterization on a genome-wide basis of genes under the control of the developmental transcription factor σE in Bacillus subtilis. The σE factor governs gene expression in the larger of the two cellular compartments (the mother cell) created by polar division during the developmental process of sporulation. Using transcriptional profiling and bioinformatics we show that 253 genes (organized in 157 operons) appear to be controlled by σE. Among these, 181 genes (organized in 121 operons) had not been previously described as members of this regulon. Promoters for many of the newly identified genes were located by transcription start site mapping. To assess the role of these genes in sporulation, we created null mutations in 98 of the newly identified genes and operons. Of the resulting mutants, 12 (in prkA, ybaN, yhbH, ykvV, ylbJ, ypjB, yqfC, yqfD, ytrH, ytrI, ytvI and yunB) exhibited defects in spore formation. In addition, subcellular localization studies were carried out using in-frame fusions of several of the genes to the coding sequence for GFP. A majority of the fusion proteins localized either to the membrane surrounding the developing spore or to specific layers of the spore coat, although some fusions showed a uniform distribution in the mother cell cytoplasm. Finally, we used comparative genomics to determine that 46 of the σE-controlled genes in B.subtilis were present in all of the Gram-positive endospore-forming bacteria whose genome has been sequenced, but absent from the genome of the closely related but not endospore-forming bacterium Listeria monocytogenes, thereby defining a core of conserved sporulation genes of probable common ancestral origin. Our findings set the stage for a comprehensive understanding of the contribution of a cell-specific transcription factor to development and morphogenesis.
Bibliographical noteFunding Information:
We thank Katerina Ragkousi and Peter Setlow, and Sarah Trewhitt, Haridasan Chirakkal and Anne Moir for communicating results prior to publication. We are grateful to Virginie Molle for sharing results prior to publication and assistance in the production of the microarrays. We thank Paul Fawcett for helpful comments on the manuscript, Tyler Aldredge, Keith Morneau and Rachel Erlich from the Bauer Center for Genomics Research at Harvard University for advice, Robert Britton at the Massachusetts Institute of Technology for help at an early stage of the project and members of the laboratory for helpful discussions. P.E. was a post-doctoral fellow of the Swiss National Science Foundation and of the Human Frontier Science Program. S.T.J., E.M.C. and J.S.L. were supported by grant DMS 0094613 from the National Science Foundation and grant R01 HG02518-01 from the National Institutes of Health. C.v.O. was supported by NIH NRSA fellowship GM20165. J.E.G.-P. acknowledges the support of the Ministerio de Educacion y Cienca Post-doctoral Fellowship (Spain). M.F. was supported by a grant-in-aid for research abroad from the Ministry of Education, Science and Culture (Japan). S.B.-Y. was a post-doctoral fellow of the Human Frontier Science Program. This work was supported by National Institutes of Health grant GM18568 to R.L.
- Bacillus subtilis
- Bacterial genomics
- Protein localization
- Sigma factors