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Journal of Bacteriology, January 2006, p. 532-541, Vol. 188, No. 2
0021-9193/06/$08.00+0     doi:10.1128/JB.188.2.532-541.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Genes for Small, Noncoding RNAs under Sporulation Control in Bacillus subtilis{dagger}

Jessica M. Silvaggi,1 John B. Perkins,2 and Richard Losick1*

Department of Molecular and Cellular Biology, The Biological Laboratories, Harvard University, Cambridge, Massachusetts 02138,1 DSM Nutritional Products, Ltd., Biotechnology R&D, P.O. Box 3255, Bldg 203/20A, CH-4002 Basel, Switzerland2

Received 14 September 2005/ Accepted 24 October 2005

The process of sporulation in the bacterium Bacillus subtilis is known to involve the programmed activation of several hundred protein-coding genes. Here we report the discovery of previously unrecognized genes under sporulation control that specify small, non-protein-coding RNAs (sRNAs). Genes for sRNAs were identified by transcriptional profiling with a microarray bearing probes for intergenic regions in the genome and by use of a comparative genomics algorithm that predicts regions of conserved RNA secondary structure. The gene for one such sRNA, SurA, which is located in the region between yndK and yndL, was induced at the start of development under the indirect control of the master regulator for entry into sporulation, Spo0A. The gene for a second sRNA, SurC, located in the region between dnaJ and dnaK, was switched on at a late stage of sporulation by the RNA polymerase sigma factor {sigma}K, which directs gene transcription in the mother cell compartment of the developing sporangium. Finally, a third intergenic region, that between polC and ylxS, which specified several sRNAs, including two transcripts produced under the control of the forespore-specific sigma factor {sigma}G and a third transcript generated by {sigma}K, was identified. Our results indicate that the full repertoire of sporulation-specific gene expression involves the activation of multiple genes for small, noncoding RNAs.

* Corresponding author. Mailing address: Department of Molecular and Cellular Biology, The Biological Laboratories, 16 Divinity Ave., Harvard University, Cambridge, MA 02138. Phone: (617) 495-4905. Fax: (617) 496-4642. E-mail: losick{at}mcb.harvard.edu.

{dagger} Supplemental material for this article may be found at http://jb.asm.org/.

Journal of Bacteriology, January 2006, p. 532-541, Vol. 188, No. 2
0021-9193/06/$08.00+0     doi:10.1128/JB.188.2.532-541.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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