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Identification and characterization of novel small RNAs in the aspS–yrvM intergenic region of the Bacillus subtilis genome

Institute of Biological Sciences, University of Tsukuba, Tsukuba-shi, Ibaraki 305-8572, Japan¹
Department of Molecular and Cellular Biology, The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 01238, USA²

Author for correspondence: Kouji Nakamura. Tel: +81 298 53 6419. Fax: +81 298 53 7723. e-mail: nakamura.kouji{at}nifty.ne.jp

A novel RNA species was isolated from Bacillus subtilis, and its sequence was determined and mapped to its genetic position. This RNA was termed BS190 RNA from the length of its mature form (190 nt), and the gene encoding it is located within the aspS–yrvM intergenic region of the B. subtilis genome. Northern blotting revealed that the novel RNA species is transcribed in vegetative cells as a larger precursor (BS201 RNA, 201 nt). After transcription, the 5' end of the precursor is processed to generate the mature form, BS190 RNA. A computer-aided prediction of the secondary structure of BS190 RNA showed that it can be folded into a single hairpin structure with some bulge structures. The authors found that the growth rate of a BS190 mutant strain of B. subtilis was reduced when compared to the wild-type. A phylogenetic comparison of the sequence of the BS190 RNA gene with sequences from the databases suggests that RNA related to BS190 RNA appears to be encoded in the genomes of Bacillus halodurans and Listeria monocytogenes.

Keywords: non-coding RNA, RNA processing, RNA secondary structure

Abbreviations: scRNA, small cytoplasmic RNA; sRNA, small RNA; tmRNA, transfer-message RNA

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