Small non-coding RNAs in Streptomyces coelicolor

• Published in: Nucleic acids research Vol. 36; no. 22; pp. 7240 - 7251
• Main Authors: Swiercz, Julia P, Hindra, Bobek, Jan, Haiser, Henry J, Di Berardo, Christina, Tjaden, Brian, Elliot, Marie A
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.12.2008; Oxford Publishing Limited (England)
• Subjects: Base Sequence; Genes, Bacterial; Genomics; Molecular Sequence Data; RNA; RNA, Bacterial - chemistry; RNA, Bacterial - genetics; RNA, Bacterial - metabolism; RNA, Untranslated - chemistry; RNA, Untranslated - genetics; RNA, Untranslated - metabolism; Streptomyces coelicolor; Streptomyces coelicolor - genetics; Streptomyces coelicolor - metabolism
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkn898

In bacteria, small RNAs (sRNAs) make important regulatory contributions to an ever increasing number of cellular processes. To expand the repertoire of known sRNAs, we sought to identify novel sRNAs in the differentiating, multicellular bacterium Streptomyces coelicolor. We describe a combined bioinformatic and experimental approach that enabled the identification and characterization of nine novel sRNAs in S. coelicolor, including a cis-encoded antisense sRNA. We examined sRNA expression throughout the S. coelicolor developmental cycle, which progresses from vegetative mycelium formation, to aerial mycelium formation and finally sporulation. We further determined the effects of growth medium composition (rich versus minimal medium) on sRNA gene expression, and compared wild-type sRNA expression profiles with those of four developmental mutants. All but two of the sRNAs exhibited some degree of medium dependence, with three sRNAs being expressed exclusively during growth on one medium type. Unlike most sRNAs characterized thus far, several sRNA genes in S. coelicolor were expressed constitutively (apart from during late sporulation), suggesting a possible housekeeping role for these transcripts. Others were expressed at specific developmental stages, and their expression profiles were altered in response to developmental mutations. Expression of one sRNA in particular was dependent upon the sporulation-specific sigma factor σWhiG.