BACKGROUND: The first systematic study of small non-coding RNAs (sRNA, ncRNA) in Streptomyces is presented. Except for a few exceptions, the Streptomyces sRNAs, as well as the sRNAs in other genera of the Actinomyces group, have remained unstudied. This study was based on sequence conservation in intergenic regions of Streptomyces, localization of transcription termination factors, and genomic arrangement of genes flanking the predicted sRNAs. RESULTS: Thirty-two potential sRNAs in Streptomyces were predicted. Of these, expression of 20 was detected by microarrays and RT-PCR. The prediction was validated by a structure based computational approach. Two predicted sRNAs were found to be terminated by transcription termination factors different from the Rho-independent terminators. One predicted sRNA was identified computationally with high probability as a Streptomyces 6S RNA. Out of the 32 predicted sRNAs, 24 were found to be structurally dissimilar from known sRNAs. CONCLUSION: Streptomyces is the largest genus of Actinomyces, whose sRNAs have not been studied. The Actinomyces is a group of bacterial species with unique genomes and phenotypes. Therefore, in Actinomyces, new unique bacterial sRNAs may be identified. The sequence and structural dissimilarity of the predicted Streptomyces sRNAs demonstrated by this study serve as the first evidence of the uniqueness of Actinomyces sRNAs.

• MeSH
• Algorithms MeSH
• RNA, Bacterial chemistry   genetics   MeSH
• Species Specificity MeSH
• Genome, Bacterial MeSH
• DNA, Intergenic MeSH
• Nucleic Acid Conformation MeSH
• Models, Molecular MeSH
• RNA, Untranslated chemistry   genetics   MeSH
• Reverse Transcriptase Polymerase Chain Reaction MeSH
• Base Sequence MeSH
• Oligonucleotide Array Sequence Analysis MeSH
• Streptomyces coelicolor genetics   MeSH
• Streptomyces genetics   MeSH
• Terminator Regions, Genetic MeSH
• Computational Biology MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Validation Study MeSH
• Names of Substances
• RNA, Bacterial MeSH
• DNA, Intergenic MeSH
• RNA, Untranslated MeSH