Biocomputational prediction of small non-coding RNAs in Streptomyces

• Published in: BMC genomics Vol. 9; no. 1; p. 217
• Main Authors: Pánek, Josef, Bobek, Jan, Mikulík, Karel, Basler, Marek, Vohradský, Jiří
• Format: Journal Article
• Language: English
• Published: London BioMed Central 13.05.2008; BioMed Central Ltd; BMC
• Subjects: Actinomyces; Algorithms; Animal Genetics and Genomics; Base Sequence; Biomedical and Life Sciences; Computational Biology; DNA, Intergenic; Genetic aspects; Genome, Bacterial; Identification and classification; Life Sciences; Microarrays; Microbial Genetics and Genomics; Models, Molecular; Nucleic Acid Conformation; Oligonucleotide Array Sequence Analysis; Plant Genetics and Genomics; Proteomics; Research Article; Reverse Transcriptase Polymerase Chain Reaction; RNA; RNA, Bacterial - chemistry; RNA, Bacterial - genetics; RNA, Untranslated - chemistry; RNA, Untranslated - genetics; Species Specificity; Streptomyces; Streptomyces - genetics; Streptomyces coelicolor - genetics; Terminator Regions, Genetic; Czech Republic; sRNA Sequence; Streptomyces; Flank Gene; Transcription Termination; Genomic Arrangement
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/1471-2164-9-217

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.