Comparative analysis of non-coding RNAs in the antibiotic-producing Streptomyces bacteria.
BACKGROUND
Non-coding RNAs (ncRNAs) are key regulatory elements that control a wide range of cellular processes in all bacteria in which they have been studied. Taking advantage of recent technological innovations, we set out to fully explore the ncRNA potential of the multicellular, antibiotic-producing Streptomyces bacteria.


RESULTS
Using a comparative RNA sequencing analysis of three divergent model streptomycetes (S. coelicolor, S. avermitilis and S. venezuelae), we discovered hundreds of novel cis-antisense RNAs and intergenic small RNAs (sRNAs). We identified a ubiquitous antisense RNA species that arose from the overlapping transcription of convergently-oriented genes; we termed these RNA species 'cutoRNAs', for convergent untranslated overlapping RNAs. Conservation between different classes of ncRNAs varied greatly, with sRNAs being more conserved than antisense RNAs. Many species-specific ncRNAs, including many distinct cutoRNA pairs, were located within antibiotic biosynthetic clusters, including the actinorhodin, undecylprodigiosin, and coelimycin clusters of S. coelicolor, the chloramphenicol cluster of S. venezuelae, and the avermectin cluster of S. avermitilis.


CONCLUSIONS
These findings indicate that ncRNAs, including a novel class of antisense RNA, may exert a previously unrecognized level of regulatory control over antibiotic production in these bacteria. Collectively, this work has dramatically expanded the ncRNA repertoire of three Streptomyces species and has established a critical foundation from which to investigate ncRNA function in this medically and industrially important bacterial genus.
Department of Biology and Michael G, DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada. melliot@mcmaster.ca.
Matthew J
MJ
Moody
Rachel A
RA
Young
Stephanie E
SE
Jones
Marie A
MA
Elliot
D000898:Antibiosis / Q000235:genetics; D001483:Base Sequence; D017124:Conserved Sequence; D005798:Genes, Bacterial; D055029:Inverted Repeat Sequences; D008969:Molecular Sequence Data; D005810:Multigene Family; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D017423:Sequence Analysis, RNA; D013045:Species Specificity; D048372:Streptomyces coelicolor / Q000235:genetics*; D059467:Transcriptome
D012329:RNA, Bacterial; D022661:RNA, Untranslated