RsaOG, a new Staphylococcal family of highly transcribed non-coding RNA

The expression of trans-acting small RNAs in firmicutes has been poorly documented to date. This gap is being filled quickly in the genus Staphylococcus, which is both a model firmicute and an important human pathogen. Here we analyse RsaOG, a novel small RNA family specific to Staphylococcus and highly transcribed. This well conserved element, first discovered in a computational screen, was precisely mapped in the genome by RACE mapping and the identification of a putative transcriptional promoter. The proposed secondary structure presents two highly conserved unpaired sequences, part of which can form a pseudoknot. We suggest a possible involvement of the remaining conserved single stranded region in trans regulatory interactions.

[1]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[2]  D. Gautheret,et al.  Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. , 2001, Journal of molecular biology.

[3]  H. Margalit,et al.  Novel small RNA-encoding genes in the intergenic regions of Escherichia coli , 2001, Current Biology.

[4]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[5]  R. Novick.  Mobile genetic elements and bacterial toxinoses: the superantigen-encoding pathogenicity islands of Staphylococcus aureus. , 2003, Plasmid.

[6]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[7]  M. Bischoff,et al.  Microarray-based analysis of the Staphylococcus aureus sigmaB regulon. , 2004, Journal of bacteriology.

[8]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[9]  Peter F. Stadler,et al.  Thermodynamics of RNA-RNA Binding , 2006, German Conference on Bioinformatics.

[10]  Sam Griffiths-Jones,et al.  RALEE--RNA ALignment Editor in Emacs , 2005, Bioinform..

[11]  B. Felden,et al.  Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[12]  W. König,et al.  Genetic Classification and Distinguishing of Staphylococcus Species Based on Different Partial gap, 16S rRNA, hsp60, rpoB, sodA, and tuf Gene Sequences , 2008, Journal of Clinical Microbiology.

[13]  F. Major,et al.  The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data , 2008, Nature.

[14]  D. Gautheret,et al.  SINGLE‐PASS CLASSIFICATION OF ALL NON‐CODING SEQUENCES IN A BACTERIAL GENOME USING PHYLOGENETIC PROFILES , 2009, Genome research.

[15]  Yann Ponty,et al.  VARNA: Interactive drawing and editing of the RNA secondary structure , 2009, Bioinform..

[16]  P. François,et al.  A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation , 2009, Nucleic acids research.