A simple and efficient method to search for selected primary transcripts: non-coding and antisense RNAs in the human pathogen Enterococcus faecalis
2011 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 39, no 7, E46- p.Article in journal (Refereed) Published
Enterococcus faecalis is a commensal bacterium and a major opportunistic human pathogen. In this study, we combined in silico predictions with a novel 5'RACE-derivative method coined '5'tagRACE', to perform the first search for non-coding RNAs (ncRNAs) encoded on the E. faecalis chromosome. We used the 5'tagRACE to simultaneously probe and characterize primary transcripts, and demonstrate here the simplicity, the reliability and the sensitivity of the method. The 5'tagRACE is complementary to tiling arrays or RNA-sequencing methods, and is also directly applicable to deep RNA sequencing and should significantly improve functional studies of bacterial RNA landscapes. From 45 selected loci of the E. faecalis chromosome, we discovered and mapped 29 novel ncRNAs, 10 putative novel mRNAs and 16 antisense transcriptional organizations. We describe in more detail the oxygen-dependent expression of one ncRNA located in an E. faecalis pathogenicity island, the existence of an ncRNA that is antisense to the ncRNA modulator of the RNA polymerase, SsrS and provide evidences for the functional interplay between two distinct toxin-antitoxin modules.
Place, publisher, year, edition, pages
2011. Vol. 39, no 7, E46- p.
antitoxin, bacterial RNA, messenger RNA, RNA polymerase, TxpA toxin, unclassified drug, untranslated RNA
Condensed Matter Physics
IdentifiersURN: urn:nbn:se:kth:diva-31483DOI: 10.1093/nar/gkr012ISI: 000289628400006PubMedID: 21266481ScopusID: 2-s2.0-79954609527OAI: oai:DiVA.org:kth-31483DiVA: diva2:404315
FunderSwedish Research Council, 2006-156
QC 201103162011-03-162011-03-162012-08-22Bibliographically approved