A simple and efficient method to search for selected primary transcripts: non-coding and antisense RNAs in the human pathogen Enterococcus faecalis
| Autor: | Sean Kennedy, David Halpern, Aymeric Fouquier d'Hérouël, Françoise Wessner, Erik Aurell, Joseph Ly-Vu, Pascale Serror, Francis Repoila |
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| Přispěvatelé: | MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Royal Inst Technol, Dept Computat Biol, Albanova University Center, Institut National de la Recherche Agronomique, EGIDE-PESSOA [20014TA], transnational ERA-Net Pathogenomics program, Agence Nationale de la Recherche [ANR-06-PATHO-008-02], Sweden Science Council [2006-156], UMR1319 Institut Micalis INRA, Domaine de Vilvert, France |
| Jazyk: | angličtina |
| Rok vydání: | 2011 |
| Předmět: |
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences
RNA Untranslated EXTRACELLULAR-SUPEROXIDE PRODUCTION STAPHYLOCOCCUS-AUREUS REVEALS MESSENGER-RNA ESCHERICHIA-COLI LISTERIA-MONOCYTOGENES REGULATORY MECHANISMS CONTROLS EXPRESSION BACILLUS-SUBTILIS BIOFILM FORMATION SERINE-PROTEASE Biochemistry biophysics & molecular biology [F05] [Life sciences] chemistry.chemical_compound RNA polymerase Enterococcus faecalis Biochimie biophysique & biologie moléculaire [F05] [Sciences du vivant] Conserved Sequence Sequence Tagged Sites Genetics 0303 health sciences biology Non-coding RNA RNA Bacterial Methods Online Enterococcus faecalis/genetics/metabolism In silico Bacterial Toxins 03 medical and health sciences RNA Antisense Gene RNA Untranslated/analysis/genetics/metabolism 030304 developmental biology Bacterial Toxins/genetics RNA Antisense/analysis/genetics Messenger RNA Tiling array Base Sequence 030306 microbiology Sequence Analysis RNA RNA biology.organism_classification Oxidative Stress chemistry Genetic Loci RNA Bacterial/analysis/genetics/metabolism Peptides Peptides/genetics |
| Zdroj: | Nucleic Acids Research Nucleic Acids Research, Oxford University Press, 2011, 39 (7), pp.E46-U88. ⟨10.1093/nar/gkr012⟩ Nucleic Acids Research 7 (39), E46-U88. (2011) |
| ISSN: | 0305-1048 1362-4962 |
| DOI: | 10.1093/nar/gkr012⟩ |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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