title: Genome-wide identification of small RNAs in the opportunistic pathogen Enterococcus faecalis V583.
abstract: Small RNA molecules (sRNAs) are key mediators of virulence and stress inducible gene expressions in some pathogens. In this work we identify sRNAs in the gram positive opportunistic pathogen Enterococcus faecalis. We characterized 11 sRNAs by tiling microarray analysis, 5' and 3' RACE-PCR, and Northern blot analysis. Six sRNAs were specifically expressed at exponential phase, two sRNAs were observed at stationary phase, and three were detected during both phases. Searches of putative functions revealed that three of them (EFA0080_EFA0081 and EFB0062_EFB0063 on pTF1 and pTF2 plasmids, respectively, and EF0408_EF04092 located on the chromosome) are similar to antisense RNA involved in plasmid addiction modules. Moreover, EF1097_EF1098 shares strong homologies with tmRNA (bi-functional RNA acting as both a tRNA and an mRNA) and EF2205_EF2206 appears homologous to 4.5S RNA member of the Signal Recognition Particle (SRP) ribonucleoprotein complex. In addition, proteomic analysis of the ΔEF3314_EF3315 sRNA mutant suggests that it may be involved in the turnover of some abundant proteins. The expression patterns of these transcripts were evaluated by tiling array hybridizations performed with samples from cells grown under eleven different conditions some of which may be encountered during infection. Finally, distribution of these sRNAs among genome sequences of 54 E. faecalis strains was assessed. This is the first experimental genome-wide identification of sRNAs in E. faecalis and provides impetus to the understanding of gene regulation in this important human pathogen.
authors.affiliation: Laboratoire de Microbiologie de l'Environnement, EA956-USC INRA 2017-IFR146 ICORE, University of Caen, Caen, France.
authors.forename: Kouki
authors.initials: K
authors.lastname: Shioya
authors.forename: Charlotte
authors.initials: C
authors.lastname: Michaux
authors.forename: Carsten
authors.initials: C
authors.lastname: Kuenne
authors.forename: Torsten
authors.initials: T
authors.lastname: Hain
authors.forename: Nicolas
authors.initials: N
authors.lastname: Verneuil
authors.forename: Aurélie
authors.initials: A
authors.lastname: Budin-Verneuil
authors.forename: Thomas
authors.initials: T
authors.lastname: Hartsch
authors.forename: Axel
authors.initials: A
authors.lastname: Hartke
authors.forename: Jean-Christophe
authors.initials: JC
authors.lastname: Giard
mesh_terms: D000818:Animals; D001483:Base Sequence; D002876:Chromosomes, Bacterial / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D013293:Enterococcus faecalis / Q000235:genetics* / Q000502:physiology; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D009894:Opportunistic Infections / Q000382:microbiology*; D010957:Plasmids / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D015203:Reproducibility of Results; D013045:Species Specificity; D013312:Stress, Physiological / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D021901:DNA, Intergenic; D012329:RNA, Bacterial; D022661:RNA, Untranslated