Genome-wide identification of small RNAs in the opportunistic pathogen Enterococcus faecalis V583.

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,...

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Autores principales:	Kouki Shioya, Charlotte Michaux, Carsten Kuenne, Torsten Hain, Nicolas Verneuil, Aurélie Budin-Verneuil, Thomas Hartsch, Axel Hartke, Jean-Christophe Giard
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1ed4f6220b8249029959727815a5c431
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spelling	oai:doaj.org-article:1ed4f6220b8249029959727815a5c4312021-11-18T06:46:45ZGenome-wide identification of small RNAs in the opportunistic pathogen Enterococcus faecalis V583.1932-620310.1371/journal.pone.0023948https://doaj.org/article/1ed4f6220b8249029959727815a5c4312011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21912655/?tool=EBIhttps://doaj.org/toc/1932-6203Small 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.Kouki ShioyaCharlotte MichauxCarsten KuenneTorsten HainNicolas VerneuilAurélie Budin-VerneuilThomas HartschAxel HartkeJean-Christophe GiardPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 9, p e23948 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Kouki Shioya Charlotte Michaux Carsten Kuenne Torsten Hain Nicolas Verneuil Aurélie Budin-Verneuil Thomas Hartsch Axel Hartke Jean-Christophe Giard Genome-wide identification of small RNAs in the opportunistic pathogen Enterococcus faecalis V583.
description	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.
format	article
author	Kouki Shioya Charlotte Michaux Carsten Kuenne Torsten Hain Nicolas Verneuil Aurélie Budin-Verneuil Thomas Hartsch Axel Hartke Jean-Christophe Giard
author_facet	Kouki Shioya Charlotte Michaux Carsten Kuenne Torsten Hain Nicolas Verneuil Aurélie Budin-Verneuil Thomas Hartsch Axel Hartke Jean-Christophe Giard
author_sort	Kouki Shioya
title	Genome-wide identification of small RNAs in the opportunistic pathogen Enterococcus faecalis V583.
title_short	Genome-wide identification of small RNAs in the opportunistic pathogen Enterococcus faecalis V583.
title_full	Genome-wide identification of small RNAs in the opportunistic pathogen Enterococcus faecalis V583.
title_fullStr	Genome-wide identification of small RNAs in the opportunistic pathogen Enterococcus faecalis V583.
title_full_unstemmed	Genome-wide identification of small RNAs in the opportunistic pathogen Enterococcus faecalis V583.
title_sort	genome-wide identification of small rnas in the opportunistic pathogen enterococcus faecalis v583.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/1ed4f6220b8249029959727815a5c431
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Genome-wide identification of small RNAs in the opportunistic pathogen Enterococcus faecalis V583.

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