Cargando…
Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria
BACKGROUND: Small regulatory RNAs (sRNAs) are widely found in bacteria and play key roles in many important physiological and adaptation processes. Studying their evolution and screening for events of coevolution with other genomic features is a powerful way to better understand their origin and ass...
Autores principales: | , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5689173/ https://www.ncbi.nlm.nih.gov/pubmed/29145803 http://dx.doi.org/10.1186/s12864-017-4242-0 |
_version_ | 1783279324868116480 |
---|---|
author | Cerutti, Franck Mallet, Ludovic Painset, Anaïs Hoede, Claire Moisan, Annick Bécavin, Christophe Duval, Mélodie Dussurget, Olivier Cossart, Pascale Gaspin, Christine Chiapello, Hélène |
author_facet | Cerutti, Franck Mallet, Ludovic Painset, Anaïs Hoede, Claire Moisan, Annick Bécavin, Christophe Duval, Mélodie Dussurget, Olivier Cossart, Pascale Gaspin, Christine Chiapello, Hélène |
author_sort | Cerutti, Franck |
collection | PubMed |
description | BACKGROUND: Small regulatory RNAs (sRNAs) are widely found in bacteria and play key roles in many important physiological and adaptation processes. Studying their evolution and screening for events of coevolution with other genomic features is a powerful way to better understand their origin and assess a common functional or adaptive relationship between them. However, evolution and coevolution of sRNAs with coding genes have been sparsely investigated in bacterial pathogens. RESULTS: We designed a robust and generic phylogenomics approach that detects correlated evolution between sRNAs and protein-coding genes using their observed and inferred patterns of presence-absence in a set of annotated genomes. We applied this approach on 79 complete genomes of the Listeria genus and identified fifty-two accessory sRNAs, of which most were present in the Listeria common ancestor and lost during Listeria evolution. We detected significant coevolution between 23 sRNA and 52 coding genes and inferred the Listeria sRNA-coding genes coevolution network. We characterized a main hub of 12 sRNAs that coevolved with genes encoding cell wall proteins and virulence factors. Among them, an sRNA specific to L. monocytogenes species, rli133, coevolved with genes involved either in pathogenicity or in interaction with host cells, possibly acting as a direct negative post-transcriptional regulation. CONCLUSIONS: Our approach allowed the identification of candidate sRNAs potentially involved in pathogenicity and host interaction, consistent with recent findings on known pathogenicity actors. We highlight four sRNAs coevolving with seven internalin genes, some of which being important virulence factors in Listeria. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-017-4242-0) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5689173 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-56891732017-11-24 Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria Cerutti, Franck Mallet, Ludovic Painset, Anaïs Hoede, Claire Moisan, Annick Bécavin, Christophe Duval, Mélodie Dussurget, Olivier Cossart, Pascale Gaspin, Christine Chiapello, Hélène BMC Genomics Research Article BACKGROUND: Small regulatory RNAs (sRNAs) are widely found in bacteria and play key roles in many important physiological and adaptation processes. Studying their evolution and screening for events of coevolution with other genomic features is a powerful way to better understand their origin and assess a common functional or adaptive relationship between them. However, evolution and coevolution of sRNAs with coding genes have been sparsely investigated in bacterial pathogens. RESULTS: We designed a robust and generic phylogenomics approach that detects correlated evolution between sRNAs and protein-coding genes using their observed and inferred patterns of presence-absence in a set of annotated genomes. We applied this approach on 79 complete genomes of the Listeria genus and identified fifty-two accessory sRNAs, of which most were present in the Listeria common ancestor and lost during Listeria evolution. We detected significant coevolution between 23 sRNA and 52 coding genes and inferred the Listeria sRNA-coding genes coevolution network. We characterized a main hub of 12 sRNAs that coevolved with genes encoding cell wall proteins and virulence factors. Among them, an sRNA specific to L. monocytogenes species, rli133, coevolved with genes involved either in pathogenicity or in interaction with host cells, possibly acting as a direct negative post-transcriptional regulation. CONCLUSIONS: Our approach allowed the identification of candidate sRNAs potentially involved in pathogenicity and host interaction, consistent with recent findings on known pathogenicity actors. We highlight four sRNAs coevolving with seven internalin genes, some of which being important virulence factors in Listeria. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-017-4242-0) contains supplementary material, which is available to authorized users. BioMed Central 2017-11-16 /pmc/articles/PMC5689173/ /pubmed/29145803 http://dx.doi.org/10.1186/s12864-017-4242-0 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Cerutti, Franck Mallet, Ludovic Painset, Anaïs Hoede, Claire Moisan, Annick Bécavin, Christophe Duval, Mélodie Dussurget, Olivier Cossart, Pascale Gaspin, Christine Chiapello, Hélène Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria |
title | Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria |
title_full | Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria |
title_fullStr | Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria |
title_full_unstemmed | Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria |
title_short | Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria |
title_sort | unraveling the evolution and coevolution of small regulatory rnas and coding genes in listeria |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5689173/ https://www.ncbi.nlm.nih.gov/pubmed/29145803 http://dx.doi.org/10.1186/s12864-017-4242-0 |
work_keys_str_mv | AT ceruttifranck unravelingtheevolutionandcoevolutionofsmallregulatoryrnasandcodinggenesinlisteria AT malletludovic unravelingtheevolutionandcoevolutionofsmallregulatoryrnasandcodinggenesinlisteria AT painsetanais unravelingtheevolutionandcoevolutionofsmallregulatoryrnasandcodinggenesinlisteria AT hoedeclaire unravelingtheevolutionandcoevolutionofsmallregulatoryrnasandcodinggenesinlisteria AT moisanannick unravelingtheevolutionandcoevolutionofsmallregulatoryrnasandcodinggenesinlisteria AT becavinchristophe unravelingtheevolutionandcoevolutionofsmallregulatoryrnasandcodinggenesinlisteria AT duvalmelodie unravelingtheevolutionandcoevolutionofsmallregulatoryrnasandcodinggenesinlisteria AT dussurgetolivier unravelingtheevolutionandcoevolutionofsmallregulatoryrnasandcodinggenesinlisteria AT cossartpascale unravelingtheevolutionandcoevolutionofsmallregulatoryrnasandcodinggenesinlisteria AT gaspinchristine unravelingtheevolutionandcoevolutionofsmallregulatoryrnasandcodinggenesinlisteria AT chiapellohelene unravelingtheevolutionandcoevolutionofsmallregulatoryrnasandcodinggenesinlisteria |