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Evolution of the IRF Family in Salmonids

Interferon regulatory factors (IRFs) as a family, are major regulators of the innate antiviral response in vertebrates principally involved in regulating the expression of interferons (IFNs) and interferon-stimulated genes (ISGs). To date, nine IRFs have been identified in mammals with a 10th member...

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Autores principales: Clark, Thomas C., Boudinot, Pierre, Collet, Bertrand
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7915476/
https://www.ncbi.nlm.nih.gov/pubmed/33567584
http://dx.doi.org/10.3390/genes12020238
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author Clark, Thomas C.
Boudinot, Pierre
Collet, Bertrand
author_facet Clark, Thomas C.
Boudinot, Pierre
Collet, Bertrand
author_sort Clark, Thomas C.
collection PubMed
description Interferon regulatory factors (IRFs) as a family, are major regulators of the innate antiviral response in vertebrates principally involved in regulating the expression of interferons (IFNs) and interferon-stimulated genes (ISGs). To date, nine IRFs have been identified in mammals with a 10th member also found in several avian and fish species. Through genome mining and phylogenetic analysis, we identified and characterised 23 irf genes in 6 salmonid species. This larger repertoire of IRF in salmonids results from two additional whole-genome duplications which occurred in early teleosts and salmonids, respectively. Synteny analysis was then used to identify and confirm which paralogues belonged to each subgroup and a new nomenclature was assigned to the salmonid IRFs. Furthermore, we present a full set of Real-Time PCR primers for all rainbow trout IRFs, confirmed by sequencing to ensure paralogue specificity. RT PCR was then used to examine the response of all trout irf genes in vivo, following Vibrio anguillarum and poly I:C stimulation, indicating potential functional divergence between paralogues. Overall, this study presents a comprehensive overview of the IRF family in salmonids and highlights some novel roles for the salmonid-specific IRFs in immunity.
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spelling pubmed-79154762021-03-01 Evolution of the IRF Family in Salmonids Clark, Thomas C. Boudinot, Pierre Collet, Bertrand Genes (Basel) Article Interferon regulatory factors (IRFs) as a family, are major regulators of the innate antiviral response in vertebrates principally involved in regulating the expression of interferons (IFNs) and interferon-stimulated genes (ISGs). To date, nine IRFs have been identified in mammals with a 10th member also found in several avian and fish species. Through genome mining and phylogenetic analysis, we identified and characterised 23 irf genes in 6 salmonid species. This larger repertoire of IRF in salmonids results from two additional whole-genome duplications which occurred in early teleosts and salmonids, respectively. Synteny analysis was then used to identify and confirm which paralogues belonged to each subgroup and a new nomenclature was assigned to the salmonid IRFs. Furthermore, we present a full set of Real-Time PCR primers for all rainbow trout IRFs, confirmed by sequencing to ensure paralogue specificity. RT PCR was then used to examine the response of all trout irf genes in vivo, following Vibrio anguillarum and poly I:C stimulation, indicating potential functional divergence between paralogues. Overall, this study presents a comprehensive overview of the IRF family in salmonids and highlights some novel roles for the salmonid-specific IRFs in immunity. MDPI 2021-02-08 /pmc/articles/PMC7915476/ /pubmed/33567584 http://dx.doi.org/10.3390/genes12020238 Text en © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Clark, Thomas C.
Boudinot, Pierre
Collet, Bertrand
Evolution of the IRF Family in Salmonids
title Evolution of the IRF Family in Salmonids
title_full Evolution of the IRF Family in Salmonids
title_fullStr Evolution of the IRF Family in Salmonids
title_full_unstemmed Evolution of the IRF Family in Salmonids
title_short Evolution of the IRF Family in Salmonids
title_sort evolution of the irf family in salmonids
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7915476/
https://www.ncbi.nlm.nih.gov/pubmed/33567584
http://dx.doi.org/10.3390/genes12020238
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