Single-nucleotide polymorphisms (SNP) mining and their effect on the tridimensional protein structure prediction in a set of immunity-related expressed sequence tags (EST) in Atlantic salmon (Salmo salar)

Vallejos Vidal, Eva Carolina|||0000-0002-3091-2700; Reyes-Cerpa, Sebastián|||0000-0002-7676-1266; Rivas-Pardo, Jaime Andrés; Maisey, Kevin|||0000-0002-7423-6329; Yáñez, José M.|||0000-0002-6612-4087; Valenzuela, Hector; Cea, Pablo A.; Castro-Fernandez, Victor; Tort Bardolet, Lluís|||0000-0002-3907-722X; Sandino, Ana María|||0000-0002-3862-3743; Imarai, Mónica|||0000-0001-8767-9180; Reyes-López, Felipe E.|||0000-0002-5001-457X

Single-nucleotide polymorphisms (SNP) mining and their effect on the tridimensional protein structure prediction in a set of immunity-related expressed sequence tags (EST) in Atlantic salmon (Salmo salar)

Single-nucleotide polymorphisms (SNPs) are single genetic code variations considered one of the most common forms of nucleotide modifications. Such SNPs can be located in genes associated to immune response and, therefore, they may have direct implications over the phenotype of susceptibility to inf...

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Autores:	Vallejos Vidal, Eva Carolina\|\|\|0000-0002-3091-2700, Reyes-Cerpa, Sebastián\|\|\|0000-0002-7676-1266, Rivas-Pardo, Jaime Andrés, Maisey, Kevin\|\|\|0000-0002-7423-6329, Yáñez, José M.\|\|\|0000-0002-6612-4087, Valenzuela, Hector, Cea, Pablo A., Castro-Fernandez, Victor, Tort Bardolet, Lluís\|\|\|0000-0002-3907-722X, Sandino, Ana María\|\|\|0000-0002-3862-3743, Imarai, Mónica\|\|\|0000-0001-8767-9180, Reyes-López, Felipe E.\|\|\|0000-0002-5001-457X
Tipo de recurso:	artículo
Fecha de publicación:	2020
País:	España
Institución:	Universitat Autònoma de Barcelona
Repositorio:	Dipòsit Digital de Documents de la UAB
Idioma:	inglés
OAI Identifier:	oai:ddd.uab.cat:252505
Acceso en línea:	https://ddd.uab.cat/record/252505 https://dx.doi.org/urn:doi:10.3389/fgene.2019.01406
Access Level:	acceso abierto
Palabra clave:	Single-nucleotide polymorphism Immune response Synonymous SNP Nonsynonymous SNP Homology modeling 3D protein structure Molecular dynamics simulation Salmo salar

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repository_id_str
spelling	Single-nucleotide polymorphisms (SNP) mining and their effect on the tridimensional protein structure prediction in a set of immunity-related expressed sequence tags (EST) in Atlantic salmon (Salmo salar)Vallejos Vidal, Eva Carolina\|\|\|0000-0002-3091-2700Reyes-Cerpa, Sebastián\|\|\|0000-0002-7676-1266Rivas-Pardo, Jaime AndrésMaisey, Kevin\|\|\|0000-0002-7423-6329Yáñez, José M.\|\|\|0000-0002-6612-4087Valenzuela, HectorCea, Pablo A.Castro-Fernandez, VictorTort Bardolet, Lluís\|\|\|0000-0002-3907-722XSandino, Ana María\|\|\|0000-0002-3862-3743Imarai, Mónica\|\|\|0000-0001-8767-9180Reyes-López, Felipe E.\|\|\|0000-0002-5001-457XSingle-nucleotide polymorphismImmune responseSynonymous SNPNonsynonymous SNPHomology modeling3D protein structureMolecular dynamics simulationSalmo salarSingle-nucleotide polymorphisms (SNPs) are single genetic code variations considered one of the most common forms of nucleotide modifications. Such SNPs can be located in genes associated to immune response and, therefore, they may have direct implications over the phenotype of susceptibility to infections affecting the productive sector. In this study, a set of immune-related genes (cc motif chemokine 19 precursor [ ccl19 ], integrin β2 (itβ2, also named cd18), glutathione transferase omega-1 [ gsto-1 ], heat shock 70 KDa protein [ hsp70 ], major histocompatibility complex class I [ mhc-I ]) were analyzed to identify SNPs by data mining. These genes were chosen based on their previously reported expression on infectious pancreatic necrosis virus (IPNV)-infected Atlantic salmon phenotype. The available EST sequences for these genes were obtained from the Unigene database. Twenty-eight SNPs were found in the genes evaluated and identified most of them as transition base changes. The effect of the SNPs located on the 5'-untranslated region (UTR) or 3'-UTR upon transcription factor binding sites and alternative splicing regulatory motifs was assessed and ranked with a low-medium predicted FASTSNP score risk. Synonymous SNPs were found on itβ2 (c.2275G > A), gsto-1 (c.558G > A), and hsp70 (c.1950C > T) with low FASTSNP predicted score risk. The difference in the relative synonymous codon usage (RSCU) value between the variant codons and the wild-type codon (ΔRSCU) showed one negative (hsp70 c.1950C > T) and two positive ΔRSCU values (itβ2 c.2275G > A; gsto-1 c.558G > A), suggesting that these synonymous SNPs (sSNPs) may be associated to differences in the local rate of elongation. Nonsynonymous SNPs (nsSNPs) in the gsto-1 translatable gene region were ranked, using SIFT and POLYPHEN web-tools, with the second highest (c.205A > G; c484T > C) and the highest (c.499T > C; c.769A > C) predicted score risk possible. Using homology modeling to predict the effect of these nonsynonymous SNPs, the most relevant nucleotide changes for gsto-1 were observed for the nsSNPs c.205A > G, c484T > C, and c.769A > C. Molecular dynamics was assessed to analyze if these GSTO-1 variants have significant differences in their conformational dynamics, suggesting these SNPs could have allosteric effects modulating its catalysis. Altogether, these results suggest that candidate SNPs identified may play a crucial potential role in the immune response of Atlantic salmon. 22020-01-0120202020-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/252505https://dx.doi.org/urn:doi:10.3389/fgene.2019.01406reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengopen accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:2525052026-06-06T12:50:31Z
dc.title.none.fl_str_mv	Single-nucleotide polymorphisms (SNP) mining and their effect on the tridimensional protein structure prediction in a set of immunity-related expressed sequence tags (EST) in Atlantic salmon (Salmo salar)
title	Single-nucleotide polymorphisms (SNP) mining and their effect on the tridimensional protein structure prediction in a set of immunity-related expressed sequence tags (EST) in Atlantic salmon (Salmo salar)
spellingShingle	Single-nucleotide polymorphisms (SNP) mining and their effect on the tridimensional protein structure prediction in a set of immunity-related expressed sequence tags (EST) in Atlantic salmon (Salmo salar) Vallejos Vidal, Eva Carolina\|\|\|0000-0002-3091-2700 Single-nucleotide polymorphism Immune response Synonymous SNP Nonsynonymous SNP Homology modeling 3D protein structure Molecular dynamics simulation Salmo salar
title_short	Single-nucleotide polymorphisms (SNP) mining and their effect on the tridimensional protein structure prediction in a set of immunity-related expressed sequence tags (EST) in Atlantic salmon (Salmo salar)
title_full	Single-nucleotide polymorphisms (SNP) mining and their effect on the tridimensional protein structure prediction in a set of immunity-related expressed sequence tags (EST) in Atlantic salmon (Salmo salar)
title_fullStr	Single-nucleotide polymorphisms (SNP) mining and their effect on the tridimensional protein structure prediction in a set of immunity-related expressed sequence tags (EST) in Atlantic salmon (Salmo salar)
title_full_unstemmed	Single-nucleotide polymorphisms (SNP) mining and their effect on the tridimensional protein structure prediction in a set of immunity-related expressed sequence tags (EST) in Atlantic salmon (Salmo salar)
title_sort	Single-nucleotide polymorphisms (SNP) mining and their effect on the tridimensional protein structure prediction in a set of immunity-related expressed sequence tags (EST) in Atlantic salmon (Salmo salar)
dc.creator.none.fl_str_mv	Vallejos Vidal, Eva Carolina\|\|\|0000-0002-3091-2700 Reyes-Cerpa, Sebastián\|\|\|0000-0002-7676-1266 Rivas-Pardo, Jaime Andrés Maisey, Kevin\|\|\|0000-0002-7423-6329 Yáñez, José M.\|\|\|0000-0002-6612-4087 Valenzuela, Hector Cea, Pablo A. Castro-Fernandez, Victor Tort Bardolet, Lluís\|\|\|0000-0002-3907-722X Sandino, Ana María\|\|\|0000-0002-3862-3743 Imarai, Mónica\|\|\|0000-0001-8767-9180 Reyes-López, Felipe E.\|\|\|0000-0002-5001-457X
author	Vallejos Vidal, Eva Carolina\|\|\|0000-0002-3091-2700
author_facet	Vallejos Vidal, Eva Carolina\|\|\|0000-0002-3091-2700 Reyes-Cerpa, Sebastián\|\|\|0000-0002-7676-1266 Rivas-Pardo, Jaime Andrés Maisey, Kevin\|\|\|0000-0002-7423-6329 Yáñez, José M.\|\|\|0000-0002-6612-4087 Valenzuela, Hector Cea, Pablo A. Castro-Fernandez, Victor Tort Bardolet, Lluís\|\|\|0000-0002-3907-722X Sandino, Ana María\|\|\|0000-0002-3862-3743 Imarai, Mónica\|\|\|0000-0001-8767-9180 Reyes-López, Felipe E.\|\|\|0000-0002-5001-457X
author_role	author
author2	Reyes-Cerpa, Sebastián\|\|\|0000-0002-7676-1266 Rivas-Pardo, Jaime Andrés Maisey, Kevin\|\|\|0000-0002-7423-6329 Yáñez, José M.\|\|\|0000-0002-6612-4087 Valenzuela, Hector Cea, Pablo A. Castro-Fernandez, Victor Tort Bardolet, Lluís\|\|\|0000-0002-3907-722X Sandino, Ana María\|\|\|0000-0002-3862-3743 Imarai, Mónica\|\|\|0000-0001-8767-9180 Reyes-López, Felipe E.\|\|\|0000-0002-5001-457X
author2_role	author author author author author author author author author author author
dc.subject.none.fl_str_mv	Single-nucleotide polymorphism Immune response Synonymous SNP Nonsynonymous SNP Homology modeling 3D protein structure Molecular dynamics simulation Salmo salar
topic	Single-nucleotide polymorphism Immune response Synonymous SNP Nonsynonymous SNP Homology modeling 3D protein structure Molecular dynamics simulation Salmo salar
description	Single-nucleotide polymorphisms (SNPs) are single genetic code variations considered one of the most common forms of nucleotide modifications. Such SNPs can be located in genes associated to immune response and, therefore, they may have direct implications over the phenotype of susceptibility to infections affecting the productive sector. In this study, a set of immune-related genes (cc motif chemokine 19 precursor [ ccl19 ], integrin β2 (itβ2, also named cd18), glutathione transferase omega-1 [ gsto-1 ], heat shock 70 KDa protein [ hsp70 ], major histocompatibility complex class I [ mhc-I ]) were analyzed to identify SNPs by data mining. These genes were chosen based on their previously reported expression on infectious pancreatic necrosis virus (IPNV)-infected Atlantic salmon phenotype. The available EST sequences for these genes were obtained from the Unigene database. Twenty-eight SNPs were found in the genes evaluated and identified most of them as transition base changes. The effect of the SNPs located on the 5'-untranslated region (UTR) or 3'-UTR upon transcription factor binding sites and alternative splicing regulatory motifs was assessed and ranked with a low-medium predicted FASTSNP score risk. Synonymous SNPs were found on itβ2 (c.2275G > A), gsto-1 (c.558G > A), and hsp70 (c.1950C > T) with low FASTSNP predicted score risk. The difference in the relative synonymous codon usage (RSCU) value between the variant codons and the wild-type codon (ΔRSCU) showed one negative (hsp70 c.1950C > T) and two positive ΔRSCU values (itβ2 c.2275G > A; gsto-1 c.558G > A), suggesting that these synonymous SNPs (sSNPs) may be associated to differences in the local rate of elongation. Nonsynonymous SNPs (nsSNPs) in the gsto-1 translatable gene region were ranked, using SIFT and POLYPHEN web-tools, with the second highest (c.205A > G; c484T > C) and the highest (c.499T > C; c.769A > C) predicted score risk possible. Using homology modeling to predict the effect of these nonsynonymous SNPs, the most relevant nucleotide changes for gsto-1 were observed for the nsSNPs c.205A > G, c484T > C, and c.769A > C. Molecular dynamics was assessed to analyze if these GSTO-1 variants have significant differences in their conformational dynamics, suggesting these SNPs could have allosteric effects modulating its catalysis. Altogether, these results suggest that candidate SNPs identified may play a crucial potential role in the immune response of Atlantic salmon.
publishDate	2020
dc.date.none.fl_str_mv	2 2020-01-01 2020 2020-01-01
dc.type.none.fl_str_mv	Article http://purl.org/coar/resource_type/c_6501 VoR http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv	info:eu-repo/semantics/article
format	article
dc.identifier.none.fl_str_mv	https://ddd.uab.cat/record/252505 https://dx.doi.org/urn:doi:10.3389/fgene.2019.01406
url	https://ddd.uab.cat/record/252505 https://dx.doi.org/urn:doi:10.3389/fgene.2019.01406
dc.language.none.fl_str_mv	Inglés eng
language_invalid_str_mv	Inglés
language	eng
dc.rights.none.fl_str_mv	open access http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv	info:eu-repo/semantics/openAccess
rights_invalid_str_mv	open access http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv	openAccess
dc.format.none.fl_str_mv	application/pdf
dc.source.none.fl_str_mv	reponame:Dipòsit Digital de Documents de la UAB instname:Universitat Autònoma de Barcelona
instname_str	Universitat Autònoma de Barcelona
reponame_str	Dipòsit Digital de Documents de la UAB
collection	Dipòsit Digital de Documents de la UAB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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Single-nucleotide polymorphisms (SNP) mining and their effect on the tridimensional protein structure prediction in a set of immunity-related expressed sequence tags (EST) in Atlantic salmon (Salmo salar)

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