SARS-CoV-2 codon usage bias downregulates host expressed genes with similar codon usage

Autores
Alonso, Andrés M.; Diambra, Luis Aníbal
Año de publicación
2020
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Severe acute respiratory syndrome is quickly spreading throughout the world and was declared as a pandemic by the World Health Organisation (WHO). The pathogenic agent is a new coronavirus (SARS-CoV-2) that infects pulmonary cells with great effectiveness. In this study we focus on the codon composition for the viral proteins synthesis and its relationship with the proteins synthesis of the host. Our analysis reveals that SARS-CoV-2 preferred codons have poor representation of G or C nucleotides in the third position, a characteristic which could conduct to an unbalance in the tRNAs pools of the infected cells with serious implications in host protein synthesis. By integrating this observation with proteomic data from infected cells, we observe a reduced translation rate of host proteins associated with highly expressed genes, and that they share the codon usage bias of the virus. The functional analysis of these genes suggests that this mechanism of epistasis contributes to understand some deleterious collateral effect as result of the viral replication. In this manner, our finding contribute to the understanding of the SARS-CoV-2 pathogeny and could be useful for the design of a vaccine based on the live attenuated strategy.
Centro Regional de Estudios Genómicos
Materia
Biología
SARS-CoV-2
Codon usage bias
Codon optimality
Translational control
Pathogeny
Vaccine design
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
SEDICI (UNLP)
Institución
Universidad Nacional de La Plata
OAI Identificador
oai:sedici.unlp.edu.ar:10915/135183

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network_name_str SEDICI (UNLP)
spelling SARS-CoV-2 codon usage bias downregulates host expressed genes with similar codon usageAlonso, Andrés M.Diambra, Luis AníbalBiologíaSARS-CoV-2Codon usage biasCodon optimalityTranslational controlPathogenyVaccine designSevere acute respiratory syndrome is quickly spreading throughout the world and was declared as a pandemic by the World Health Organisation (WHO). The pathogenic agent is a new coronavirus (SARS-CoV-2) that infects pulmonary cells with great effectiveness. In this study we focus on the codon composition for the viral proteins synthesis and its relationship with the proteins synthesis of the host. Our analysis reveals that SARS-CoV-2 preferred codons have poor representation of G or C nucleotides in the third position, a characteristic which could conduct to an unbalance in the tRNAs pools of the infected cells with serious implications in host protein synthesis. By integrating this observation with proteomic data from infected cells, we observe a reduced translation rate of host proteins associated with highly expressed genes, and that they share the codon usage bias of the virus. The functional analysis of these genes suggests that this mechanism of epistasis contributes to understand some deleterious collateral effect as result of the viral replication. In this manner, our finding contribute to the understanding of the SARS-CoV-2 pathogeny and could be useful for the design of a vaccine based on the live attenuated strategy.Centro Regional de Estudios Genómicos2020info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionArticulohttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://sedici.unlp.edu.ar/handle/10915/135183enginfo:eu-repo/semantics/altIdentifier/issn/2296-634Xinfo:eu-repo/semantics/altIdentifier/doi/10.3389/fcell.2020.00831info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)reponame:SEDICI (UNLP)instname:Universidad Nacional de La Platainstacron:UNLP2025-09-29T11:32:36Zoai:sedici.unlp.edu.ar:10915/135183Institucionalhttp://sedici.unlp.edu.ar/Universidad públicaNo correspondehttp://sedici.unlp.edu.ar/oai/snrdalira@sedici.unlp.edu.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:13292025-09-29 11:32:37.109SEDICI (UNLP) - Universidad Nacional de La Platafalse
dc.title.none.fl_str_mv SARS-CoV-2 codon usage bias downregulates host expressed genes with similar codon usage
title SARS-CoV-2 codon usage bias downregulates host expressed genes with similar codon usage
spellingShingle SARS-CoV-2 codon usage bias downregulates host expressed genes with similar codon usage
Alonso, Andrés M.
Biología
SARS-CoV-2
Codon usage bias
Codon optimality
Translational control
Pathogeny
Vaccine design
title_short SARS-CoV-2 codon usage bias downregulates host expressed genes with similar codon usage
title_full SARS-CoV-2 codon usage bias downregulates host expressed genes with similar codon usage
title_fullStr SARS-CoV-2 codon usage bias downregulates host expressed genes with similar codon usage
title_full_unstemmed SARS-CoV-2 codon usage bias downregulates host expressed genes with similar codon usage
title_sort SARS-CoV-2 codon usage bias downregulates host expressed genes with similar codon usage
dc.creator.none.fl_str_mv Alonso, Andrés M.
Diambra, Luis Aníbal
author Alonso, Andrés M.
author_facet Alonso, Andrés M.
Diambra, Luis Aníbal
author_role author
author2 Diambra, Luis Aníbal
author2_role author
dc.subject.none.fl_str_mv Biología
SARS-CoV-2
Codon usage bias
Codon optimality
Translational control
Pathogeny
Vaccine design
topic Biología
SARS-CoV-2
Codon usage bias
Codon optimality
Translational control
Pathogeny
Vaccine design
dc.description.none.fl_txt_mv Severe acute respiratory syndrome is quickly spreading throughout the world and was declared as a pandemic by the World Health Organisation (WHO). The pathogenic agent is a new coronavirus (SARS-CoV-2) that infects pulmonary cells with great effectiveness. In this study we focus on the codon composition for the viral proteins synthesis and its relationship with the proteins synthesis of the host. Our analysis reveals that SARS-CoV-2 preferred codons have poor representation of G or C nucleotides in the third position, a characteristic which could conduct to an unbalance in the tRNAs pools of the infected cells with serious implications in host protein synthesis. By integrating this observation with proteomic data from infected cells, we observe a reduced translation rate of host proteins associated with highly expressed genes, and that they share the codon usage bias of the virus. The functional analysis of these genes suggests that this mechanism of epistasis contributes to understand some deleterious collateral effect as result of the viral replication. In this manner, our finding contribute to the understanding of the SARS-CoV-2 pathogeny and could be useful for the design of a vaccine based on the live attenuated strategy.
Centro Regional de Estudios Genómicos
description Severe acute respiratory syndrome is quickly spreading throughout the world and was declared as a pandemic by the World Health Organisation (WHO). The pathogenic agent is a new coronavirus (SARS-CoV-2) that infects pulmonary cells with great effectiveness. In this study we focus on the codon composition for the viral proteins synthesis and its relationship with the proteins synthesis of the host. Our analysis reveals that SARS-CoV-2 preferred codons have poor representation of G or C nucleotides in the third position, a characteristic which could conduct to an unbalance in the tRNAs pools of the infected cells with serious implications in host protein synthesis. By integrating this observation with proteomic data from infected cells, we observe a reduced translation rate of host proteins associated with highly expressed genes, and that they share the codon usage bias of the virus. The functional analysis of these genes suggests that this mechanism of epistasis contributes to understand some deleterious collateral effect as result of the viral replication. In this manner, our finding contribute to the understanding of the SARS-CoV-2 pathogeny and could be useful for the design of a vaccine based on the live attenuated strategy.
publishDate 2020
dc.date.none.fl_str_mv 2020
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
Articulo
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dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/issn/2296-634X
info:eu-repo/semantics/altIdentifier/doi/10.3389/fcell.2020.00831
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
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repository.name.fl_str_mv SEDICI (UNLP) - Universidad Nacional de La Plata
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