Cargando…
The evolution of codon usage in structural and non-structural viral genes: The case of Avian coronavirus and its natural host Gallus gallus
To assess the codon evolution in virus–host systems, Avian coronavirus and its natural host Gallus gallus were used as a model. Codon usage (CU) was measured for the viral spike (S), nucleocapsid (N), nonstructural protein 2 (NSP2) and papain-like protease (PL(pro)) genes from a diverse set of A. co...
Autor principal: | |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier B.V.
2013
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7114390/ https://www.ncbi.nlm.nih.gov/pubmed/24091362 http://dx.doi.org/10.1016/j.virusres.2013.09.033 |
_version_ | 1783513875201654784 |
---|---|
author | Brandão, Paulo Eduardo |
author_facet | Brandão, Paulo Eduardo |
author_sort | Brandão, Paulo Eduardo |
collection | PubMed |
description | To assess the codon evolution in virus–host systems, Avian coronavirus and its natural host Gallus gallus were used as a model. Codon usage (CU) was measured for the viral spike (S), nucleocapsid (N), nonstructural protein 2 (NSP2) and papain-like protease (PL(pro)) genes from a diverse set of A. coronavirus lineages and for G. gallus genes (lung surfactant protein A, intestinal cholecystokinin, oviduct ovomucin alpha subunit, kidney vitamin D receptor and the ubiquitary beta-actin) for different A. coronavirus replicating sites. Relative synonymous codon usage (RSCU) trees accommodating all virus and host genes in a single topology showed a higher proximity of A. coronavirus CU to the respiratory tract for all genes. The codon adaptation index (CAI) showed a lower adaptation of S to G. gallus compared to NSP2, PL(pro) and N. The effective number of codons (Nc) and GC(3%) revealed that natural selection and genetic drift are the evolutionary forces driving the codon usage evolution of both A. coronavirus and G. gallus regardless of the gene being considered. The spike gene showed only one 100% conserved amino acid position coded by an A. coronavirus preferred codon, a significantly low number when compared to the three other genes (p < 0.0001). Virus CU evolves independently for each gene in a manner predicted by the protein function, with a balance between natural selection and mutation pressure, giving further molecular basis for the viruses’ ability to exploit the host's cellular environment in a concerted virus–host molecular evolution. |
format | Online Article Text |
id | pubmed-7114390 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Elsevier B.V. |
record_format | MEDLINE/PubMed |
spelling | pubmed-71143902020-04-02 The evolution of codon usage in structural and non-structural viral genes: The case of Avian coronavirus and its natural host Gallus gallus Brandão, Paulo Eduardo Virus Res Article To assess the codon evolution in virus–host systems, Avian coronavirus and its natural host Gallus gallus were used as a model. Codon usage (CU) was measured for the viral spike (S), nucleocapsid (N), nonstructural protein 2 (NSP2) and papain-like protease (PL(pro)) genes from a diverse set of A. coronavirus lineages and for G. gallus genes (lung surfactant protein A, intestinal cholecystokinin, oviduct ovomucin alpha subunit, kidney vitamin D receptor and the ubiquitary beta-actin) for different A. coronavirus replicating sites. Relative synonymous codon usage (RSCU) trees accommodating all virus and host genes in a single topology showed a higher proximity of A. coronavirus CU to the respiratory tract for all genes. The codon adaptation index (CAI) showed a lower adaptation of S to G. gallus compared to NSP2, PL(pro) and N. The effective number of codons (Nc) and GC(3%) revealed that natural selection and genetic drift are the evolutionary forces driving the codon usage evolution of both A. coronavirus and G. gallus regardless of the gene being considered. The spike gene showed only one 100% conserved amino acid position coded by an A. coronavirus preferred codon, a significantly low number when compared to the three other genes (p < 0.0001). Virus CU evolves independently for each gene in a manner predicted by the protein function, with a balance between natural selection and mutation pressure, giving further molecular basis for the viruses’ ability to exploit the host's cellular environment in a concerted virus–host molecular evolution. Elsevier B.V. 2013-12-26 2013-09-30 /pmc/articles/PMC7114390/ /pubmed/24091362 http://dx.doi.org/10.1016/j.virusres.2013.09.033 Text en Copyright © 2013 Elsevier B.V. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. |
spellingShingle | Article Brandão, Paulo Eduardo The evolution of codon usage in structural and non-structural viral genes: The case of Avian coronavirus and its natural host Gallus gallus |
title | The evolution of codon usage in structural and non-structural viral genes: The case of Avian coronavirus and its natural host Gallus gallus |
title_full | The evolution of codon usage in structural and non-structural viral genes: The case of Avian coronavirus and its natural host Gallus gallus |
title_fullStr | The evolution of codon usage in structural and non-structural viral genes: The case of Avian coronavirus and its natural host Gallus gallus |
title_full_unstemmed | The evolution of codon usage in structural and non-structural viral genes: The case of Avian coronavirus and its natural host Gallus gallus |
title_short | The evolution of codon usage in structural and non-structural viral genes: The case of Avian coronavirus and its natural host Gallus gallus |
title_sort | evolution of codon usage in structural and non-structural viral genes: the case of avian coronavirus and its natural host gallus gallus |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7114390/ https://www.ncbi.nlm.nih.gov/pubmed/24091362 http://dx.doi.org/10.1016/j.virusres.2013.09.033 |
work_keys_str_mv | AT brandaopauloeduardo theevolutionofcodonusageinstructuralandnonstructuralviralgenesthecaseofaviancoronavirusanditsnaturalhostgallusgallus AT brandaopauloeduardo evolutionofcodonusageinstructuralandnonstructuralviralgenesthecaseofaviancoronavirusanditsnaturalhostgallusgallus |