Poorly conserved p15 proteins of cileviruses retain elements of common ancestry and putative functionality: a theoretical assessment on the evolution of cilevirus genomes.
Autor(a) principal: | |
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Data de Publicação: | 2021 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
Texto Completo: | http://www.alice.cnptia.embrapa.br/alice/handle/doc/1136833 https://doi.org/10.3389/fpls.2021.771983 |
Resumo: | The genus Cilevirus groups enveloped single-stranded (+) RNA virus members of the family Kitaviridae, order Martellivirales. Proteins P15, scarcely conserved polypeptides encoded by cileviruses, have no apparent homologs in public databases. Accordingly, the open reading frames (ORFs) p15, located at the 5?-end of the viral RNA2 molecules, are considered orphan genes (ORFans). In this study, we have delved into ORFs p15 and the relatively poorly understood biochemical properties of the proteins P15 to posit their importance for viruses across the genus and theorize on their origin. We detected that the ORFs p15 are under purifying selection and that, in some viral strains, the use of synonymous codons is biased, which might be a sign of adaptation to their plant hosts. Despite the high amino acid sequence divergence, proteins P15 show the conserved motif [FY]-L-x(3)-[FL]-H-x-x-[LIV]-S-C-x-C-x(2)-C-x-G-x-C, which occurs exclusively in members of this protein family. Proteins P15 also show a common predicted 3D structure that resembles the helical scaffold of the protein ORF49 encoded by radinoviruses and the phosphoprotein C-terminal domain of mononegavirids. Based on the 3D structural similarities of P15, we suggest elements of common ancestry, conserved functionality, and relevant amino acid residues. We conclude by postulating a plausible evolutionary trajectory of ORFans p15 and the 5?-end of the RNA2 of cileviruses considering both protein fold superpositions and comparative genomic analyses with the closest kitaviruses, negeviruses, nege/kita-like viruses, and unrelated viruses that share the ecological niches of cileviruses. |
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Poorly conserved p15 proteins of cileviruses retain elements of common ancestry and putative functionality: a theoretical assessment on the evolution of cilevirus genomes.ProteínaVírusGenomaThe genus Cilevirus groups enveloped single-stranded (+) RNA virus members of the family Kitaviridae, order Martellivirales. Proteins P15, scarcely conserved polypeptides encoded by cileviruses, have no apparent homologs in public databases. Accordingly, the open reading frames (ORFs) p15, located at the 5?-end of the viral RNA2 molecules, are considered orphan genes (ORFans). In this study, we have delved into ORFs p15 and the relatively poorly understood biochemical properties of the proteins P15 to posit their importance for viruses across the genus and theorize on their origin. We detected that the ORFs p15 are under purifying selection and that, in some viral strains, the use of synonymous codons is biased, which might be a sign of adaptation to their plant hosts. Despite the high amino acid sequence divergence, proteins P15 show the conserved motif [FY]-L-x(3)-[FL]-H-x-x-[LIV]-S-C-x-C-x(2)-C-x-G-x-C, which occurs exclusively in members of this protein family. Proteins P15 also show a common predicted 3D structure that resembles the helical scaffold of the protein ORF49 encoded by radinoviruses and the phosphoprotein C-terminal domain of mononegavirids. Based on the 3D structural similarities of P15, we suggest elements of common ancestry, conserved functionality, and relevant amino acid residues. We conclude by postulating a plausible evolutionary trajectory of ORFans p15 and the 5?-end of the RNA2 of cileviruses considering both protein fold superpositions and comparative genomic analyses with the closest kitaviruses, negeviruses, nege/kita-like viruses, and unrelated viruses that share the ecological niches of cileviruses.PEDRO L. RAMOS-GONZÁLEZ, Instituto Biológico de São Paulo; TIRSO PONS, CNB-CSIC; CAMILA CHABI-JESUS, Instituto Biológico de São Paulo; GABRIELLA DIAS ARENA, Instituto Biológico de São Paulo; JULIANA DE FREITAS ASTUA, CNPMF.RAMOS-GONZÁLEZ, P. L.PONS, T.CHABI-JESUS, C.ARENA, G. D.ASTUA, J. de F.2021-11-30T15:00:24Z2021-11-30T15:00:24Z2021-11-302021info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFrontiers in Plant Science, November, 2021.1664-462Xhttp://www.alice.cnptia.embrapa.br/alice/handle/doc/1136833https://doi.org/10.3389/fpls.2021.771983enginfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPA2021-11-30T15:00:35Zoai:www.alice.cnptia.embrapa.br:doc/1136833Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestopendoar:21542021-11-30T15:00:35falseRepositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542021-11-30T15:00:35Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false |
dc.title.none.fl_str_mv |
Poorly conserved p15 proteins of cileviruses retain elements of common ancestry and putative functionality: a theoretical assessment on the evolution of cilevirus genomes. |
title |
Poorly conserved p15 proteins of cileviruses retain elements of common ancestry and putative functionality: a theoretical assessment on the evolution of cilevirus genomes. |
spellingShingle |
Poorly conserved p15 proteins of cileviruses retain elements of common ancestry and putative functionality: a theoretical assessment on the evolution of cilevirus genomes. RAMOS-GONZÁLEZ, P. L. Proteína Vírus Genoma |
title_short |
Poorly conserved p15 proteins of cileviruses retain elements of common ancestry and putative functionality: a theoretical assessment on the evolution of cilevirus genomes. |
title_full |
Poorly conserved p15 proteins of cileviruses retain elements of common ancestry and putative functionality: a theoretical assessment on the evolution of cilevirus genomes. |
title_fullStr |
Poorly conserved p15 proteins of cileviruses retain elements of common ancestry and putative functionality: a theoretical assessment on the evolution of cilevirus genomes. |
title_full_unstemmed |
Poorly conserved p15 proteins of cileviruses retain elements of common ancestry and putative functionality: a theoretical assessment on the evolution of cilevirus genomes. |
title_sort |
Poorly conserved p15 proteins of cileviruses retain elements of common ancestry and putative functionality: a theoretical assessment on the evolution of cilevirus genomes. |
author |
RAMOS-GONZÁLEZ, P. L. |
author_facet |
RAMOS-GONZÁLEZ, P. L. PONS, T. CHABI-JESUS, C. ARENA, G. D. ASTUA, J. de F. |
author_role |
author |
author2 |
PONS, T. CHABI-JESUS, C. ARENA, G. D. ASTUA, J. de F. |
author2_role |
author author author author |
dc.contributor.none.fl_str_mv |
PEDRO L. RAMOS-GONZÁLEZ, Instituto Biológico de São Paulo; TIRSO PONS, CNB-CSIC; CAMILA CHABI-JESUS, Instituto Biológico de São Paulo; GABRIELLA DIAS ARENA, Instituto Biológico de São Paulo; JULIANA DE FREITAS ASTUA, CNPMF. |
dc.contributor.author.fl_str_mv |
RAMOS-GONZÁLEZ, P. L. PONS, T. CHABI-JESUS, C. ARENA, G. D. ASTUA, J. de F. |
dc.subject.por.fl_str_mv |
Proteína Vírus Genoma |
topic |
Proteína Vírus Genoma |
description |
The genus Cilevirus groups enveloped single-stranded (+) RNA virus members of the family Kitaviridae, order Martellivirales. Proteins P15, scarcely conserved polypeptides encoded by cileviruses, have no apparent homologs in public databases. Accordingly, the open reading frames (ORFs) p15, located at the 5?-end of the viral RNA2 molecules, are considered orphan genes (ORFans). In this study, we have delved into ORFs p15 and the relatively poorly understood biochemical properties of the proteins P15 to posit their importance for viruses across the genus and theorize on their origin. We detected that the ORFs p15 are under purifying selection and that, in some viral strains, the use of synonymous codons is biased, which might be a sign of adaptation to their plant hosts. Despite the high amino acid sequence divergence, proteins P15 show the conserved motif [FY]-L-x(3)-[FL]-H-x-x-[LIV]-S-C-x-C-x(2)-C-x-G-x-C, which occurs exclusively in members of this protein family. Proteins P15 also show a common predicted 3D structure that resembles the helical scaffold of the protein ORF49 encoded by radinoviruses and the phosphoprotein C-terminal domain of mononegavirids. Based on the 3D structural similarities of P15, we suggest elements of common ancestry, conserved functionality, and relevant amino acid residues. We conclude by postulating a plausible evolutionary trajectory of ORFans p15 and the 5?-end of the RNA2 of cileviruses considering both protein fold superpositions and comparative genomic analyses with the closest kitaviruses, negeviruses, nege/kita-like viruses, and unrelated viruses that share the ecological niches of cileviruses. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-11-30T15:00:24Z 2021-11-30T15:00:24Z 2021-11-30 2021 |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/publishedVersion info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
Frontiers in Plant Science, November, 2021. 1664-462X http://www.alice.cnptia.embrapa.br/alice/handle/doc/1136833 https://doi.org/10.3389/fpls.2021.771983 |
identifier_str_mv |
Frontiers in Plant Science, November, 2021. 1664-462X |
url |
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1136833 https://doi.org/10.3389/fpls.2021.771983 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa) instacron:EMBRAPA |
instname_str |
Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
instacron_str |
EMBRAPA |
institution |
EMBRAPA |
reponame_str |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
collection |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
repository.name.fl_str_mv |
Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
repository.mail.fl_str_mv |
cg-riaa@embrapa.br |
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1794503512970756096 |