Poorly Conserved P15 Proteins of Cileviruses Retain Elements of Common Ancestry and Putative Functionality: A Theoretical Assessment on the Evolution of Cilevirus Genomes

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 a...

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Autores principales: Pedro L. Ramos-González, Tirso Pons, Camila Chabi-Jesus, Gabriella Dias Arena, Juliana Freitas-Astua
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Publicado: Frontiers Media S.A. 2021
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spelling oai:doaj.org-article:dea69065e1364cbfaaba225d3204bee32021-11-05T11:54:56ZPoorly Conserved P15 Proteins of Cileviruses Retain Elements of Common Ancestry and Putative Functionality: A Theoretical Assessment on the Evolution of Cilevirus Genomes1664-462X10.3389/fpls.2021.771983https://doaj.org/article/dea69065e1364cbfaaba225d3204bee32021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fpls.2021.771983/fullhttps://doaj.org/toc/1664-462XThe 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-GonzálezTirso PonsCamila Chabi-JesusCamila Chabi-JesusGabriella Dias ArenaJuliana Freitas-AstuaJuliana Freitas-AstuaFrontiers Media S.A.articleKitaviridaeorphan ORFstructure-based phylogenetic analysissynonymous codon usage biashorizontal gene transferDichorhavirusPlant cultureSB1-1110ENFrontiers in Plant Science, Vol 12 (2021)
institution DOAJ
collection DOAJ
language EN
topic Kitaviridae
orphan ORF
structure-based phylogenetic analysis
synonymous codon usage bias
horizontal gene transfer
Dichorhavirus
Plant culture
SB1-1110
spellingShingle Kitaviridae
orphan ORF
structure-based phylogenetic analysis
synonymous codon usage bias
horizontal gene transfer
Dichorhavirus
Plant culture
SB1-1110
Pedro L. Ramos-González
Tirso Pons
Camila Chabi-Jesus
Camila Chabi-Jesus
Gabriella Dias Arena
Juliana Freitas-Astua
Juliana Freitas-Astua
Poorly Conserved P15 Proteins of Cileviruses Retain Elements of Common Ancestry and Putative Functionality: A Theoretical Assessment on the Evolution of Cilevirus Genomes
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.
format article
author Pedro L. Ramos-González
Tirso Pons
Camila Chabi-Jesus
Camila Chabi-Jesus
Gabriella Dias Arena
Juliana Freitas-Astua
Juliana Freitas-Astua
author_facet Pedro L. Ramos-González
Tirso Pons
Camila Chabi-Jesus
Camila Chabi-Jesus
Gabriella Dias Arena
Juliana Freitas-Astua
Juliana Freitas-Astua
author_sort Pedro L. Ramos-González
title Poorly Conserved P15 Proteins of Cileviruses Retain Elements of Common Ancestry and Putative Functionality: A Theoretical Assessment on the Evolution of Cilevirus Genomes
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
publisher Frontiers Media S.A.
publishDate 2021
url https://doaj.org/article/dea69065e1364cbfaaba225d3204bee3
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