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2021
Ramos-González, Pedro L.; Pons, Tirso; Chabi-Jesus, Camila; Arena, Gabriella Dias; Freitas-Astua, Juliana
In: Frontiers in Plant Science, vol. 12, pp. 2542, 2021, ISSN: 1664462X.
Abstract | Links | BibTeX | Tags: Dichorhavirus, Horizontal gene transfer, Kitaviridae, miniproteins, orphan ORF, small ORF, structure-based phylogenetic analysis, synonymous codon usage bias
@article{nokey,
title = {Poorly Conserved P15 Proteins of Cileviruses Retain Elements of Common Ancestry and Putative Functionality: A Theoretical Assessment on the Evolution of Cilevirus Genomes},
author = {Pedro L. Ramos-González and Tirso Pons and Camila Chabi-Jesus and Gabriella Dias Arena and Juliana Freitas-Astua},
doi = {10.3389/FPLS.2021.771983/BIBTEX},
issn = {1664462X},
year = {2021},
date = {2021-01-01},
journal = {Frontiers in Plant Science},
volume = {12},
pages = {2542},
publisher = {Frontiers Media S.A.},
abstract = {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.},
keywords = {Dichorhavirus, Horizontal gene transfer, Kitaviridae, miniproteins, orphan ORF, small ORF, structure-based phylogenetic analysis, synonymous codon usage bias},
pubstate = {published},
tppubtype = {article}
}
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.
Ramos-González, Pedro L.; Pons, Tirso; Chabi-Jesus, Camila; Arena, Gabriella Dias; Freitas-Astua, Juliana
In: Frontiers in Plant Science, vol. 12, pp. 2542, 2021, ISSN: 1664462X.
Abstract | Links | BibTeX | Tags: Dichorhavirus, Horizontal gene transfer, Kitaviridae, miniproteins, orphan ORF, small ORF, structure-based phylogenetic analysis, synonymous codon usage bias
@article{nokey,
title = {Poorly Conserved P15 Proteins of Cileviruses Retain Elements of Common Ancestry and Putative Functionality: A Theoretical Assessment on the Evolution of Cilevirus Genomes},
author = {Pedro L. Ramos-González and Tirso Pons and Camila Chabi-Jesus and Gabriella Dias Arena and Juliana Freitas-Astua},
doi = {10.3389/FPLS.2021.771983/BIBTEX},
issn = {1664462X},
year = {2021},
date = {2021-01-01},
journal = {Frontiers in Plant Science},
volume = {12},
pages = {2542},
publisher = {Frontiers Media S.A.},
abstract = {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.},
keywords = {Dichorhavirus, Horizontal gene transfer, Kitaviridae, miniproteins, orphan ORF, small ORF, structure-based phylogenetic analysis, synonymous codon usage bias},
pubstate = {published},
tppubtype = {article}
}
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.
2020
Pierry, Paulo Marques; Uceda-Campos, Guillermo; Feitosa-Junior, Oseias Rodrigues; Martins-Junior, Joaquim; Santana, Wesley Oliveira; Coletta-Filho, Helvécio Della; Zaini, Paulo Adriano; Silva, Aline Maria
Genetic Diversity of Xylella fastidiosa Plasmids Assessed by Comparative Genomics Journal Article
In: Tropical Plant Pathology, vol. 45, iss. 3, pp. 342-360, 2020, ISSN: 19832052.
Abstract | Links | BibTeX | Tags: Conjugative plasmid, Horizontal gene transfer, Phytopathogen, Plasmid classification, Relaxase, Type IV coupling protein
@article{Pierry2020,
title = {Genetic Diversity of Xylella fastidiosa Plasmids Assessed by Comparative Genomics},
author = {Paulo Marques Pierry and Guillermo Uceda-Campos and Oseias Rodrigues Feitosa-Junior and Joaquim Martins-Junior and Wesley Oliveira Santana and Helvécio Della Coletta-Filho and Paulo Adriano Zaini and Aline Maria Silva},
url = {https://link.springer.com/article/10.1007/s40858-020-00359-4},
doi = {10.1007/S40858-020-00359-4/METRICS},
issn = {19832052},
year = {2020},
date = {2020-01-01},
journal = {Tropical Plant Pathology},
volume = {45},
issue = {3},
pages = {342-360},
publisher = {Springer},
abstract = {Plasmids are a major source of horizontal gene transfer among bacteria contributing to their evolution and ecology. The known collection of plasmids carried by the plant pathogen Xylella fastidiosa increases as new strains from different origins and hosts are sampled and sequenced. Here we performed an extensive comparison of 61 publicly available sequences annotated as plasmids belonging to 38 X. fastidiosa strains isolated from different plant species and distinct geographical locations. Twenty-six strains exhibited at least one plasmid and up to four plasmids were found in a single strain. Plasmids sizes varied widely from 1.3 kbp to 64.3 kbp, ranging from 1 to 70 protein-coding sequences (CDS) encompassing 324 orthologs. Based on the presence of specific mobility proteins such as relaxases and type 4 secretion system-related genes, respectively 40 and 8 of the X. fastidiosa plasmids were classified as conjugative and mobilizable, while 13 were classified as non-mobilizable. X. fastidiosa plasmids did not carry known antibiotic resistance or virulence genes, and their stability seems to take advantage of toxin/antitoxin systems. The comparative analyses described here revealed similarity among plasmids of X. fastidiosa from different subspecies, geographical regions, and hosts, as well as with sequences found in plasmids from other bacterial species. Altogether, our results provide an in silico analysis of X. fastidiosa plasmid content and their main features, with applications in future studies of epidemiology, ecology, and evolution of this phytopathogen.},
keywords = {Conjugative plasmid, Horizontal gene transfer, Phytopathogen, Plasmid classification, Relaxase, Type IV coupling protein},
pubstate = {published},
tppubtype = {article}
}
Plasmids are a major source of horizontal gene transfer among bacteria contributing to their evolution and ecology. The known collection of plasmids carried by the plant pathogen Xylella fastidiosa increases as new strains from different origins and hosts are sampled and sequenced. Here we performed an extensive comparison of 61 publicly available sequences annotated as plasmids belonging to 38 X. fastidiosa strains isolated from different plant species and distinct geographical locations. Twenty-six strains exhibited at least one plasmid and up to four plasmids were found in a single strain. Plasmids sizes varied widely from 1.3 kbp to 64.3 kbp, ranging from 1 to 70 protein-coding sequences (CDS) encompassing 324 orthologs. Based on the presence of specific mobility proteins such as relaxases and type 4 secretion system-related genes, respectively 40 and 8 of the X. fastidiosa plasmids were classified as conjugative and mobilizable, while 13 were classified as non-mobilizable. X. fastidiosa plasmids did not carry known antibiotic resistance or virulence genes, and their stability seems to take advantage of toxin/antitoxin systems. The comparative analyses described here revealed similarity among plasmids of X. fastidiosa from different subspecies, geographical regions, and hosts, as well as with sequences found in plasmids from other bacterial species. Altogether, our results provide an in silico analysis of X. fastidiosa plasmid content and their main features, with applications in future studies of epidemiology, ecology, and evolution of this phytopathogen.