New insights into the evolutionary features of viral overlapping genes by discriminant analysis.
Ancestral reading frame
Apoptin
Codon usage
Computer simulation
De novo reading Frame
Homologs
Multivariate statistics
SARS-CoV-2
Therapeutic proteins
Virus evolution
Journal
Virology
ISSN: 1096-0341
Titre abrégé: Virology
Pays: United States
ID NLM: 0110674
Informations de publication
Date de publication:
07 2020
07 2020
Historique:
received:
20
03
2020
accepted:
29
03
2020
entrez:
27
5
2020
pubmed:
27
5
2020
medline:
30
5
2020
Statut:
ppublish
Résumé
Overlapping genes originate by a mechanism of overprinting, in which nucleotide substitutions in a pre-existing frame induce the expression of a de novo protein from an alternative frame. In this study, I assembled a dataset of 319 viral overlapping genes, which included 82 overlaps whose expression is experimentally known and the respective 237 homologs. Principal component analysis revealed that overlapping genes have a common pattern of nucleotide and amino acid composition. Discriminant analysis separated overlapping from non-overlapping genes with an accuracy of 97%. When applied to overlapping genes with known genealogy, it separated ancestral from de novo frames with an accuracy close to 100%. This high discriminant power was crucial to computationally design variants of de novo viral proteins known to possess selective anticancer toxicity (apoptin) or protection against neurodegeneration (X protein), as well as to detect two new potential overlapping genes in the genome of the new coronavirus SARS-CoV-2.
Identifiants
pubmed: 32452417
pii: S0042-6822(20)30060-X
doi: 10.1016/j.virol.2020.03.007
pmc: PMC7157939
pii:
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
51-66Informations de copyright
Copyright © 2020 Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of competing interest None.
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