ArticlePLoS computational biology2013
Viral proteins originated de novo by overprinting can be identified by codon usage: application to the "gene nursery" of Deltaretroviruses.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers, 1 of them a synthesis that pooled it.
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Who cites it
48 citing papers in PubMed, 1 synthesis or guideline pooled it, 71 citations in OpenAlex.
- Pooled it
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- Evolution of primate T-cell leukemia virus type 1 accessory genes and functional divergence of its antisense proteins.PLoS pathogens · 2025Article
- De Novo Genes.Annual review of genetics · 2024Review
- Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins.Genome research · 2024Article
- Creation of the HIV-1 antisense geneMicrobiology spectrum · 2024Article
- CodingDiv: analyzing SNP-level microdiversity to discriminate between coding and noncoding regions in viral genomes.Bioinformatics (Oxford, England) · 2023Article
- Reekeekee- and roodoodooviruses, two differentVirus evolution · 2023Article
- Mechanisms of protein evolution.Protein science : a publication of the Protein Society · 2022Review
- Spacer Domain in Hepatitis B Virus Polymerase: Plugging a Hole or Performing a Role?Journal of virology · 2022Review
- Overlapping genes in natural and engineered genomes.Nature reviews. Genetics · 2022Review
- Computational methods for inferring location and genealogy of overlapping genes in virus genomes: approaches and applications.Current opinion in virology · 2022Review
- Article
- Biological factors in the synthetic construction of overlapping genes.BMC genomics · 2021Article
- The Effects of Sequence Length and Composition of Random Sequence Peptides on the Growth ofGenes · 2021Article
- Article
- The HIV-1 Antisense Gene ASP: The New Kid on the Block.Vaccines · 2021Review
- New insights into the evolutionary features of viral overlapping genes by discriminant analysis.Virology · 2020Article
- The HIV-1 Antisense Protein ASP Is a Transmembrane Protein of the Cell Surface and an Integral Protein of the Viral Envelope.Journal of virology · 2019Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
A well-known mechanism through which new protein-coding genes originate is by modification of pre-existing genes, e.g. by duplication or horizontal transfer. In contrast, many viruses generate protein-coding genes de novo, via the overprinting of a new reading frame onto an existing ("ancestral") frame. This mechanism is thought to play an important role in viral pathogenicity, but has been poorly explored, perhaps because identifying the de novo frames is very challenging. Therefore, a new approach to detect them was needed. We assembled a reference set of overlapping genes for which we could reliably determine the ancestral frames, and found that their codon usage was significantly closer to that of the rest of the viral genome than the codon usage of de novo frames. Based on this observation, we designed a method that allowed the identification of de novo frames based on their codon usage with a very good specificity, but intermediate sensitivity. Using our method, we predicted that the Rex gene of deltaretroviruses has originated de novo by overprinting the Tax gene. Intriguingly, several genes in the same genomic region have also originated de novo and encode proteins that regulate the functions of Tax. Such "gene nurseries" may be common in viral genomes. Finally, our results confirm that the genomic GC content is not the only determinant of codon usage in viruses and suggest that a constraint linked to translation must influence codon usage.
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Registered trials
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