Overlapping Genes in Viral Genomes

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "General Virology".

Deadline for manuscript submissions: 25 September 2024 | Viewed by 952

Special Issue Editors


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Guest Editor
School of Medicine, Johns Hopkins University, Baltimore, MA, USA
Interests: HIV-1 persistence; HIV-1 cure; the HIV-1 antisense gene; ASP

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Guest Editor
Department of Chemistry, Life Sciences and Environmental Sustainability, Università di Parma, Parma, Italy
Interests: overlapping genes; genetic code; reading frames; HIV; SARS-CoV-2

Special Issue Information

Dear Colleagues,

To ensure their successful replication and spread, viruses must overcome formidable challenges. Among them are the ability to take over and coerce the host’s machinery to their advantage, and the capacity to elude or subvert the host’s antiviral defenses. What is more impressive is the fact that to achieve these tasks, viruses can rely on a significantly smaller number of genes than the cells they invade. Most often, the creation of new viral genes cannot involve an increase in the size of their genomes, which otherwise would put them at risk of not being able to fit into the viral capsid. However, viruses have mastered a clever alternative strategy to achieve their goals, namely overlapping genes. Viral genomes often include multiple genes encoded in different reading frames of the same genomic region, and in both orientations. This strategy presents advantages (such as unchanged genome size) and disadvantages (such as reciprocal constraints on gene evolution). Nevertheless, the widespread use of overlapping genes in all realms of viruses suggests that this is a successful strategy from an evolutionary standpoint. In this Special Issue of Viruses, we invite you to share your findings on this intriguing and under-appreciated strategy.

Dr. Fabio Romerio
Dr. Angelo Pavesi
Guest Editors

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Keywords

  • viral genomes
  • overlapping genes
  • sense overlap
  • antisense overlap
  • reading frames
  • host/virus interaction

Published Papers (1 paper)

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Research

18 pages, 7186 KiB  
Article
Parvovirus B19 and Human Parvovirus 4 Encode Similar Proteins in a Reading Frame Overlapping the VP1 Capsid Gene
by David G. Karlin
Viruses 2024, 16(2), 191; https://doi.org/10.3390/v16020191 - 26 Jan 2024
Viewed by 691
Abstract
Viruses frequently contain overlapping genes, which encode functionally unrelated proteins from the same DNA or RNA region but in different reading frames. Yet, overlapping genes are often overlooked during genome annotation, in particular in DNA viruses. Here we looked for the presence of [...] Read more.
Viruses frequently contain overlapping genes, which encode functionally unrelated proteins from the same DNA or RNA region but in different reading frames. Yet, overlapping genes are often overlooked during genome annotation, in particular in DNA viruses. Here we looked for the presence of overlapping genes likely to encode a functional protein in human parvovirus B19 (genus Erythroparvovirus), using an experimentally validated software, Synplot2. Synplot2 detected an open reading frame, X, conserved in all erythroparvoviruses, which overlaps the VP1 capsid gene and is under highly significant selection pressure. In a related virus, human parvovirus 4 (genus Tetraparvovirus), Synplot2 also detected an open reading frame under highly significant selection pressure, ARF1, which overlaps the VP1 gene and is conserved in all tetraparvoviruses. These findings provide compelling evidence that the X and ARF1 proteins must be expressed and functional. X and ARF1 have the exact same location (they overlap the region of the VP1 gene encoding the phospholipase A2 domain), are both in the same frame (+1) with respect to the VP1 frame, and encode proteins with similar predicted properties, including a central transmembrane region. Further studies will be needed to determine whether they have a common origin and similar function. X and ARF1 are probably translated either from a polycistronic mRNA by a non-canonical mechanism, or from an unmapped monocistronic mRNA. Finally, we also discovered proteins predicted to be expressed from a frame overlapping VP1 in other species related to parvovirus B19: porcine parvovirus 2 (Z protein) and bovine parvovirus 3 (X-like protein). Full article
(This article belongs to the Special Issue Overlapping Genes in Viral Genomes)
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