Computational methods for inferring location and genealogy of overlapping genes in virus genomes: approaches and applications

Pavesi, Angelo

doi:10.1016/j.coviro.2021.10.009

Cited by 1 publication

(2 citation statements)

References 47 publications

(94 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our findings confirm (if that were needed) that overlapping genes remain to be discovered in DNA viruses (we know of at least another case already flagged by sequence analyses, in human bocavirus [ 57 ]). We encourage all virologists who sequence genomes to look for overlapping genes using the simple tools and strategies presented here, as well as other available software to predict overlapping genes, which are complementary (for a review, [ 12 ]). This is perfectly feasible if you are a bench virologist lacking programming skills (like the author), since all analyses were performed using web-based, relatively user-friendly programs (see Section 2 ) on a standard laptop computer.…”

Section: Discussionmentioning

confidence: 99%

“…Overlapping ORFs are frequently overlooked in viral genomes [ 11 ]. It is possible, in principle, to predict merely from sequence analyses whether a protein is expressed from an overlapping ORF, provided that the protein confers a beneficial function to the virus [ 12 ]. In that case, the additional selection pressure caused on the sequence of the reading frame that it overlaps results in a lower rate of synonymous codon substitution in that second frame [ 13 , 14 ].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Parvovirus B19 and Human Parvovirus 4 Encode Similar Proteins in a Reading Frame Overlapping the VP1 Capsid Gene

Karlin

2024

Viruses

View full text Add to dashboard Cite

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).

show abstract

Section: Discussionmentioning

confidence: 99%