Evidence of pervasive biologically functional secondary structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses

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dc.contributor.authorMuhire, Brejnev Muhizi
dc.contributor.authorGolden, Michael
dc.contributor.authorTanov, Emil Pavlov
dc.contributor.authorHarkins, Gordon William
dc.contributor.authorMurrell, Ben
dc.contributor.authorLefeuvre, Pierre
dc.contributor.authorLett, Jean-Michel
dc.contributor.authorGray, Alistair
dc.contributor.authorPoon, Art Y. F.
dc.contributor.authorNgandu, Nobubelo Kwanele
dc.contributor.authorSemegni, Yves
dc.contributor.authorMonjane, Adérito Luis
dc.contributor.authorVarsani, Arvind
dc.contributor.authorShepherd, Dionne Natalie
dc.contributor.authorMartin, Darren Patrick
dc.date.accessioned2017-07-12T10:42:08Z
dc.date.available2017-07-12T10:42:08Z
dc.date.issued2013
dc.description.abstractSingle-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here.en_US
dc.description.accreditationDepartment of HE and Training approved list
dc.identifier.citationMuhire, B. M. et al. (2013). Evidence of pervasive biologically functional secondary structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses. Journal of Virology, 88 (4): 1972–1989en_US
dc.identifier.issn0022-538X
dc.identifier.urihttp://hdl.handle.net/10566/3062
dc.language.isoenen_US
dc.publisherAmerican Society for Microbiologyen_US
dc.rightsPublisher retains copyright. Authors may archive the published version in their institutional repository.
dc.source.urihttp://dx.doi.org/10.1128/JVI.03031-13
dc.subjectEvidenceen_US
dc.subjectSingle-stranded DNAen_US
dc.subjectGenomes of Eukaryotic Single-Stranded DNA Virusesen_US
dc.subjectPervasive Biologically Functional Secondary Structuresen_US
dc.titleEvidence of pervasive biologically functional secondary structures within the Genomes of Eukaryotic Single-Stranded DNA Virusesen_US
dc.typeArticleen_US

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