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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
agricultural and biological sciences
Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses
Journal of Virology, Volume 88, No. 4, Year 2014
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Description
Single-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. © 2014, American Society for Microbiology.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC3911531/bin/supp_88_4_1972__index.html
https://efashare.b-cdn.net/share/pmc/articles/PMC3911531/bin/JVI.03031-13_zjv999098642so1.pdf
Authors & Co-Authors
Muhire, Brejnev Muhizi
South Africa, Cape Town
University of Cape Town
Golden, Michael
South Africa, Cape Town
University of Cape Town
Murrell, Ben
United States, La Jolla
University of California, San Diego
Lefeuvre, Pierre F.
France, Saint-denis
Université de la Réunion
Lett, Jean Michel
France, Saint-denis
Université de la Réunion
Gray, A.
South Africa, Cape Town
University of Cape Town
Poon, Art Y.F.
Canada, Vancouver
British Columbia Centre for Excellence in Hiv-aids
Canada, Vancouver
The University of British Columbia
Ngandu, Nobubelo Kwanele
South Africa, Cape Town
University of Cape Town
Semegni, Y.
South Africa, Bellville
Cape Peninsula University of Technology
Tanov, Emil Pavlov
South Africa, Bellville
University of the Western Cape
Monjane, Adérito Luis
South Africa, Cape Town
University of Cape Town
Harkins, Gordon William
South Africa, Bellville
University of the Western Cape
Varsani, Arvind
New Zealand, Christchurch
University of Canterbury
South Africa, Cape Town
University of Cape Town
Shepherd, Dionne Natalie
South Africa, Cape Town
University of Cape Town
Martin, Darren Patrick
South Africa, Cape Town
University of Cape Town
Statistics
Citations: 39
Authors: 15
Affiliations: 8
Identifiers
Doi:
10.1128/JVI.03031-13
ISSN:
0022538X
e-ISSN:
10985514
Research Areas
Genetics And Genomics