Evidence of pervasive biologically functional secondary-structures within the genomes of eukaryotic single-stranded DNA viruses

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dc.contributor.authorMuhire, B M
dc.contributor.authorGolden, M
dc.contributor.authorMurrell, B
dc.contributor.authorLefeuvre, P
dc.contributor.authorLett, J-M
dc.contributor.authorGray, A
dc.contributor.authorPoon, Art Y F
dc.contributor.authorNgandu, N K
dc.contributor.authorSemegni, Y
dc.contributor.authorTanov, E P
dc.contributor.authorMonjane, A L
dc.contributor.authorHarkins, G W
dc.contributor.authorVarsani, A
dc.contributor.authorShepherd, D N
dc.contributor.authorMartin, D P
dc.date.accessioned2016-08-11T14:34:42Z
dc.date.available2016-08-11T14:34:42Z
dc.date.issued2013
dc.date.updated2016-08-11T12:58:19Z
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. What is unknown, however, is (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 andGeminiviridae, and analysed these for evidence of natural selection favouring 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 it is 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 uncharacterised structural elements that likely have important functions within some of the ssDNA virus genomes analysed here.en_ZA
dc.identifierhttp://dx.doi.org/10.1128/JVI.03031-13
dc.identifier.apacitationMuhire, B. M., Golden, M., Murrell, B., Lefeuvre, P., Lett, J., Gray, A., ... Martin, D. P. (2013). Evidence of pervasive biologically functional secondary-structures within the genomes of eukaryotic single-stranded DNA viruses. <i>Journal of Virology</i>, http://hdl.handle.net/11427/21202en_ZA
dc.identifier.chicagocitationMuhire, B M, M Golden, B Murrell, P Lefeuvre, J-M Lett, A Gray, Art Y F Poon, et al "Evidence of pervasive biologically functional secondary-structures within the genomes of eukaryotic single-stranded DNA viruses." <i>Journal of Virology</i> (2013) http://hdl.handle.net/11427/21202en_ZA
dc.identifier.citationMuhire, B. M., Golden, M., Murrell, B., Lefeuvre, P., Lett, J. M., Gray, A., ... & Monjane, A. L. (2014). Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses. Journal of virology, 88(4), 1972-1989.en_ZA
dc.identifier.issn0022-538Xen_ZA
dc.identifier.ris TY - Journal Article AU - Muhire, B M AU - Golden, M AU - Murrell, B AU - Lefeuvre, P AU - Lett, J-M AU - Gray, A AU - Poon, Art Y F AU - Ngandu, N K AU - Semegni, Y AU - Tanov, E P AU - Monjane, A L AU - Harkins, G W AU - Varsani, A AU - Shepherd, D N AU - Martin, D P AB - 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. What is unknown, however, is (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 andGeminiviridae, and analysed these for evidence of natural selection favouring 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 it is 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 uncharacterised structural elements that likely have important functions within some of the ssDNA virus genomes analysed here. DA - 2013 DB - OpenUCT DP - University of Cape Town J1 - Journal of Virology LK - https://open.uct.ac.za PB - University of Cape Town PY - 2013 SM - 0022-538X T1 - Evidence of pervasive biologically functional secondary-structures within the genomes of eukaryotic single-stranded DNA viruses TI - Evidence of pervasive biologically functional secondary-structures within the genomes of eukaryotic single-stranded DNA viruses UR - http://hdl.handle.net/11427/21202 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/21202
dc.identifier.vancouvercitationMuhire BM, Golden M, Murrell B, Lefeuvre P, Lett J, Gray A, et al. Evidence of pervasive biologically functional secondary-structures within the genomes of eukaryotic single-stranded DNA viruses. Journal of Virology. 2013; http://hdl.handle.net/11427/21202.en_ZA
dc.languageengen_ZA
dc.publisherAmerican Society for Microbiologyen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.sourceJournal of Virologyen_ZA
dc.source.urihttp://jvi.asm.org/
dc.titleEvidence of pervasive biologically functional secondary-structures within the genomes of eukaryotic single-stranded DNA virusesen_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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