Evidence of pervasive biologically functional secondary-structures within the genomes of eukaryotic single-stranded DNA viruses (2014)

View/ Open
Type of Content
Journal ArticlePublisher
University of Canterbury. Biological SciencesUniversity of Canterbury. Biomolecular Interaction Centre
Collections
- Science: Journal Articles [1139]
Authors
Abstract
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.
Citation
Muhire, B.M., Golden, M., Murrell, B., Lefeuvre, P., Lett, J-M., Gray, A., Poon, A.Y.F., Ngandu, N.K., Semegni, Y., Tanov, E.P., Monjane, A.L., Harkins, G.W., Varsani, A., Shepherd, D.N., Martin, D.P. (2014) Evidence of pervasive biologically functional secondary-structures within the genomes of eukaryotic single-stranded DNA viruses. Journal of Virology, 88(4), pp. 1972–1989.This citation is automatically generated and may be unreliable. Use as a guide only.
ANZSRC Fields of Research
31 - Biological sciences::3105 - Genetics::310508 - Genome structure and regulationRelated items
Showing items related by title, author, creator and subject.
-
The global distribution of Banana bunchy top virus reveals little evidence for frequent recent, human-mediated long distance dispersal events
Stainton, D.; Martin, D.P.; Muhire, B.M.; Lolohea, S.; Halafihi, M.; Lepoint, P.; Blomme, G.; Crew, K.S.; Sharman, M.; Kraberger, S.; Dayaram, A.; Walters, M.; Collings, D.A.; Mabvakure, B.; Lemey, P.; Harkins, G.W.; Thomas, J.E.; Varsani, A. (University of Canterbury. Biological Sciences, 2015)Banana bunchy top virus (BBTV; family Nanoviridae, genus Babuvirus) is a multi-component single-stranded DNA virus, which infects banana plants in many regions of the world, often resulting in large-scale crop losses. We ... -
Pervasive chimerism in the replication-associated proteins of uncultured single-stranded DNA viruses
Kazlauskas D; Varsani A; Krupovic M (2018)© 2018 by the authors. Licensee MDPI, Basel, Switzerland. Numerous metagenomic studies have uncovered a remarkable diversity of circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses, ... -
Virus discovery in all three major lineages of terrestrial arthropods highlights the diversity of single-stranded DNA viruses associated with invertebrates
Baker CCM; Cassill DL; Storer C; Varsani A; Breitbart M; Rosario K; Mettel K; Benner BE; Johnson R; Scott C; Yusseff-Vanegas, SZ (2018)© 2018 Rosario et al. Viruses encoding a replication-associated protein (Rep) within a covalently closed, single-stranded (ss)DNA genome are among the smallest viruses known to infect eukaryotic organisms, including ...