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

Muhizi Muhire Brejnev, Golden Michael, Murrell Ben, Lefeuvre Pierre, Lett Jean-Michel, Gray Alistair J.A., Poon Art Y.F., Kwanele Ngandu Nobubelo, Semegni Jean-Yves, Tanov Emil Pavlov, Monjane Adérito Luis, Harkins Gordon William, Varsani Arvind, Shepherd Dionne Natalie, Martin Darren Patrick. 2014. Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses. Journal of Virology, 88 (4) : 1972-1989.

Quartile : Q1, Sujet : VIROLOGY

Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Psychologie-éthologie-ergonomie

Résumé : 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.

Classification Agris : H20 - Maladies des plantes

Champ stratégique Cirad : Axe 4 (2014-2018) - Santé des animaux et des plantes

Auteurs et affiliations

• Muhizi Muhire Brejnev, UCT (ZAF)
• Golden Michael, Institute of Infectious Diseases and Molecular Medicine (ZAF)
• Murrell Ben, UCR (USA)
• Lefeuvre Pierre, CIRAD-BIOS-UMR PVBMT (REU)
• Lett Jean-Michel, CIRAD-BIOS-UMR PVBMT (REU)
• Gray Alistair J.A., UCT (ZAF)
• Poon Art Y.F., University of British Columbia (CAN)
• Kwanele Ngandu Nobubelo, Institute of Infectious Diseases and Molecular Medicine (ZAF)
• Semegni Jean-Yves, Cape Peninsula University of Technology (ZAF)
• Tanov Emil Pavlov, University of the Western Cape (ZAF)
• Monjane Adérito Luis, UCT (ZAF)
• Harkins Gordon William, University of the Western Cape (ZAF)
• Varsani Arvind, University of Canterbury (NZL)
• Shepherd Dionne Natalie, UCT (ZAF)
• Martin Darren Patrick, Institute of Infectious Diseases and Molecular Medicine (ZAF)

Source : Cirad - Agritrop (https://agritrop.cirad.fr/573047/)

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