Mechanisms for RNA Capture by ssDNA Viruses: Grand Theft RNA
- 628 Downloads
Viruses contain three common types of packaged genomes; double-stranded DNA (dsDNA), RNA (mostly single and occasionally double stranded) and single-stranded DNA (ssDNA). There are relatively straightforward explanations for the prevalence of viruses with dsDNA and RNA genomes, but the evolutionary basis for the apparent success of ssDNA viruses is less clear. The recent discovery of four ssDNA virus genomes that appear to have been formed by recombination between co-infecting RNA and ssDNA viruses, together with the high mutation rate of ssDNA viruses provide possible explanations. RNA–DNA recombination allows ssDNA viruses to access much broader sequence space than through nucleotide substitution and DNA–DNA recombination alone. Multiple non-exclusive mechanisms, all due to the unique replication of ssDNA viruses, are proposed for this unusual RNA capture. RNA capture provides an explanation for the evolutionary success of the ssDNA viruses and may help elucidate the mystery of integrated RNA viruses in viral and cellular DNA genomes.
KeywordsRecombination Evolution Rep protein Endonuclease Ligase RNA–DNA ligation
Thanks to the Stedman lab for stimulating discussions and Geoff Diemer and Christoph Deeg comments on this manuscript. Thanks also to Ian Hewson and Lauren McDaniel for sharing data before publication. Thanks to Mya Breitbart, Sandy Lazarowitz and Bentley Fane for stimulating discussions. This work was supported by the Gordon and Betty Moore Foundation, the US National Science Foundation Microbial Observatories Program, Grant number MCB 0702020, and Portland State University.
- Acheson NH (2011) Fundamentals of Molecular Virology. Wiley, New YorkGoogle Scholar
- Fane BA, Brentlinger KL, Burch AD, Chen M, Hafenstein S, Moore E, Novak CR, Uchiyama A (2006) ΦX174 et al., the Microviridae. In: Calendar R (ed) The Bacteriophages, 2nd edn. Oxford University Press, New York, pp 129–145Google Scholar
- Hewson I, Ng G, Li W, LaBarre BA, Aguirre I, Barbosa JG, Breitbart M, Greco AW, Kearns CM, Looi A, Schaffner LR, Thompson PD, Hairston NG Jr (2013) Metagenomic identification, seasonal dynamics and potential transmission mechanisms of a Daphnia-associated putative RNA–DNA hybrid virus in two temperate lakes. Limnol Ocean (in press)Google Scholar
- Holmes EC (2009) The evolution and emergence of RNA viruses. Oxford University Press, New YorkGoogle Scholar
- King AMQ, Lefkowitz E, Adams MJ, Carstens EB (eds) (2011) Virus Taxonomy : Ninth Report of the International Committee on Taxonomy of Viruses. Academic Press, San DiegoGoogle Scholar
- McDaniel L, Rosario K, Breitbart M, Paul J (2013) Comparative metagenomics : Natural populations of induced prophages demonstrate highly unique, lower diversity viral sequences. Env Microbiol (in press)Google Scholar
- Morens DM, Fauci AS (2012) Emerging infectious diseases in 2012: 20 years after the Institute of Medicine report. mBio 3 e00494-12. doi: 10.1128/mBio.00494-12
- Villarreal LP (2004) Viruses and the evolution of life. ASM Press, WashingtonGoogle Scholar
- Watson J, Baker T, Bell S, Gann A, Levine M, Losick R (2014) Molecular Biology of the Gene. Cold Spring Harbor Press, New YorkGoogle Scholar