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Nucleic Acids Research Advance Access originally published online on December 17, 2007
Nucleic Acids Research 2008 36(4):1057-1071; doi:10.1093/nar/gkm1036
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Nucleic Acids Research, 2008, Vol. 36, No. 4 1057-1071
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

The cucumovirus 2b gene drives selection of inter-viral recombinants affecting the crossover site, the acceptor RNA and the rate of selection

Bu-Jun Shi1,2,*, Robert H. Symons2,{dagger} and Peter Palukaitis3

1Australian Centre for Plant Functional Genomics, University of Adelaide, 2School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA 5064, Australia and 3Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK

*To whom correspondence should be addressed. Tel: +61 8 83037168; Fax: +61 8 83037102; Email: bujun.shi{at}acpfg.com.au

Correspondence may also be addressed to Peter Palukaitis. Tel: +44 1382 568523; Fax: +44 1382 568575; Email: Peter.Palukaitis{at}scri.ac.uk

Received August 27, 2007. Revised October 30, 2007. Accepted October 30, 2007.

RNA–RNA recombination is an important pathway in virus evolution and has been described for many viruses. However, the factors driving recombination or promoting the selection of recombinants are still unclear. Here, we show that the small movement protein (2b) was able to promote selection of RNA 1/2–RNA 3 recombinants within a chimeric virus having RNAs 1 and 2 from cucumber mosaic virus, and RNA 3 from the related tomato aspermy virus, along with heterologous 2b genes. The source of the 2b also determined the selection of the acceptor RNA and the crossover site, as well as affecting the rate of selection of the recombinant RNAs. The nature of the RNA 3 also influenced the selection of the recombinant RNAs. A 163-nt tandem repeat in RNA 3 significantly affected the rate of selection of the recombinant RNA, while a single nucleotide within the repeat affected the crossover site. The recombination occurred in a non-random manner, involved no intermediates and probably was generated via a copy-choice mechanism during (+) strand RNA synthesis.

{dagger}Deceased.


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