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Journal of Virology, September 1998, p. 6967-6978, Vol. 72, No. 9
0022-538X/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.

Recombination in the 5' Leader of Murine Leukemia Virus Is Accurate and Influenced by Sequence Identity with a Strong Bias toward the Kissing-Loop Dimerization Region

Jacob Giehm Mikkelsen,1 Anders H. Lund,1 Mogens Duch,1 and Finn Skou Pedersen1,2,*

Department of Molecular and Structural Biology1 and Department of Medical Microbiology and Immunology,2 University of Aarhus, DK-8000 Aarhus, Denmark

Received 4 December 1997/Accepted 24 May 1998

Retroviral recombination occurs frequently during reverse transcription of the dimeric RNA genome. By a forced recombination approach based on the transduction of Akv murine leukemia virus vectors harboring a primer binding site knockout mutation and the entire 5' untranslated region, we studied recombination between two closely related naturally occurring retroviral sequences. On the basis of 24 independent template switching events within a 481-nucleotide target sequence containing multiple sequence identity windows, we found that shifting from vector RNA to an endogenous retroviral RNA template during minus-strand DNA synthesis occurred within defined areas of the genome and did not lead to misincorporations at the crossover site. The nonrandom distribution of recombination sites did not reflect a bias for specific sites due to selection at the level of marker gene expression. We address whether template switching is affected by the length of sequence identity, by palindromic sequences, and/or by putative stem-loop structures. Sixteen of 24 sites of recombination colocalized with the kissing-loop dimerization region, and we propose that RNA-RNA interactions between palindromic sequences facilitate template switching. We discuss the putative role of the dimerization domain in the overall structure of the reverse-transcribed RNA dimer and note that related mechanisms of template switching may be found in remote RNA viruses.

* Corresponding author. Mailing address: Department of Molecular and Structural Biology, University of Aarhus, C. F. Moellers Allé, Bldg. 130, DK-8000 Aarhus, Denmark. Phone: 45 89422614. Fax: 45 86196500. E-mail: fsp{at}mbio.aau.dk.

Journal of Virology, September 1998, p. 6967-6978, Vol. 72, No. 9
0022-538X/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.


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