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J. Biol. Chem., Vol. 280, Issue 10, 8748-8755, March 11, 2005

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Viral RNA-directed RNA Polymerases Use Diverse Mechanisms to Promote Recombination between RNA Molecules^*

Alexander B. Chetverin, Damir S. Kopein, Helena V. Chetverina, Alexander A. Demidenko, and Victor I. Ugarov

From the Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia

An earlier developed purified cell-free system was used to explore the potential of two RNA-directed RNA polymerases (RdRps), Q phage replicase and the poliovirus 3Dpol protein, to promote RNA recombination through a primer extension mechanism. The substrates of recombination were fragments of complementary strands of a Q phage-derived RNA, such that if aligned at complementary 3'-termini and extended using one another as a template, they would produce replicable molecules detectable as RNA colonies grown in a Q replicase-containing agarose. The results show that while 3Dpol efficiently extends the aligned fragments to produce the expected homologous recombinant sequences, only nonhomologous recombinants are generated by Q replicase at a much lower yield and through a mechanism not involving the extension of RNA primers. It follows that the mechanisms of RNA recombination by poliovirus and Q RdRps are quite different. The data favor an RNA transesterification reaction catalyzed by a conformation acquired by Q replicase during RNA synthesis and provide a likely explanation for the very low frequency of homologous recombination in Q phage.

Received for publication, November 9, 2004 , and in revised form, December 17, 2004.

^* This work was supported by the program "Molecular and Cell Biology" of the Russian Academy of Sciences, Russian Foundation for Basic Research Grant 02-04-48320, International Association for the promotion of co-operation with scientists from the New Independent States of the former Soviet Union Grant 01-2012, a grant from the Ministry of Industry, Science and Technology of the Russian Federation, and an International Research Scholar's award from the Howard Hughes Medical Institute (to A. B. C.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

Present address: University of Chicago, Chicago, IL 60637.

To whom correspondence should be addressed: Institute of Protein Research, Pushchino, Moscow Region, Russia 142290. Tel.: 7-0967-73-2524; Fax: 7-095-924-0493; E-mail: alexch{at}vega.protres.ru.

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