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J. Biol. Chem., Vol. 278, Issue 48, 48084-48091, November 28, 2003

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RNA Packaging Device of Double-stranded RNA Bacteriophages, Possibly as Simple as Hexamer of P4 Protein^*

Denis E. Kainov, Markus Pirttimaa, Roman Tuma, Sarah J. Butcher, George J. Thomas, Jr.¶, Dennis H. Bamford||, and Eugene V. Makeyev**

From the Department of Biosciences and Institute of Biotechnology, FIN-00014, University of Helsinki, Finland and the ^¶Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri, Kansas City, Missouri 64110

Genomes of complex viruses have been demonstrated, in many cases, to be packaged into preformed empty capsids (procapsids). This reaction is performed by molecular motors translocating nucleic acid against the concentration gradient at the expense of NTP hydrolysis. At present, the molecular mechanisms of packaging remain elusive due to the complex nature of packaging motors. In the case of the double-stranded RNA bacteriophage 6 from the Cystoviridae family, packaging of single-stranded genomic precursors requires a hexameric NTPase, P4. In the present study, the purified P4 proteins from two other cystoviruses, 8 and 13, were characterized and compared with 6 P4. All three proteins are hexameric, single-stranded RNA-stimulated NTPases with / folds. Using a direct motor assay, we found that 8 and 13 P4 hexamers translocate 5' to 3' along ssRNA, whereas the analogous activity of 6 P4 requires association with the procapsid. This difference is explained by the intrinsically high affinity of 8 and 13 P4s for nucleic acids. The unidirectional translocation results in RNA helicase activity. Thus, P4 proteins of Cystoviridae exhibit extensive similarity to hexameric helicases and are simple models for studying viral packaging motor mechanisms.

Received for publication, June 30, 2003 , and in revised form, August 28, 2003.

^* This work was supported by the Academy of Finland ("Finnish Centre of Excellence Program 2000–2005" Grants 172623 (to R. T.), 178778 (to S. J. B.), and 1202855 and 1202108 (to D. H. B.)) and National Institutes of Health Grant GM50776 (to G. J. T.). 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.

Fellow of the National Graduate School in Informational and Structural Biology.

^** Present address: Dept. of Molecular and Cellular Biology, Harvard University, 7 Divinity Ave., Cambridge, MA 02138.

^|| To whom correspondence should be addressed: P.O. Box 56, Viikinkaari 5, FIN-00014, University of Helsinki, Finland. Tel.: 358-9-191-59100; Fax: 358-9-191-59098; E-mail: dbamford{at}mappi.helsinki.fi.

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