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Journal of Virology, April 2009, p. 2976-2988, Vol. 83, No. 7
0022-538X/09/$08.00+0     doi:10.1128/JVI.02040-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

5' cis Elements Direct Nodavirus RNA1 Recruitment to Mitochondrial Sites of Replication Complex Formation{triangledown}

Priscilla M. Van Wynsberghe1,{dagger} and Paul Ahlquist1,2*

Institute for Molecular Virology,1 Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 537062

Received 26 September 2008/ Accepted 5 January 2009

Positive-strand RNA viruses replicate their genomes on intracellular membranes, usually in conjunction with virus-induced membrane rearrangements. For the nodavirus flock house virus (FHV), we recently showed that multifunctional FHV replicase protein A induces viral RNA template recruitment to a membrane-associated state, but the site(s) and function of this recruitment were not determined. By tagging viral RNA with green fluorescent protein, we show here in Drosophila cells that protein A recruits FHV RNA specifically to the outer mitochondrial membrane sites of RNA replication complex formation. Using Drosophila cells and yeast cells, which also support FHV replication, we also defined the cis-acting regions that direct replication and template recruitment for FHV genomic RNA1. RNA1 nucleotides 68 to 205 were required for RNA replication and directed efficient protein A-mediated RNA recruitment in both cell types. RNA secondary structure prediction, structure probing, and phylogenetic comparisons in this region identified two stable, conserved stem-loops with nearly identical loop sequences. Further mutational analysis showed that both stem-loops and certain flanking sequences were required for RNA1 recruitment, negative-strand synthesis, and subsequent positive-strand amplification in yeast and Drosophila cells. Thus, we have shown that protein A recruits RNA1 templates to mitochondria, as expected for RNA replication, and identified a new RNA1 cis element that is necessary and sufficient for RNA1 template recognition and recruitment to these mitochondrial membranes for negative-strand RNA1 synthesis. These results establish RNA recruitment to the sites of replication complex formation as an essential, distinct, and selective early step in nodavirus replication.

* Corresponding author. Mailing address: Institute for Molecular Virology, University of Wisconsin-Madison, 1525 Linden Dr., Madison, WI 53706-1596. Phone: (608) 263-5916. Fax: (608) 265-9214. E-mail: ahlquist{at}facstaff.wisc.edu

{triangledown} Published ahead of print on 14 January 2009.

{dagger} Present address: Department of Biology, University of California, San Diego, La Jolla, CA 92093.

Journal of Virology, April 2009, p. 2976-2988, Vol. 83, No. 7
0022-538X/09/$08.00+0     doi:10.1128/JVI.02040-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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