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Title: A stem–loop structure in the 59 untranslated region of bean pod mottle virus RNA2 is specifically required for RNA2 accumulation

item LIN, J - The Ohio State University
item ALI, A - The Ohio State University
item CHEN, P - The Ohio State University
item GHABRIAL, S - University Of Kentucky
item FINER, J - The Ohio State University
item DORRANCE, A - The Ohio State University
item Redinbaugh, Margaret - Peg
item QU, F - The Ohio State University

Submitted to: Journal of General Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/30/2013
Publication Date: 6/1/2013
Publication URL:
Citation: Lin, J., Ali, A.K., Chen, P., Ghabrial, S., Finer, J., Dorrance, A., Redinbaugh, M.G., Qu, F. 2013. A stem–loop structure in the 59 untranslated region of bean pod mottle virus RNA2 is specifically required for RNA2 accumulation. Journal of General Virology. 94:1415-1420.

Interpretive Summary: For virus infection to occur in a host, the viral genome must replicate or be reproduced. This key step in the virus 'life cycle' depends on factors in both the host and and virus. For many viruses, this step is carried out primarily by a viral protein called an RNA-dependent RNA polymerase (RdRP). A second viral protein, called an auxiliary protein is important for making sites, called viral replication complexes (VRC), within the infected host cell that shield the virus replication process from host defenses. The question of how viral nucleic acids are brought to the VRC is understood for some viruses, but had not been investigated for the agriculturally important pathogen, Bean pod mottle virus. This viral genome has two segments, RNA1 which contains the RDRP and RNA2 which requires the RDRP from RNA1 for it's replication. We found that a part of RNA2 at the one end (5') of the genome segment that does not encode a protein was required for RNA2 replication. Further, we identified this portion of the viral RNA segment forms a structure called a hairpin loop. When this structure can form in plants, the viral RNA can replicate. We hypothesize that the structure is important for guiding the RNA2 to the VRC for virus replication.

Technical Abstract: Bean pod mottle virus (BPMV) is a bipartite, positive-sense (+) RNA plant virus of the family Secoviridae. Its RNA1 encodes all proteins needed for genome replication and is capable of autonomous replication. By contrast, BPMV RNA2 must utilize RNA1-encoded proteins for replication. Here, we sought to identify RNA elements in RNA2 required for its replication. The exchange of 59 untranslated regions (UTRs) between genome segments revealed an RNA2-specific element in its 59 UTR. Further mapping localized a 66 nucleotide region that was predicted to fold into an RNA stem–loop structure, designated SLC. Additional functional analysis indicated the importance of the middle portion of the stem and an adjacent two-base mismatch. This is the first report of a cis-acting RNA element in RNA2 of a bipartite secovirus.