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Journal of Virology, October 2006, p. 10045-10054, Vol. 80, No. 20
0022-538X/06/$08.00+0     doi:10.1128/JVI.00991-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

trans Regulation of Cap-Independent Translation by a Viral Subgenomic RNA

Ruizhong Shen ,^1,3,, Aurélie M. Rakotondrafara,^2,3, and W. Allen Miller^1,2,3,4*

Interdepartmental Genetics Program,¹ Molecular, Cellular and Developmental Biology Program,² Plant Pathology Department,³ Biochemistry, Biophysics and Molecular Biology Department, Iowa State University, Ames, Iowa 50011⁴

Received 13 May 2006/ Accepted 24 July 2006

Many positive-strand RNA viruses generate 3'-coterminal subgenomic mRNAs to allow translation of 5'-distal open reading frames. It is unclear how viral genomic and subgenomic mRNAs compete with each other for the cellular translation machinery. Translation of the uncapped Barley yellow dwarf virus genomic RNA (gRNA) and subgenomic RNA1 (sgRNA1) is driven by the powerful cap-independent translation element (BTE) in their 3' untranslated regions (UTRs). The BTE forms a kissing stem-loop interaction with the 5' UTR to mediate translation initiation at the 5' end. Here, using reporter mRNAs that mimic gRNA and sgRNA1, we show that the abundant sgRNA2 inhibits translation of gRNA, but not sgRNA1, in vitro and in vivo. This trans inhibition requires the functional BTE in the 5' UTR of sgRNA2, but no translation of sgRNA2 itself is detectable. The efficiency of translation of the viral mRNAs in the presence of sgRNA2 is determined by proximity to the mRNA 5' end of the stem-loop that kisses the 3' BTE. Thus, the gRNA and sgRNA1 have "tuned" their expression efficiencies via the site in the 5' UTR to which the 3' BTE base pairs. We conclude that sgRNA2 is a riboregulator that switches off translation of replication genes from gRNA while permitting translation of structural genes from sgRNA1. These results reveal (i) a new level of control of subgenomic-RNA gene expression, (ii) a new role for a viral subgenomic RNA, and (iii) a new mechanism for RNA-mediated regulation of translation.

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* Corresponding author. Mailing address: Plant Pathology Department, Iowa State University, 351 Bessey Hall, Ames, Iowa 50011. Phone: (515) 294-2436. Fax: (515) 294-9420. E-mail: wamiller{at}iastate.edu.

R.S. and A.M.R. contributed equally to the study.

Present address: Department of Medicine/Gastroenterology, University of Alabama at Birmingham, Birmingham, AL 35294.

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Journal of Virology, October 2006, p. 10045-10054, Vol. 80, No. 20
0022-538X/06/$08.00+0     doi:10.1128/JVI.00991-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

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