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Published online 12 March 2004

Nucleic Acids Research, 2004, Vol. 32, No. 5 1721-1730
© 2004 Oxford University Press

Conservation of RNA structures enables TNV and BYDV 5' and 3' elements to cooperate synergistically in cap-independent translation

Frank Meulewaeter*, Rosalinde van Lipzig, Alexander P. Gultyaev1,2, Cornelis W. A. Pleij1, Daniel Van Damme, Marc Cornelissen and Gerben van Eldik

Bayer BioScience N.V., J. Plateaustraat 22, B-9000, Gent, Belgium, 1 Leiden Institute of Chemistry, Gorlaeus Laboratories, 2300 RA Leiden, The Netherlands and 2 Section Theoretical Biology, Institute of Biology, Leiden University, Kaiserstraat 63, 2311 GP Leiden, The Netherlands

*To whom correspondence should be addressed. Tel: +32 9 235 84 38, Fax: +32 9 224 06 94; Email: frank.meulewaeter{at}bayercropscience.com
Present address:
Daniel Van Damme, Department of Plant Systems Biology, VIB / Ghent University, Technologiepark 927, B-9052 Gent, Belgium

The subgenomic RNA 2 of tobacco necrosis virus A (TNV sgRNA2) encodes the viral coat protein, is unpolyadenylated and presumably uncapped. Here, we show that TNV sgRNA2 is translated cap independently. This cap-independent translation requires the leader and a 140 nt element of the trailer both in wheat germ extract and in tobacco protoplasts. Similar to barley yellow dwarf virus (BYDV), the TNV 5' and 3' elements stimulate translation synergistically. Computer-aided phylogenetic analysis of the secondary structure of the TNV trailer revealed that the 3' translation element is part of a major conserved stem–loop that contains similarities to structures in the BYDV 3' translation element. These data suggest that the translation mechanisms of TNV sgRNA2 and BYDV RNA are related. To further characterize this relationship, we tested whether cooperativity exists between TNV sgRNA2 and BYDV 5' and 3' elements. We found that the TNV sgRNA2 5' element stimulates translation synergistically with the BYDV 3' element in vitro. This finding is the first evidence for conservation of structures that enable a 5'–3' interaction stimulating cap-independent translation.


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