Nucleic Acids Research, 2002, Vol. 30, No. 19 4232-4240
© 2002 Oxford University Press
Structural variation and functional importance of a D-loop–T-loop interaction in valine-accepting tRNA-like structures of plant viral RNAs
Group Genexpress, Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands, 1 Group Theoretical Biology and Phylogenetics, Institute of Evolutionary and Ecological Sciences, Leiden University, Leiden, The Netherlands and 2 Department of Biophysical Structural Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
*To whom correspondence should be addressed. Tel: +31 71 527 4769; Fax: +31 71 527 4340; Email: c.pley{at}chem.leidenuniv.nl
Valine-accepting tRNA-like structures (TLSs) are found at the 3' ends of the genomic RNAs of most plant viruses belonging to the genera Tymovirus, Furovirus, Pomovirus and Pecluvirus, and of one Tobamovirus species. Sequence alignment of these TLSs suggests the existence of a tertiary D-loop–T-loop interaction consisting of 2 bp, analogous to those in the elbow region of canonical tRNAs. The conserved G18·
55 pair of regular tRNAs is found to covary in these TLSs between G·U (possibly also modified to G·) and A·G. We have mutated the relevant bases in turnip yellow mosaic virus (TYMV) and examined the mutants for symptom development on Chinese cabbage plants and for accumulation of genetic reversions. Development of symptoms is shown to rely on the presence of either A·G or G·U in the original mutants or in revertants. This finding supports the existence and functional importance of this tertiary interaction. The fact that only G·U and A·G are accepted at this position appears to result from steric and energetic limitations related to the highly compact nature of the elbow region. We discuss the implications of these findings for the various possible functions of the valine-accepting TLS.
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