THE ROLE OF THE PSEUDOKNOT AT THE 3'-END OF TURNIP YELLOW MOSAIC-VIRUS RNA IN MINUS-STRAND SYNTHESIS BY THE VIRAL RNA-DEPENDENT RNA-POLYMERASE

The tRNA-like structure at the 3' end of turnip yellow mosaic virus (T YMV) RNA was studied in order to determine the role of this structure in the initiation of minus-strand synthesis in vitro. Deletions in the 5'-to 3' direction up to the pseudoknot structure did not result in a decrease of transcription efficiency. However, transcription efficien cy was reduced twofold when a fragment of 21 nucleotides, comprising t he 3'-terminal hairpin, was used as a template, tRNA(Phe) from yeast, Escherichia coli 5S rRNA, and the 3'-terminal 208 nucleotides of alfal fa mosaic virus RNA 3 could not be transcribed by the RNA-dependent RN A polymerase (RdRp) of TYMV. Various mutations in the sequences of loo p regions L1 and L2 or of stem region S1 of the pseudoknot were tested to further investigate the importance of the pseudoknot structure. Th e results were compared with those obtained in an earlier study on ami noacylation with the same mutants tR, M. W. Mans, M. H. van Steeg, P. W. G. Verlaan, C. W. A. Pleij, and L. Bosch. J. Mol. Biol, 223:221-232 : 1992). Mutants which still harbor a stable pseudoknot, as proven by probing its structure, have a transcription efficiency very close to t hat of the wild-type virus. Disruption of the pseudoknot structure, ho wever, gives rise to a drop in transcription efficiency to about 50%, No indications of base-specific interactions between L1, L2, or S1 of the pseudoknot and the RdRp were found.