FIG. 1.

Sequences and proposed secondary structures of TYMV and PCV TLSs. The main structural features of the TLSs are depicted on the TYMV structure: T and D loops analogous to those of tRNAs, the acceptor/T arm pseudoknot indicated by helical segments S1 and S2 and connecting loops L1 and L2, and the major valine identity nucleotides (arrowheads) in the anticodon loop (anticodon underlined), which are recognized by valyl-tRNA synthetase. The nucleotide in reverse shading in the PCV RNA2 TLS is one of the two nucleotides that differ from the PCV RNA2 TLS sequence. The other difference, a single nucleotide deletion in the anticodon of PCV RNA2, is shown with a dash. The stem-loop (5′-SL) structure shown beside the PCV RNA1 TLS is present at the 5′ end of the PCV RNA1 and -2 TLS RNAs used for in vitro valylation assays and is represented by “SL” in each structure. Nucleotides shown in lowercase at the 3′ ends of the PCV RNA1 and -2 TLSs are of nonviral origin, derived from the MluI and HindIII linearization, respectively, of plasmid templates used to make the infectious transcripts used in in vivo replication experiments. Those nucleotides are not present in the SLTLS transcripts used for valylation assays. During plant cell inoculation, the additional nucleotides are thought to be removed by exonuclease action and repair of the 3′ CCA by CCA nucleotidyltransferase or by internal initiation during minus-strand synthesis. The mutations introduced into the RNA1 and RNA2 anticodons are indicated below the structures. TLS nucleotides are numbered from the 3′ A of the viral sequences.