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. 2004 Mar 12;32(5):1721–1730. doi: 10.1093/nar/gkh338

Figure 3.

Figure 3

TNV sgRNA2 contains phylogenetically conserved structural elements with similarities to those in the RNA of BYDV. (A) TNV sgRNA2 trailer can fold into a phylogenetically conserved structure that contains similarities to the structure present in the BYDV 3′ translation element. The predicted foldings of TNV-A, TNV-D and TNV-DH, and the folding of the translation-stimulatory nucleotides 4837–4901 of the BYDV RNA (19) are shown. I–IV are the major stem–loops formed in the TNV sgRNA2 trailer. X, Y and Z are the small stem–loop structures in BYDV and their homologous stem–loops in the TNV sgRNA2 trailer (X and Z), comprising the small regions of complementarity to the leader (circled bases) as described earlier by Guo et al. (16). 18S indicates complementary region to the 18S ribosomal RNA. The arrows indicate the TNV sgRNA2 trailer region containing the translation-stimulatory sequences. (B) The proposed leader–trailer interactions are phylogenetically conserved in TNV RNAs. Comparison of the predicted stem–loop structures in the leaders and putative interactions with the trailers for the TNV-A genomic and subgenomic RNAs, BYDV RNA [as described by Guo et al. (16)], and the genomic RNAs of TNV-D, TNV-DH. Circles indicate the complementary nucleotides, and the dashed lines indicate the putative interactions. Covariations between TNV-A, TNV-D and TNV-DH are indicated with squares. Nucleotide numbering for the TNV RNAs is according to the position in sgRNA2 for the full trailer sequence, and indicates the position of the nucleotides within the RNA for which the putative leader–trailer interaction is shown (1,4). Numbering between parentheses indicates the position within TNV sgRNA2. Nucleotide positions in the genomic RNA are indicated for BYDV (29), TNV-D (20) and TNV-DH (21).