Conserved RNA secondary structure in Cherry virus A 5′-UTR associated with translation regulation

Figures

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  Fig. 1. Genetic structure and diversity of CVA. A Neighbor-joining phylogenetic tree of 75 CVA variants. B 3D PCA (PC1, PC2, and PC3) of 75 CVA variants using identified SNPs as markers. CVA variants from the same subgroup clustered together

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  Fig. 2. Nucleotide diversity in different groups on the whole genome. Polyline height represents nucleotide diversity, and the x-axis represents genome position. Dotted lines divide the genome into different functional regions

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  Fig. 3. Motifs in the four CVA 5′-UTR types. Similar motifs are marked in red, and different motifs are marked in turquoise. The red motif sequence is more conservative, and the turquoise motif sequence is the hypervariable region. Green motifs were absent in type 2

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  Fig. 4. Secondary structures in the four CVA 5′-UTR types. A-D correspond to 5′-UTR types 1–4, respectively. The red line indicates the conserved RNA structure

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  Fig. 5. Effects of CVA 5′-UTR types and mutation of CR on translation of the FLuc reporter gene. A FLuc reporter constructs containing CVA 5′-UTR types. Red nucleotides indicate the mutation sites. B Effects of CVA 5′-UTR types and mutation of CR on FLuc translation

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  Fig. 6. In-line structure probing of CVA 5′-UTR-Type-1. A Susceptibility of residues at the CVA 5′-UTR-Type-1 to in-line cleavage. OH, ladder generated from treatment with NaOH; Tm, partial RNaseT1 digest to denote location of guanosine; In-line, in-line cleavage of the fragment. The intensity of each band is proportional to the flexibility of the residue at that location. Green solid triangles point to the weaker cleavage sites, where as red solid triangles point to the stronger cleavage sites. CR, conserved sequence and RNA structure region. B Susceptibility of residues in the putative structure of CVA 5′-UTR-Type-1 to in-line cleavage. Green and red nucleotides indicate the single-strand characteristic, whereas red nucleotides indicate strongly marked cleavage based on the in-line probing pattern