The amazing diversity of cap-independent translation elements in the 3'-untranslated regions of plant viral RNAs

Abstract

Many plant viral RNAs lack the 5'-cap structure that is required on all host mRNAs for interacting with essential translation initiation factors. Instead, uncapped viral RNAs take over the host translation machinery by harbouring sequences that functionally replace the 5'-cap. Recent reports reveal at least eight different classes of CITE (cap-independent translation element) located in the 3'-UTRs (untranslated regions) of various viruses. We describe how the structure and behaviour of each class of element differs from the other classes, suggesting that they recruit translation factors and, ultimately, the ribosome by diverse mechanisms. These results greatly expand our understanding of ways in which mRNAs can recruit ribosomes, and they provide insight into the regulation of virus gene expression.

Figure 1. Sequences and secondary structures of representative members of six classes of plant viral 3′-CITE

Bold bases are known to or predicted to base-pair to the 5′-UTR. Bold italics indicate conserved sequences. (A) STNV TED, known only in STNV-1 [37] and STNV-2 [42] RNAs. (B) The BTE, found in all members of the Luteovirus [10], Dianthovirus [19], and Necrovirus [20,21] genera, and in two umbraviruses. (C) The TBSV CITE, found in nine members of genus Tombusvirus [23]. (D) The predicted MNeSV CITE secondary structure is [25] also predicted for MNSV. (E) The PTE, also present in PEMV RNA 2. (F) Predicted structure of the BRV RNA2 CITE [32]. Shaded text indicates the stop codon of the RNA 2 ORF.

Figure 2. Model for 3′-CITE recruitment of translational machinery to viral mRNA

Using the BYDV BTE as an example, eIF4F and possibly other factors bind the 3′-CITE. Long-distance base-pairing juxtaposes the CITE-bound factors near the 5′-end. This delivers eIF4F and possibly other factors to the 5′-end, where they interact with the ribosome to facilitate scanning.