Stimulation of stop codon readthrough: frequent presence of an extended 3' RNA structural element

Firth, Andrew E.; Wills, Norma M.; Gesteland, Raymond F.; Atkins, John F.

Stop codon RT is also utilized by members of the plant virus taxa Tombusviridae, Luteoviridae, Benyvirus and Tobamovirus but the RT signals for these viruses had previously been grouped separately from those utilized by the alphaviruses, coltiviruses, tobraviruses, pecluviruses, furoviruses and pomoviruses (excepting pomovirus RNA2), and our analysis likewise supported this distinction at the level of extended 3 0 -adjacent synonymous site conservation (34) . In the case of the tobamoviruses, greatly enhanced synonymous site conservation is seen from codons À1 to +3 relative to the UAG stop codon, and the motif xxA-UAG-CAA-UUA-xxG is completely conserved in the 105 sequences analyzed (despite lack of amino acid conservation at the À1 and +3 codons). However, more extended conservation of the type seen in the alphaviruses was not observed (Figure 4 ). In the luteoviruses and poleroviruses (family Luteoviridae), the stop codon context AAA-UAG-GUA is completely conserved in all except one of 247 sequences analyzed (rose spring dwarf-associated virus, EU024678, has GAA-UGA-CGG), and enhanced synonymous site conservation was also observed over several further codons, especially codons À1 to +5. However, while this region may well interact with distal elements as discussed in ref. (45) , the extended 3 0 -adjacent conservation of the type seen in the alphaviruses was not observed in the Luteoviridae (Figure 4) . The highly conserved local nucleotide contexts of the different RT sites mentioned here have been noted, discussed and characterized in detail in a number of previous works (34 and references therein). A compilation of our own sequence analysis is given in the Supplementary Data and, to our knowledge, represents the largest such compilation to date.