Conservation of RNA structures enables TNV and BYDV 5' and 3' elements to cooperate synergistically in cap-independent translation

Abstract

The subgenomic RNA 2 of tobacco necrosis virus A (TNV sgRNA2) encodes the viral coat protein, is unpolyadenylated and presumably uncapped. Here, we show that TNV sgRNA2 is translated cap independently. This cap-independent translation requires the leader and a 140 nt element of the trailer both in wheat germ extract and in tobacco protoplasts. Similar to barley yellow dwarf virus (BYDV), the TNV 5' and 3' elements stimulate translation synergistically. Computer-aided phylogenetic analysis of the secondary structure of the TNV trailer revealed that the 3' translation element is part of a major conserved stem-loop that contains similarities to structures in the BYDV 3' translation element. These data suggest that the translation mechanisms of TNV sgRNA2 and BYDV RNA are related. To further characterize this relationship, we tested whether cooperativity exists between TNV sgRNA2 and BYDV 5' and 3' elements. We found that the TNV sgRNA2 5' element stimulates translation synergistically with the BYDV 3' element in vitro. This finding is the first evidence for conservation of structures that enable a 5'-3' interaction stimulating cap-independent translation.

Tombusvirus recruitment of host translational machinery via the 3′ UTR

“…For BYDV, a model incorporating the 39CITE binding to both eIF4Fs and the 59 UTR (i.e., a 59 UTR/39CITE/eIF interaction) has been proposed to explain how 39CITE-bound eIFs could access the 59-end of a viral message, where they likely mediate recruitment of the 43S ribosomal subunit (Guo et al 2001;Rakotondrafara et al 2006;Treder et al 2008). This type of RNA/RNA/protein (RRP) model for 39CITE function has also been suggested for several other virus genera (Gazo et al 2004;Meulewaeter et al 2004;Shen and Miller 2004;Karetnikov et al 2006;Karetnikov and Lehto 2008;Truniger et al 2008;Xu and White 2009), including tombusviruses (Fabian and White 2006). However, the factor(s) that presumably binds to tombusvirus 39CITEs has yet to be identified.…”

“…These RNA structures have been termed 39-cap-independent translational enhancers (39CITEs) (Miller et al 2007). Functional 39CITEs have been reported for the aureusvirus Cucumber leafspot virus (CLSV) (Xu and White 2009); the carmoviruses Turnip crinkle virus (TCV) (Qu and Morris 2000;Stupina et al 2008), Hibiscus chlorotic ringspot virus (HCRSV) (Koh et al 2002), and Melon necrotic spot virus (MNSV) (Truniger et al 2008); the dianthovirus Red clover necrotic mosaic virus (RCNMV) (Mizumoto et al 2003); the necroviruses Tobacco necrosis virus (TNV) (Shen and Miller 2004;Meulewaeter et al 2004) and Satellite tobacco necrosis virus (STNV) (Danthinne et al 1993;Timmer et al 1993;Meulewaeter et al 1998); the panicovirus Panicum mosaic virus (PMV) (Batten et al 2006); the tombusviruses Tomato bushy stunt virus (TBSV) (Wu and White 1999), Carnation Italian ringspot virus (CIRV) (Nicholson and White 2008), and Maize necrotic streak virus (MNeSV) (Scheets and Redinbaugh 2006); the luteovirus Barley yellow dwarf virus (BYDV) (Wang and Miller 1995;Wang et al 1997); and the umbravirus Pea enation mosaic virus (PEMV) (Wang et al 2009). Of these, detailed RNA structure/function analyses of 39CITEs in BYDV (Guo et al 2000), TBSV White 2004, 2006), TCV (Stupina et al 2008;Zuo et al 2010), and PEMV (Wang et al 2009) have led to sound RNA secondary structure models for these elements.…”

A Distinct Class of Internal Ribosomal Entry Site in Members of the Kobuvirus and Proposed Salivirus and Paraturdivirus Genera of the Picornaviridae

“…There is direct evidence for the recombinational transfer of the ϳ300-nt-long 3= UTR of grapevine chrome mosaic virus RNA-1 to tomato black ring virus RNA-2 (40), and a similar phenomenon could account for the presence of structurally related and functionally exchangeable translational enhancers known as Barley yellow dwarf virus (BYDV)-like translation elements in the 3= UTRs of members of Luteovirus, Dianthovirus, Necrovirus, and Umbravirus genera (50,86), of the sequence-and structurally related 3=-cap-independent translational enhancer (3=CITE) in the 3= UTRs of members of Tombusvirus, Aureusvirus, and Carmovirus genera (53), and of the stem-loop 2-like motif (s2m) in the 3= end of the genome of some species in Astroviridae, Caliciviridae, Coronaviridae, and Picornaviridae (37,77).…”

Oscillating kissing stem–loop interactions mediate 5′ scanning-dependent translation by a viral 3′-cap-independent translation element

“…Here we report on a different type of cap-independent translation element discovered in certain uncapped nonpolyadenylated plant viral and satellite RNAs including the Luteoviruses (Wang et al 1997) and members of the Tombusviridae family (Timmer et al 1993;Wu and White 1999;Mizumoto et al 2003;Meulewaeter et al 2004;Shen and Miller 2004;Batten et al 2006;Scheets and Redinbaugh 2006). Unlike IRES-mediated translation, the cap-independent translation element is present in the 39-untranslated region, yet translation initiation occurs at the AUG closest to the 59-end of the mRNA (Kneller et al 2006).…”