Cap- and poly(A)-independent initiation in translation in Viruses

Several groups of positive-strand RNA viruses containRNAs that are neither capped nor polyadenylated. These viruses have evolved alternative strategies for translation that use 3′-UTR enhancer elements to recruit eIF4F or eIFiso4F and/or to base pair with their 5′-UTRs for loading

the 43S preinitiation complex at the 5′- start site. Satellite tobacco necrosis virus (STNV – a positive strand RNA necrovirus) RNA contains within its 3′-UTR (just after the termination codon of the coat protein coding region) a translational enhancer domain (TED) that promotes efficient cap-independent translation when combined with the STNV 5′-UTR (for STNV-1 strain see Timmer etal. 1993). Although TED can functionally substitute for a 5′-cap structure, its function in vitro is dependent on the presence of eIF4F and eIFiso4F (Timmer et al. 1993). Indeed TED specifically binds eIF4E and eIF4iso4Ein vitro (van Lipzig et al. 2002; Gazo et al. 2004), while the 5′-UTR of STNV-1 has the potential to base pair with TED and the 3′-end of 18S rRNA (Timmer et al. 1993).

Thus to promote cap-independent translation initiation, TED recruits the 43S preinitiation complex by binding canonical cap-binding factors at the 3′-UTR, while potential base pairing between the viral 5′- and 3′-UTRs would be required for transfer of this 43S complex to the 5′-UTR to locate the initiation codon. The existence of the 3′- to 5′-UTR pathway to recruit the translational machinery is probably not unique to STNV TED, but is likely to apply to other enhancer elements present within the 3′-UTRs of other non-capped, non-polyadenylated virus RNAs. Barley yellow dwarf virus (BYDV – a luteovirus) RNA also lacks a 5′-cap structure and poly (A) tail, but it harbors a cap-independent BYDV translational element (BTE) functionally similar to TED within the 3′-UTR (Wang et al. 1997; Guo et al. 2000). A BYDV like BTE is present in all Luteoviruses, as well as in Dianthovirus [Red clover necrotic mosaic virus (RCNMV), Mizumoto et al. 2003] and Necrovirus [tobacco necrosis virus (TNV), Meulewaeter et al. 2004; Shen and Miller 2004], and contains the conserved sequence CGGAUCCUGGGAAACAGG, which also functions when placed in the 5′-UTR. In its natural location this sequence has the potential to base pair to the 5′-UTR (Wang et al. 1997; Guo et al. 2000, 2001). BTE can recruit the translation machinery to the 3′-end and deliver it to the 5′-UTR by a 3′–5′ RNA interaction (Wang et al. 1997).

The delivery of the translational machinery to the 5′-end can occur due to long-distance kissing-loop interactions between RNA hairpins in BTE and the 5′-UTR (Guo et al. 2001). Thus, TED and BTE behave in a similar way to strongly stimulate cap-independent translation, without exhibiting any conservation of sequence or secondary structure. Whether BTE or TED require participation of canonical translation initiation factors for their action remains to be investigated. Another distinct enhancer element identified in Tombusvirus, Tomato bushy stunt virus (TBSV), has been termed the 3′-cap-independent translational enhancer. The TBSV 5′-UTR folds into a complex RNA structure, which was recently demonstrated to physically interact with the 3′CITE in vitro (Fabian and White 2004). Formation of 5′–3′ RNA interactions correlates well with efficient translation in vivo and might support the transfer of the translational machinery from the 3′ to the 5′-end of the RNA as suggested for BTE and TED (Figure 5).

 3′ cap-independent translational enhancer (3′ CITE)-mediated translation. a | General 3′ CITE model showing the long-range interaction (indicated by the double-headed arrow) that positions the eukaryotic translation initiation factor 4F (eIF4F)-bound 3′ CITE close to the 5′ end of the genome, where it enables eIF4F-mediated recruitment of the 40S ribosomal subunit to the 5′ end to initiate translation. Interacting sequences are shown in green. b | Dual 3′ CITE model. Pea enation mosaic virus (PEMV) contains two different types of 3′ CITE: a panicum mosaic virus-like translational enhancer (PTE), which is located in the 3′UTR and binds to eIF4F; and a kissing-loop T-shaped structure (kl-TSS), which is positioned immediately upstream and binds directly to the 60S ribosome subunit and mediates long-distance RNA–RNA base pairing with a 5′-proximal hairpin. c–e | Internal ribosome entry site (IRES)-mediated translation. c | The foot-and-mouth disease virus (FMDV) IRES is stimulated by the 3′ UTR, which engages in long-range contacts with two regions in the 5′ UTR: the IRES and a region that has been shown to be involved in genome replication, which is known as the S-region. The specific sequences that are involved in this interaction have not been identified and the interaction with the S-region may modulate genome replication. d | The 3′-terminal hexamer CGGCCC in classical swine fever virus (CSFV) is a negative modulator of IRES-mediated translation and may confer its inhibition by pairing with a ribosome-binding region in the IRES, thus blocking ribosome binding. e | Hepatitis C virus (HCV) IRES activity is negatively regulated by an interaction between helix IIId of the IRES and a bulge in the structure 5BSL3.2, which is located in the coding region of non-structural protein 5B (NS5B). The same bulge in 5BSL3.2 also interacts with a genomic sequence around position 9110 of the genome, and the terminal loop of 5BSL3.2 can pair with the 3′ SL2 element located in the 3′ UTR, which may modulate genome replication. These interactions may coordinate viral translation and genome replication.