Viruses from the family Bromoviridae and the genera Tobamovirus and Tymovirus possess a 5′ cap structure but lack a 3′ poly(A) tail. In contrast, they contain tRNA-like structures (TLSs) at their 3′ termini that perform many viral processes, such as (i) serving as a telomere by interacting with CTP:ATP nucleotidyl transferase which adds CCA in a non-templated fashion to the 3′ end (Rao et al., 1989), (ii) regulation of negative strand synthesis (Dreher, 2009), (iii) translation enhancement (Gallie and Walbot, 1990; Choi et al., 2002; Matsuda and Dreher, 2004), and (iv) packaging of the viral RNA in the virion (Annamalai and Rao, 2007). Three basic types of 3′ terminal TLS have been described in the genomes of Turnip yellow mosaic virus (TYMV; genus Tymovirus, family Tymoviridae), TMV and Brome mosaic virus (BMV; genus Bromovirus, family Bromoviridae). Because of their multiple functions, it has been difficult to tease out the mechanisms of each role, but the translational enhancement structures and mechanisms have been well characterized for TMV and TYMV (Table 1).

The TYMV TLS requires aminoacylation of the 3′-CCA terminus for maximal translational efficiency and the 5′ cap synergistically promotes this activity (Matsuda et al., 2004). Translational enhancement maps principally to the TLS, although the upstream adjacent pseudoknot is important for optimal translation, possibly serving as a sequence spacer (Matsuda and Dreher, 2004). The aminoacylated TLS binds to eukaryotic elongation factor 1A (eEF1A) and is a substrate for tRNA-modifying enzymes (Dreher and Goodwin, 1998; Matsuda et al., 2004) mimicking tRNA activity. The 5′-proximal AUG in the TYMV genome serves as start codon for a 69 kDa ORF (p69), and the second AUG is the start codon for the main polyprotein ORF (p206) with which ORF p69 overlaps. Based on only in vitro translation assays, Barends et al. (2004) proposed a “Trojan Horse” model of translation initiation in which the aminoacylated TLS delivers its amino acid to the start codon of the polyprotein ORF. However, the Dreher lab provided in vitro and in vivo evidence that a more likely mechanism is classical leaky scanning, except that the efficiency of initiation at the second AUG correlated with its proximity to the first AUG (Matsuda and Dreher, 2006). In addition, the translation efficiency of the polyprotein ORF depended on a 5′ cap, and not the 3′ TLS. This and additional data support an “initiation coupling” model in which the close proximity (7 nt) of the two AUG codons is necessary for maximum translation of the polyprotein ORF (Matsuda and Dreher, 2007).

How the TLS interacts with the 5′ end to stimulate translation in the scanning-dependent manner is suggested by the crystal structure of the TYMV TLS. The TLS has a tRNA-like shape, but it uses a very different set of intramolecular interactions (Colussi et al., 2015). These interactions allow the TLS to switch conformations and to interact with the ribosome, docking within it to regulate the folding and unfolding state to permit dual functionality in viral translation and replication. This leads us to hypothesize that TLS recruits the ribosome, which is delivered to the 5′-UTR by communication with the 5′ end through the cap-eIF4E-eIF4G-eIF3-40S chain of interactions.

A different function for tRNA mimicry occurs in the only IRES that occurs naturally between ORFs: the intergenic region (IGR) IRES of dicistroviruses (Wilson et al., 2000; Khong et al., 2016). In the IGR IRES, a pseudoknot mimics the structure of the anticodon loop of a tRNA basepaired to a codon in mRNA, facilitating instant elongation as the ribosome joins the viral RNA with no initiation steps (Costantino et al., 2008).

In the case of BMV RNA, its 3′-UTR has been shown to provide translation enhancement, and the disruption of its TLS reduced translation in vitro (Barends et al., 2004). On the other hand, the TMV TLS is structurally similar to the TYMV TLS and functions as minus-strand promoter (Chapman and Kao, 1999), but it does not mediate translation enhancement. However, the 3′-UTR of TMV contains an upstream pseudoknot domain that stimulates translation in a way that is replaceable by a poly(A) tail (Gallie et al., 1991; Leathers et al., 1993). Additionally, TMV RNA also harbors in its 5′-UTR the 68-nt omega (Ω) sequence which highly stimulates cap-dependent translation (Gallie and Kado, 1989). Ω is recognized by the heat shock protein 101 (HSP101), mediating translational activity (Wells et al., 1998) and interacts with eIF4F via eIF4G (Gallie, 2002, 2016). Similarly, the Brassicaceae-specific eIFiso4G2 isoform also contributes in Ω-mediated translation, unlike eIFiso4G which did not affect Ω-dependent translation (Gallie, 2016). These results suggest that eIFiso4G2 exhibits more functional similarity with eIF4G than eIFiso4G. Regarding translational activity, Ω is one of the most efficient mRNA leaders in vitro and in vivo and it was used for biotechnological applications such as transgene expression (Gallie et al., 1987; Fan et al., 2012).

The non-polyadenylated Alfalfa mosaic virus (AMV, genus Alfamovirus, family Bromoviridae) RNA requires the viral CP for efficient translation and infection. The 3′-UTR of AMV also plays a role in translation due to its ability to bind the CP, adopting the CP-binding (CPB) conformation. This binding avoids the minus-strand promoter activity and enhances translation, possibly acting as a mimic of the poly(A) tail (Olsthoorn et al., 1999). The CPB structure folds into a series of stem-loops separated by an AUGC motif and mutations in this motif led to the loss of binding to CP, correlating with reduction of translation in protoplasts (Reusken and Bol, 1996; Neeleman et al., 2004). The crystal structure of CP-bound RNA revealed a novel RNA fold in which RNA forms two hairpins separated by the linker AUGC motif and oriented in right angles (Guogas et al., 2004). The presence of the CP promotes the base pairing between linker motifs, leading a compact structure. Moreover, pulldown assays revealed that the CP interacts with eIF4G/eIFiso4G subunits (Krab et al., 2005). This interaction may stimulate mRNA circularization in a similar fashion as found for rotaviruses (Groft and Burley, 2002). In addition to the CPB form, AMV RNAs 3′ termini also fold into a pseudoknot structure that resembles a TLS conformation. The 3′-UTR can be recognized by a tRNA-specific enzyme and by the viral replicase and this recognition is inhibited by the addition of CP (Olsthoorn et al., 1999; Chen and Olsthoorn, 2010). Thus, it suggests that TLS conformation acts as a minus-strand promoter and the CP interaction and pseudoknot stability may regulate a conformational switch between translation and replication (Chen and Olsthoorn, 2010).

Members of the Tombusviridae and Luteoviridae plant virus families lack both 5′ cap and 3′ poly(A) elements, but contain in their 3′ ends structured RNA elements capable of enhancing translation in the absence of cap (cap-independent translation elements, CITEs). Most 3′-CITEs have in common their ability to bind translation initiation factors of the eIF4E or eIF4G families, as well as the presence of small sequence stretches within or near the 3′-CITE capable of base-pairing to sequences in the 5′-UTR of the mRNA to establish long-distance RNA:RNA interactions (Table 1). By definition, 3′-CITEs functionally substitute for the 5′ cap with high efficiency. They recruit translation initiation factors leading to ribosome entry at or near the 5′ terminus followed by ribosome scanning to the initiation codon (Fabian and White, 2004; Rakotondrafara and Miller, 2008; Nicholson and White, 2011); therefore, in contrast to IRESes, 3′-CITEs do not promote internal ribosome entry. To date, seven different classes of 3′-CITEs have been described (Simon and Miller, 2013; Miras et al., 2014) which share little secondary structure and sequence similarity. Due to space limitations and a previous comprehensive review on 3′-CITEs (Simon and Miller, 2013), we will describe only briefly each 3′-CITE and recent updates.

The first 3′-CITE was discovered in Satellite tobacco necrosis virus (STNV) and is located in a 120-nt sequence termed translation enhancer domain (TED) (Danthinne et al., 1993; Timmer et al., 1993; Meulewaeter et al., 1998). The TED is predicted to form a long stem-loop with several internal bulges (Van Lipzig et al., 2002). This element was shown to be functional in enhancing translation in vitro and in vivo. TED binds eIF4F or eIFiso4F (Gazo et al., 2004), and is proposed to interact with the 5′-UTR via a predicted RNA:RNA long-distance interaction with the apical loop of the 5′ end. However, mutations that disrupted this potential long-distance base-pairing reduced translation only slightly, and covarying mutations designed to restore base pairing did not restore translation to wild type levels (Meulewaeter et al., 1998). The STNV 3′-CITE confers cap-independent translation in vitro when it is moved to the 5′-UTR of an uncapped reporter (Meulewaeter et al., 1998). Another member of the Tombusviridae family, Pelargonium line pattern virus (PLPV, genus Carmovirus) was recently shown to harbor a 3′-CITE in the TED class (Blanco-Pérez et al., 2016). In this case, PLPV TED was shown to require a long-range RNA:RNA kissing stem-loop interaction with a hairpin in the coding sequence of the PLPV p27 ORF for efficient translational activity (Blanco-Pérez et al., 2016).

The shortest CITEs are the I-shaped structures (ISS) present in the 3′-UTRs of Maize necrotic spot virus (MNeSV, Tombusvirus, family Tombusviridae) and Melon necrotic spot virus (MNSV, genus Carmovirus, family Tombusviridae) (Truniger et al., 2008; Nicholson et al., 2010; Miras et al., 2016), and are apparently similar in secondary structure to the TED. MNeSV ISS has been shown to preferentially interact with the eIF4E subunit of eIF4F. As for TED and most other CITEs, base pairing between the 3′-CITE and the 5′-UTR is predicted to deliver the translation factor to the 5′ end, facilitating recruitment of the 43S preinitiation complex (Nicholson et al., 2010). In support of this model, it has been shown that the interacting 5′-UTR:I-shaped 3′-CITE of MNeSV together with eIF4F form a complex in vitro. In addition, ribosome toe printing demonstrated that while bound to eIF4F, the I-shaped CITE can simultaneously base pair with the 5′-UTR and recruit ribosomes to the 5′ end of the viral fragment (Nicholson et al., 2010).

In the case of MNSV ISS, genetic evidence for interaction of the ISS with eIF4E has been shown in melon. A single amino acid change in melon eIF4E strongly reduces translation efficiency controlled by MNSV ISS and makes melon resistant to MNSV infection (Nieto et al., 2006; Truniger et al., 2008). The minimal 3′-CITE sequence, named Ma5TE (MNSValpha5-like translation enhancer), was mapped to a 45 nt region. In vitro binding assays revealed that Ma5TE forms a complex with eIF4F and this interaction was mapped to a conserved guanosine residue located in a Ma5TE internal loop (Miras et al., 2016). Additionally, mutational analyses in eIF4E residues involved in its interaction with eIF4G showed that eIF4F complex formation is necessary for efficient cap-independent translation driven by Ma5TE (Miras et al., 2016). Identification of a new resistant-breaking isolate of MNSV revealed a new class of 3′-CITE, the CXTE, which was acquired from Cucurbit aphid-borne yellows virus (CABYV, genus Polerovirus, family Luteoviridae) Xinjiang by interfamilial recombination, conferring to the recipient MNSV isolate the advantage to translate efficiently and infect resistant melon varieties (Miras et al., 2014). Thus, the 3′-UTR of this MNSV isolate harbors two 3′-CITEs, Ma5TE, and CXTE, with CXTE secondary RNA structure folding into two helices protruding from a central hub. Both 3′-CITEs are active in susceptible melon, while only the CXTE functions in resistant melon and in the absence of eIF4E (Miras et al., 2014).

The Barley yellow dwarf virus-like translation element (BTE) is one of the best-characterized 3′-CITEs and is found in all members of the Luteovirus, Dianthovirus, Alphanecrovirus, Betanecrovirus, and Umbravirus genera (Wang et al., 2010; Simon and Miller, 2013). All BTEs share a long basal helix from which two to five additional helices radiate (Figure 1). BTEs contain a highly conserved 17-nucleotide sequence GGAUCCUGGGAAACAGG that includes SL-I (formed by pairing of underline bases). The BTE binds preferentially to the eIF4G subunit of the eIF4F heterodimer (Treder et al., 2008). The eIF4G-binding site in the BTE was revealed by SHAPE footprinting, which showed that eIF4G protects SL-I and nearby bases around base of the hub from which all helices protrude (Kraft et al., 2013). Addition of eIF4E enhanced the level of protection and stimulated translation by about 25%. Deletion analysis of eIF4G revealed that only the core domain (including eIF4A and eIF3 binding sites, but lacking the eIF4E and PABP binding sites) and an adjacent upstream RNA binding domain are necessary for binding to the BTE and to stimulate translation (Kraft et al., 2013; Zhao et al., 2017).

A long-distance kissing stem-loop interaction between a loop in the BTE and the 5′-UTR is required for BTE-mediated translation (Guo et al., 2001). This long-distance RNA:RNA interaction can be replaced by complementary non-viral sequences outside the BTE (Rakotondrafara et al., 2006). This interaction is conserved among all BTEs except the BTE of Red clover necrotic mosaic virus (RCNMV, genus Dianthovirus, family Tombusviridae), in which mutations in potential complementary loops had no effect on translation and possess the longest BTE and 3′-CITE (Sarawaneeyaruk et al., 2009).

After eIF4F binds the BTE, it appears that the eIF4A helicase, eIF4B plus ATP bind in order to recruit the 40S subunit directly to the BTE. The long-distance base pairing would then deliver the 40S complex to the 5′ end for scanning to the first AUG (Sharma et al., 2015; Figure 2A). This differs from a previous model in which it was proposed that the long-distance base pairing places the factors near the 5′ end, at which point the 40S complex is recruited (Rakotondrafara et al., 2006). However, the dependence on helicase activity may support an older model in which a six base tract in the 17 nt conserved sequence (GAUCCU) base pairs directly to 18S rRNA at the position where the Shine-Dalgarno sequence is located in prokaryotic ribosomal RNA (Wang et al., 1997). Because much of this tract is base paired internally in both the BTE and in 18S rRNA, the helicase activity may be required to disrupt this base pairing, freeing the complementary tracts in the BTE and 18S rRNA to base pair to each other. This base pairing would recruit the 40S subunit directly to the BTE (Figure 2A). However, recently the presence of eIF4A, eIF4B and ATP was also found to enhance the binding affinity of the BTE to eIF4G in the absence of the ribosome (Zhao et al., 2017). This enhanced binding affinity may be the consequence of helicase activity of eIF4A/eIF4G/ATP altering BTE structure. This greater affinity of eIF4G to the BTE may facilitate efficient recruitment of the 40S subunit by conventional factor interactions without need for base pairing to ribosomal RNA (Figure 2B). Future experiments are necessary to determine which model is correct. On the other hand, RCNMV possesses an A-rich sequence (ARS) with strong affinity to PABP in addition to its BTE in its 3′-UTR. Both sequences, ARS and 3′-CITE, have been shown to coordinately recruit eIF4F/ eIFiso4F and the 40S ribosomal subunit to the viral RNA (Iwakawa et al., 2012).

Tomato bushy stunt virus (TBSV, genus Tombusvirus, family Tombusviridae) and other viruses belonging to the genus Tombusvirus, contain 3′-CITEs resembling Y-shaped structure (YSS), formed by three helical regions. The efficiency of translation controlled by the YSS of TBSV depends on a long-distance interaction with the 5′-UTR of the genome. Mutational analysis of TBSV YSS showed that alterations in junction residues between helices and in a large asymmetric bulge in the major supporting stem disrupted translation (Fabian and White, 2004, 2006). Moreover, the YSS of Carnation Italian ringspot virus (CIRV, genus Dianthovirus, family Tombusviridae) requires addition of the eIF4F or eIFiso4F complex to a factor-depleted wheat germ extract to promote efficient translation (Nicholson et al., 2013). Translation assays showed the ability of the CIRV YSS to function efficiently in vitro and in vivo, whereas TBSV YSS was detectable only in in vivo, suggesting that this difference is due to a misfolding in the TBSV RNA and the lack of eIFs required in translation (Fabian and White, 2004).

The Panicum mosaic virus-like Translation Enhancer (PTE) was first identified in Panicum mosaic virus (PMV, genus Panicovirus, family Tombusviridae) (Batten et al., 2006) and later in Pea enation mosaic virus 2 (PEMV2, genus Umbravirus, family Tombusviridae) (Wang et al., 2009b). The PEMV2 PTE consists of a three-way branched helix with a large G-rich bulge in the main stem (Wang et al., 2009b). The formation of a magnesium-dependent pseudoknot between the G-rich bulge and a C-rich sequence at the three-helix junction of the PTE is critical for translation and eIF4E recruitment by the PTE (Wang et al., 2011). Unlike most other CITEs, the PEMV2 PTE may not participate in a long-distance RNA:RNA interaction with the 5′-UTR. Instead, upstream of the PTE, there is an element, the kl-TSS, that participates in a long range RNA:RNA interaction with a 5′ proximal hairpin located in the p33 ORF (Gao et al., 2012).

Most other PTEs contain a loop predicted to base pair to the 5′-UTR. Indeed, Saguaro cactus virus (SCV, genus Carmovirus, family Tombusviridae), harbors a PTE which participates in a long-distance RNA:RNA interaction with a hairpin located in the p26 ORF (Chattopadhyay et al., 2011). Interestingly, the sequence involved in the interaction has the same conserved motif found in carmovirus TED-like elements and I-shaped structures (Simon and Miller, 2013).

The 3′-UTR of another member of the Tombusviridae family, Turnip crinkle virus (TCV, genus Carmovirus, family Tombusviridae), contains an internal T-shaped structure (TSS) that consists of three hairpins, two pseudoknots and multiple unpaired single stranded linker regions (Zuo et al., 2010). Interestingly, the TSS resembles a three-dimensional tRNA-like structure (Zuo et al., 2010). The TCV TSS recruits and binds the 60S subunit of the 80S ribosome (Stupina et al., 2008). For this element, no base pairing between 3′-CITE and 5′-UTR has been identified. It was proposed that the ribosomal subunits form a protein bridge with the UTRs, where the 40S subunit binds the 5′-UTR and the 60S subunit binds the TSS (Stupina et al., 2008). Two additional TSSs were found in the PEMV2 3′-UTR, one upstream of the PTE and another near to the 3′ terminus (Gao et al., 2013). Interestingly, both TSSs can also bind the 60S ribosomal subunit and although they are essential for virus accumulation in vivo, mutations that disrupted the downstream TSS had no effect in translation (Gao et al., 2013, 2014). However, when this TSS element was positioned proximal to the reporter ORF enhanced translational activity. This report points out the importance of the reporter constructs in the identification of 3′-CITE that participate in translation. A recent report showed that TCV RdRp binds to A-rich sequence upstream of the TSS and using optical tweezers and steered molecular dynamic simulations showed that elements of TSS unfold when it is interacting with RdRp which may promote the conformational switch between translation and replication (Le et al., 2017).

More classes of 3′-CITE await discovery, as the 3′ UTRs of several members of the Tombusviridae contain no structure that obviously resembles a known 3′-CITE (Simon and Miller, 2013). Thus, viruses have evolved a plethora of structures to achieve the same goal: recruitment of eIF4F and ultimately the ribosome to their RNAs.

Many plant viruses utilize programmed ribosomal frameshifting (PRS) to translate overlapping ORFs. This recoding event can occur in the + or − direction relative to the normal 0 frame of mRNA translation by shifting the ribosome in one or two nucleotides forward or backward. Productive frameshifting normally competes poorly with standard decoding, so the efficiency of frameshifting in viruses varies from 1% in BYDV to 82% in cardioviruses (Barry and Miller, 2002; Finch et al., 2015). Thus far, most frameshifting by plant viruses is in the -1 direction. These include members of the Sobemovirus, Umbravirus, and Dianthovirus genera and the Luteoviridae family (Brault and Miller, 1992; Demler et al., 1993; Kujawa et al., 1993; Mäkinen et al., 1995; Kim et al., 1999; Lucchesi et al., 2000; Barry and Miller, 2002; Tamm et al., 2009). Members of the non-related family Closteroviridae (genus Closterovirus, Crinivirus and Ampelovirus) are predicted to use a +1 frameshift to synthesize their viral replicases (Agranovsky et al., 1994; Karasev et al., 1995; Melzer et al., 2008).

The -1 PRS usually requires two signals in the mRNA, a slippery sequence of the type X_XXY_YYZ, where X normally represents any nucleotide, Y represents A or U and Z represents A, C or U (gaps delimit codons in the original 0 frame); and a downstream secondary structure element separated from the slippery sequence by a spacer region of 5-9 nt (Dinman, 2012). In plant viruses these structural elements, acting as stimulators of frameshifting, fall into three structural classes: an apical loop with a bulge, a compact hairpin-type pseudoknot or a stem-loop (Figure 3) (reviewed by Miller and Giedroc, 2010).

The -1 PRS stimulatory elements of BYDV, PEMV-RNA2 and RCNMV fold into a stem-loop with an internal bulge in a similar manner (Kim et al., 1999; Paul et al., 2001; Barry and Miller, 2002; Gao and Simon, 2015). For BYDV, this element participates in a long-distance interaction with the apical loop of a stem-loop located in the 3′-UTR (about 4 kb downstream of the frameshift site). This interaction is required for the low expression levels of RdRp and thus replication (Barry and Miller, 2002). Similar long-range base pairing interactions were shown in RNAs of RCNMV and PEMV2 (Tajima et al., 2011; Gao and Simon, 2015). For PEMV2 RNA, this interaction modifies the lower stem of the structure, possibly due to a rise of its stability or the approximation of other sequence near the 3′ end. Curiously, the distant −1 PRS element of PEMV2 RNA appeared to inhibit, rather than stimulate frameshifting, because in its absence, the frameshift rate increased 72% with respect to the wild type viral genome (Gao and Simon, 2015).

On the other hand, the frameshift stimulatory elements from poleroviruses Beet western yellows virus, Potato leaf roll virus and Sugarcane yellow leaf virus (BWYV, PLRV, and ScYLV, family Luteoviridae, genus Polerovirus) and PEMV1 (family Luteoviridae, genus Enamovirus) form h-type pseudoknots (Egli et al., 2002; Cornish et al., 2005; Pallan et al., 2005; Giedroc and Cornish, 2009). The frameshift regulatory element of BWYV was the first to be determined at atomic resolution showing a compact pseudoknot with a triple-stranded region (Egli et al., 2002). It was suggested that pseudoknots provide a kinetic barrier to the ribosome and that the unfolding of this element correlates with frameshifting stimulation (Giedroc and Cornish, 2009).

Stop-codon readthrough is a common strategy found in plant viruses to encode protein variants with an extended C-terminus from the same RNA. During readthrough, some ribosomes do not stop at the stop codon but continue until the next termination codon. Members of the Tombusviridae, Luteoviridae and Virgaviridae families employ readthrough of UGA and UAG stop codons in their replicase and coat protein genes. Flanking nucleotides as well as long-range RNA-RNA interactions influence stop-codon readthrough (Figure 3; Firth and Brierley, 2012; Nicholson and White, 2014). Depending on the sequence motifs and the stop codon, three types of readthrough can be described: The type I motif employs a UAG codon in the replicase gene and is followed by the consensus motif CARYYA (where R is a purine and Y is a pyrimidine) (Skuzeski et al., 1991); this type is used by tobamoviruses, benyviruses and pomoviruses (Pelham, 1978; Firth and Brierley, 2012). The type II motif is used by tobraviruses, pecluviruses, furoviruses and pomoviruses to generate their viral RdRp and by furoviruses to express the coat protein (Skuzeski et al., 1991; Zerfass and Beier, 1992). It involves a UGA stop codon followed by a CGG or CUA triplet and a stem-loop structure about 8 nts downstream of the stop codon (Firth et al., 2011). The type III class comprises an UAG stop codon, a downstream G or purine-rich octanucleotide and a 3′ RNA structure (Firth and Brierley, 2012) and appears in carmovirus and tombusvirus genomes. For example, the tombusvirus CIRV uses stop-codon readthrough to generate its viral RdRp and requires a long-distance interaction between an RNA structure located downstream of the readthrough site and also a sequence in the 3′-UTR (Cimino et al., 2011). Tobacco necrosis virus-D (TNV-D, genus Betanecrovirus, family Tombusviridae) employs a complex series of downstream interactions. A stable bulged readthrough stem-loop (RTSL) immediately downstream of the leaky stop codon contains a G-rich bulge which must base pair to a distant readthrough element (DRTE) located 3 kb downstream in the structure required for replication initiation (Newburn et al., 2014). A pseudoknot immediately 3′ to the RTSL, and a stem-loop adjacent 5′ to the DRTE in the 3′-UTR are also necessary for optimal readthrough (Newburn and White, 2017). The long-distance interactions within the viral genome required for frameshifting and readthrough may play a regulatory role as switch between translation and replication (Cimino et al., 2011), by allowing replicase entering at the 3′ end of the genome to stop its own translation 3–4 kb upstream, as it disrupts this essential long-distance interaction (Miller and White, 2006).

Readthrough of the CP stop codon of viruses from the Luteoviridae family appears to use a fourth class of cis-acting signals (Brown et al., 1996). The stop codon is usually UAG, but can be UGA or UAA. Instead, readthrough requires a tract of 8–16 repeats of CCXXXX beginning about 8 nt downstream of stop codon and requires additional sequence about 700–750 nt downstream in the coding region of the readthrough ORF, in the example of BYDV (Brown et al., 1996). Although the resulting CP-readthrough protein fusion is not essential for virus particle assembly or infectivity it is assembled into the virion and is required for persistent, circulative aphid transmission (Brault et al., 1995; Chay et al., 1996).