Mechanism of Initiation Site Selection Promoted by the Human Rhinovirus 2 Internal Ribosome Entry Site

Translation initiation site usage on the human rhinovirus 2 internal ribosome entry site (IRES) has been examined in a mixed reticulocyte lysate/HeLa cell extract system. There are two relevant AUG triplets, both in a base-paired hairpin structure (domain VI), with one on the 5′ side at nucleotide (nt) 576, base paired with the other at nt 611, which is the initiation site for polyprotein synthesis. A single residue was inserted in the apical loop to put AUG-576 in frame with AUG-611, and in addition another in-frame AUG was introduced at nt 593. When most of the IRES was deleted to generate a monocistronic mRNA, the use of these AUGs conformed to the scanning ribosome model: improving the AUG-576 context increased initiation at this site and decreased initiation at downstream sites, whereas the converse was seen when AUG-576 was mutated to GUA; and AUG-593, when present, took complete precedence over AUG-611. Under IRES-dependent conditions, by contrast, much less initiation occurred at AUG-576 than in a monocistronic mRNA with the same AUG-576 context, mutation of AUG-576 decreased initiation at downstream sites by ∼70%, and introduction of AUG-593 did not completely abrogate initiation at AUG-611, unless the apical base pairing in domain VI was destroyed by point mutations. These results indicate that ribosomes first bind at the AUG-576 site, but instead of initiating there, most of them are transferred to AUG-611, the majority by strictly linear scanning and a substantial minority by direct transfer, which is possibly facilitated by the occasional persistence of base pairing in the apical part of the domain VI stem.Until the recent discovery of animal picornaviruses with internal ribosome entry sites (IRESs) resembling that of hepatitis C virus, most picornavirus IRESs have been classified into two groups (1, 17): type 1 (exemplified by entero- and rhinoviruses) and type 2 (cardio- and aphthoviruses). Primary sequences and especially secondary structures are strongly conserved within each group but there is very little similarity between the two groups apart from an AUG triplet at the 3′ end of the IRES (as defined by deletion analysis), which is preceded by a ∼25 nucleotide (nt) pyrimidine-rich tract (17). In type 2 IRESs, notably encephalomyocarditis virus (EMCV), this AUG triplet is the authentic initiation codon for viral polyprotein synthesis, and the totality of the evidence indicates that all ribosomes bind at, or very close to, this AUG and that all initiate translation at this site (18, 19). The foot-and-mouth disease virus (FMDV), although a type 2 IRES, is not quite so straightforward in that a minority of initiation events occur at the AUG immediately downstream of the oligopyrimidine tract, and the rest occur at the next AUG, 84 nt downstream (3, 45).In contrast, initiation on type 1 IRESs seems much more complicated and rather puzzling. The first puzzling feature is that there is very little, if any, initiation at the AUG just downstream of the oligopyrimidine tract, at nt 586 in poliovirus type 1 (PV-1) (39), and the initiation site for polyprotein synthesis is the next AUG further downstream, at a distance of ∼160 nt in enteroviruses and ∼35 nt in rhinoviruses (17). Nevertheless, AUG-586 is important for efficient initiation at the authentic polyprotein initiation site. Mutation of AUG-586 in a PV-1 infectious clone was found to be quasi-infectious (42), while mutation of the equivalent site in PV-2 conferred a small-plaque phenotype and reduced initiation at the polyprotein initiation site by ∼70% in both in vitro assays and in transfection assays (32, 33, 37).This observation has led to the idea that ribosomes first bind at AUG-586, but instead of initiating at this site, virtually all of them get transferred to the polyprotein initiation site (17). This raises questions as to the nature of the transfer process. Because insertion of an AUG codon between PV-1 nt 586 and the authentic initiation site conferred a small-plaque phenotype and because all large-plaque pseudo-revertants had lost the inserted AUG either by deletion or point mutation (25, 26), linear scanning is likely to be important. However, as the insertion resulted in a small-plaque phenotype rather than lethality, there remains the possibility that some ribosomes were transferred directly without scanning the whole distance. This has also been suggested on the grounds that insertion of AUGs or a hairpin loop between nt 586 and the authentic initiation site of PV-1 did not seem to reduce polyprotein synthesis in vitro as much as might be expected if the authentic initiation site is accessed by strictly linear scanning (8).The final puzzle is that AUG-586 is located in a stem-loop structure, domain VI (Fig. ​(Fig.1A),1A), which is conserved in all entero- and rhinoviruses apart from bovine enterovirus. If the initiating 40S subunits do inspect AUG-586 in some way, albeit an unproductive way, this stem-loop would need to open at least partly, if not completely. This need for domain VI to be opened might be considered an impediment to efficient initiation, and yet its strong conservation suggests the opposite, namely, that it might have a positive effect. Precise deletion of the spacer downstream of AUG-586 in PV-1(Mahoney), so that polyprotein synthesis now started at 586, reduced virus yield by ∼10-fold (39), and in an independent study a deletion that brought the polyprotein initiation site to nt 586 or 580 caused a very similar growth defect in PV-1(Sabin) although the defect was considerably less in a Mahoney background (13, 27). On the other hand, two smaller deletions in PV-1(Sabin) that retained just the whole base-paired domain VI or only its 5′ side, placing the polyprotein initiation site 52 or 31 nt, respectively, downstream of AUG-586, did not confer any significant negative phenotype (13, 27). Taken together, these results would seem to imply that the base pairing in domain VI is neutral to initiation efficiency, but the primary sequence of its 5′ side may confer a moderate positive effect. In this respect it is interesting that bovine enterovirus retains most of the sequence of the 5′ side of domain VI but lacks the complementary sequence of the 3′ side.Open in a separate windowFIG. 1.(A) Sequence and base pairing of IRES domain VI of HRV-2 and PV-1(Mahoney), numbered with respect to the viral genome sequence. (B) Hypothetical model for the opening of HRV-2 domain VI in two stages, showing that in the intermediate state AUG-576 and AUG-611 are both exposed.We have reexamined these issues but in the context of human rhinovirus 2 (HRV-2), mainly because the close proximity of the polyprotein initiation site (at nt 611) to the AUG (at nt 576) just downstream of the oligopyrimidine tract makes the interpretation of results less ambiguous than is the case with enteroviruses. A recent comprehensive sequence comparison of 106 different HRV strains plus 10 field isolates shows that HRV-2 domain VI is typical of the 106 serotypes and the one field isolate that differs in domain VI from its parent strain (35). In 95% of these sequences, the number of residues between the two AUG codons is in the range of 28 to 34 nt (median, 31 nt), with five outliers at 20 or 22 nt. The two AUGs are invariably base paired in a back-to-back configuration (Fig. ​(Fig.1A),1A), and the intervening residues fold into a base-paired structure, usually with a single mismatch (Fig. ​(Fig.1A)1A) or at least one G-U codon at around the mid-point and an apical loop of 3 to 6 residues (depending on the strain). The base-paired stem of enteroviruses is considerably shorter (usually without a mismatch), and the extra length in HRV domain VI generally consists of A-U and U-A pairs (often alternating) in the apical part (Fig. ​(Fig.1A).1A). In 23% of these 107 HRV domain VI sequences, the two AUGs are in the same reading frame, and in 17 (approximately two-thirds) of these there is no in-frame stop codon between them so that any initiation at the upstream AUG would result in synthesis of a VP0 protein (and, hence, also VP4) with an N-terminal extension.We first asked whether AUG-576 in HRV-2 is similar to AUG-586 in PV-1 in that there is very little initiation at this site, and yet AUG-576 is important for efficient initiation at the downstream polyprotein initiation site. We then looked for evidence that the domain VI stem-loop opens and whether all ribosomes access the authentic initiation site (AUG-611) by strictly linear scanning from some upstream site. We conclude that most ribosomes do access AUG-611 in this way, but a significant minority may take a shortcut, which could be facilitated if the apical part of this domain remains closed and base paired, with the single mismatch in the domain VI stem possibly causing the opening of this domain to occur in two stages (Fig. ​(Fig.1B1B).