Horizontal gene transfer as a mechanism for the promiscuous acquisition of distinct classes of IRES by avian caliciviruses

Abstract In contrast to members of Picornaviridae which have long 5′-untranslated regions (5′UTRs) containing internal ribosomal entry sites (IRESs) that form five distinct classes, members of Caliciviridae typically have short 5′UTRs and initiation of translation on them is mediated by interaction of the viral 5′-terminal genome-linked protein (VPg) with subunits of eIF4F rather than by an IRES. The recent description of calicivirus genomes with 500–900nt long 5′UTRs was therefore unexpected and prompted us to examine them in detail. Sequence analysis and structural modelling of the atypically long 5′UTRs of Caliciviridae sp. isolate yc-13 and six other caliciviruses suggested that they contain picornavirus-like type 2 IRESs, whereas ruddy turnstone calicivirus (RTCV) and Caliciviridae sp. isolate hwf182cal1 calicivirus contain type 4 and type 5 IRESs, respectively. The suggestion that initiation on RTCV mRNA occurs by the type 4 IRES mechanism was confirmed experimentally using in vitro reconstitution. The high sequence identity between identified calicivirus IRESs and specific picornavirus IRESs suggests a common evolutionary origin. These calicivirus IRESs occur in a single phylogenetic branch of Caliciviridae and were likely acquired by horizontal gene transfer.


INTRODUCTION
Genetic variation in viral genomes arises from point mutation and recombination. The former allows for gradual searching through an evolutionary fitness landscape, whereas recombination is associated with large shifts that may create beneficial genetic diversity or disrupt favorable combinations of co-adapted alleles (1,2). Recombination in RNA virus genomes has been associated with increased virulence, altered host range and the emergence of viruses (3)(4)(5)(6)(7). It can occur by a replicative mechanism, in which the replication complex transfers from one template to another, or by a non-replicative mechanism in which genomes are cleaved and joined in new combinations (8). These processes can result in non-homologous recombination, by joining of fragments of similar genomes at dissimilar locations or of unrelated RNA molecules. The latter leads to horizontal gene transfer (HGT) between unrelated genomes and to the acquisition of genetic information. Analysis of HGT has focused on the transfer of protein-coding regions between viruses and from hosts (9). However, noncoding regions in viral RNA genomes, which have roles in translation, replication and encapsidation, are also heritable entities and just as for coding sequences, their evolution may also involve recombination and HGT between members of the same and even of different virus families (10)(11)(12)(13)(14)(15). 5 -Untranslated regions (5 UTRs) are of particular interest because in a number of viral mRNAs, they contain specific elements that allow the viral mRNAs to utilize non-canonical 5 end-independent mechanisms of initiation that are collectively termed 'internal ribosomal entry'.
The canonical initiation process involves attachment of 43S preinitiation complexes (comprising 40S ribosomal subunits, eIF2-GTP/ Met-tRNA i Met ternary complexes and eIFs 3, 1 and 1A) to the capped 5 -terminal region of mRNA and their subsequent scanning to the initiation codon where they stop to form 48S initiation complexes with established codon-anticodon base-pairing. Attachment is mediated by group 4 eIFs: eIF4F (which consists of the RNA helicase eIF4A, the scaffold subunit eIF4G and the cap-binding subunit eIF4E), eIF4A (which also exists in the free form), and eIF4B (which enhances the helicase activity of eIF4A). Group 4 eIFs cooperatively unwind the cap-proximal region allowing attachment of 43S complexes and also assist 43S complexes during scanning. eIFs 1 and 1A monitor the fidelity of initiation codon selection. Establishment of codon-anticodon base-pairing in the 48S complex leads to eIF5-induced hydrolysis of eIF2bound GTP, eIF5B-mediated joining of a 60S ribosomal subunit and formation of elongation-competent 80S ribosomes (16).
Internal ribosomal entry sites (IRESs) are structured RNA regions that mediate end-independent initiation of translation using a subset of the eukaryotic initiation factors (eIFs) that are required by the canonical initiation process (16). IRESs enable viral mRNAs to be translated during virus-induced shut-off of cellular translation and to evade innate immune responses that repress translation. Viral internal ribosomal entry sites (IRESs) are classified into six major groups, based on common sequence motifs and structure (Table 1). Each group uses a distinct mechanism to assemble ribosomal initiation complexes, but they are all based on non-canonical interactions of the IRES with canonical components of the translation apparatus (16,17).
Initiation on type 1, type 2 and type 5 IRESs, exemplified by poliovirus, encephalomyocarditis virus (EMCV) and Aichivirus (AV) respectively, relies on their specific interaction with the central eIF4A-binding domain of eIF4G (11,(18)(19)(20)(21)(22)(23)(24)(25). This interaction allows these IRESs to function without eIF4E and the N-terminal region of eIF4G to which it binds, for example in infected cells, when host cell translation is shut off following cleavage of eIF4G by viral proteases into this N-terminal fragment and a C-terminal fragment that binds eIF4A and eIF3. Type 1 and type 2 IRESs are ∼450 nt long and consist of five domains, designated II-VI in type 1 and H-L in type 2 IRESs. Sequence similarities between type 1 and type 2 IRESs are minimal except for a 3 -terminal Yn-Xm-AUG motif, in which a Yn pyrimidine tract (n = 8-10 nt) is separated by a spacer (m = 18-20 nt) from an AUG triplet. Type 5 IRESs are also ∼450 nt long and appear to be chimeric, containing one domain that resembles domain IV of type 1 IRESs, another that resembles domain K of type 2 IRESs, and a Yn-Xm-AUG motif. The AUG of this motif is the initiation codon for the viral polyprotein in type 2 and type 5 IRESs, although initiation can also occur downstream of it in type 2 IRESs, whereas it is sequestered within domain VI in type 1 IRESs and is only weakly active. Translation of the poliovirus polyprotein initiates ∼160 nt downstream of the motif. 48S complex formation on type 2 IRESs requires eIF2, eIF3, the central domain of eIF4G and eIF4A, and is enhanced by eIF4B (18)(19)(20); scanning to AUG codons downstream of the Yn-Xm-AUG motif additionally requires eIF1 and eIF1A (26). Initiation on type 1 IRESs requires eIF2, eIF3, eIF4A, eIF4B, the central domain of eIF4G and eIF1A, and scanning beyond the Yn-Xm-AUG motif additionally required eIF1 (25). In addition to canonical eIFs, these IRESs also commonly require specific IRES trans-acting factors (ITAFs). Thus the principal ITAF for type 1 IRESs is the poly(C) binding protein 2 whereas Type 2 IRESs require the pyrimidine tract binding protein (PTB).
Whereas the domain organization of type 1, type 2 and type 5 IRESs and their initiation mechanisms are broadly similar, the structures and mechanisms of action of type 4 and type 6 IRESs are fundamentally different from each other and from other classes of IRES. Type 4 IRESs are exemplified by hepatitis C virus (HCV) and classical swine fever virus (CSFV). The mechanism of initiation on type 4 IRESs is based on their direct specific interaction with 40S subunits, which positions the initiation codon in the ribosomal P site so that the 40S/IRES complex can recruit eIF2-GTP/Met-tRNA i Met and form a 48S complex without the involvement of group 4 eIFs (28-35). In addition to 40S subunits, type 4 IRESs also specifically inter-act with eIF3. However, in 40S/IRES/eIF3 complexes, eIF3 is displaced from its ribosomal position in the 43S complex, and instead interacts through its ribosome-binding surface exclusively with the IRES (35). As in the canonical initiation process, subunit joining on type 4 IRESs is mediated by eIF5 and eIF5B (36), but during viral infection and other stress conditions, when active eIF2 levels are reduced, eIF5B can also promote recruitment of Met-tRNA i Met independently of eIF2 (37,38). Type 4 IRESs are ∼330nt long and consist of two principal domains: domain II, which is an irregular stem-loop, and domain III, which consists of a basal pseudoknot (PK) and the branching stemloops IIIa -IIIf, several of which contain conserved motifs that are responsible for tertiary interactions within the IRES (30) and for interactions with 18S rRNA of the 40S subunit (28,29). The apical region of domain III of the IRES also interacts with eIF3 (32)(33)(34)(35). Type 4 IRESs occur in the Hepacivirus, Pestivirus and Pegivirus genera of Flaviviridae, and in over twenty genera of Picornaviridae, including Teschovirus A (formerly porcine teschovirus; genus Teschovirus) and Sapelovirus A (formerly Simian picornavirus 9; genus Sapelovirus) (e.g. 10,13,15,[39][40][41]. Type 6 IRESs are only ∼190 nt long and consists of two highly structured domains formed by three pseudoknots. They bind directly to the ribosome, and by mimicking the anticodon stem-loop of tRNA base-paired to an mRNA codon, the 3 -terminal pseudoknot enables these IRESs to initiate without the involvement of eIFs or Met-tRNA i Met even an initiation codon (16,17).
Picornaviridae and Caliciviridae are families of viruses in the order Picornavirales that have single-stranded, positivesense RNA genomes. Calicivirus genomic mRNA contain the large open reading frame ORF1 that encodes replicative proteins, followed by one to three additional ORFs that encode capsid proteins, and that are translated from subgenomic mRNA by a process that for ORF3 involves reinitiation (42,43). In contrast to picornaviruses, caliciviruses have short 5 UTRs (44) and initiation of translation on them is mediated by interaction of the viral 5 -terminal genomelinked protein (VPg) with subunits of eIF4F rather than by an IRES (45)(46)(47). Consequently, the recent identification of calicivirus genomes with 5 UTRs that are 500-900nt long (48)(49)(50)(51) was unexpected and prompted us to examine them in detail. We determined that different avian calicivirus genomes contain type 2, type 4 and type 5 IRESs that were likely acquired from picornaviruses on multiple occasions. These observations provide further evidence for HGT of noncoding RNA elements as a contributory element to viral evolution. Detailed characterization of the mechanism of initiation on the ruddy turnstone calicivirus (RTCV) IRES supported its identification as a type 4 IRES and deepened understanding of the mechanism of initiation on this class of IRES.
To assay elongation, 48S complexes were supplemented with 4.3 pmol 60S subunits, 10 pmol eIF5 and 5 pmol eIF5B, and incubated for 10 min at 37 • C. 3.75 pmol eIF1H and 4.5 pmol eEF2 were then added and incubation continued for an additional 10 min at 37 • C.

Analysis of ribosomal complexes by sucrose density gradient centrifugation
Ribosomal complexes assembled on 32 P-labelled mRNA as described above in scaled-up 100 l reaction mixtures were analysed by centrifugation through 10-30% sucrose density gradients prepared in buffer A in a Beckmann SW55 rotor at 53 000 rpm for 105 min. Ribosomal association of [ 32 P]mRNA was measured by Cerenkov counting.

Analysis of protein sequences
Sequences were aligned using MUSCLE (v3.8.31) with default settings. Gaps and ambiguously aligned regions were stripped using GBlock (v0.91b) (67) with default settings. Phylogenetic trees with 500 bootstrap resamples of the alignment data sets were generated using the maximumlikelihood method in PhyML3.1 (68). Bootstrap values for each node are given with a threshold of 70%. ORFs in the genome were predicted using ExPASy translate (https: //web.expasy.org/translate/). Individual proteins were identified by comparison with reference FCV, MNV and RHDV ORF1 polyproteins.

Avian calivirus genomes contain candidate type 2, type 4 and type 5 IRESs
The 5 UTRs of AvCV, DuCV, GTCV, PeDuCV, Wilkes virus and Caliciviridae sp. isolates yc-13 and Xftoti are related to each other and to the type 2 IRESs of the Avisivirus, Gallivirus and Sicinivirus genera of Picornaviridae. Although these caliciviruses are formally unclassified, our phylogenetic analysis ( Figure 2) is consistent with suggestions (48,51) that they may be assigned to two genera: AvCV, PeDuCV, Wilkes virus and Caliciviridae sp. isolates yc-13 and Xftoti to the genus Nacovirus and DuCV and GTCV to the genus 'Sanovirus'. The regions of greatest homology (65-67% nucleotide identity) correspond to most of the I domain and the entire J and K domains of Avisivirus  Figure S1). Consistently, they form type 2 IRES-like structures (e.g. Figure  3) with sequence motifs at locations that are known to be important for type 2 IRES function. These motifs include a pyrimidine-rich loop in domain H that interacts with PTB (73), a C-rich loop, a GNRA tetraloop and an AAA motif in apical arms of domain I (e.g. 74), an A-rich stem-loop that wedges between the minor grooves of the J and K domains (22), a bipartite sequence/ structural motif at the apex of domain J (11) and a 3 -terminal Yn-Xm-AUG motif (75). The 525nt-long RTCV 5 UTR is unrelated to other calicivirus 5 UTRs, although phylogenetic analysis of VP1 and protease-polymerase precursor amino acid sequences suggests that RTCV might be assigned to the genus 'Sanovirus'. However, nt. 170-525 are 60% identical to nt. 62-409 of the 5 UTR of Anativirus A (AnV) ( Figure 4A) of the genus Anativirus (76) which form a type 4 IRES (10). The RTCV 5 UTR also shares strong sequence identity with type 4 IRESs from avian Sapelovirus-like picornaviruses (77)(78)(79), particularly with subdomains IIId, IIIe and the pseudoknot, the most strongly conserved elements of these IRESs (13). Consistently, modelling indicated that the structure of this region of the RTCV 5 UTR ( Figure 4B) is closely related to the AnV type 4 IRES (10). Sequence differences between them are often covariant, so that the folding of structural elements is maintained by compensatory second site substitutions (Supplementary Figure S2). Both elements contain an HCV-like domain II with an internal loop near its base and GAA and AGUA sequences that form a 'loop E' motif. The apical IIIa, IIIb and IIIc subdomains in domain III form a four-way junction, although subdomain IIIa contains an 'UUUUU' loop instead of the apical 'AGUA' loop found in the HCV IRES. Domain IIId contains the apical GGG motif that engages with the ES7 element of 18S rRNA (29,35) and that is an invariant feature of all type 4 IRESs, and domain IIIe has an apical GACA tetraloop that could engage in a tertiary interaction with G 474 (cf. 30) ( Figure 4B). The pseudoknot at the base of RTCV domain III closely resembles the pseudoknot in the AnV IRES.
The 5 UTR of Caliciviridae sp. isolate hwf182cal1 (731 nt. long) shares a high level of nucleotide identity with elements of the 5 UTRs of Oscivirus A2 (80) and Passerivirus (27) that form type 5 IRESs. Homology extends from nt.162 at the 5 border of domain I to the initiation codon, and reaches ∼60% nucleotide identity from nt. 215-667, which include domain J (equivalent to domain IV of type 1 IRESs), domain K (equivalent to domain J of type 2 IRESs), the polypyrimidine tract and domain L (11).

The mechanism of initiation on the RTCV mRNA
We selected the RTCV 5 UTR, which contains a putative type 4 IRES, as a candidate to validate the identification and classification of putative IRESs in calicivirus 5 UTRs. To confirm that the RTCV 5 UTR contains an IRES, it was inserted between ORF1 and ORF2 in dicistronic DC RTCV mRNA ( Figure 5A). To avoid any possibility of reinitiation after translation of the first cistron, the RTCV 5 UTR was also preceded by a stable 5 -terminal hairpin ( G = -32.4 kcal/mol) that prevents canonical initiation (81). The RTCV 5 UTR promoted efficient translation of the second cistron in rabbit reticulocyte lysate (RRL) ( Figure 5B, lane 2), indicating that the RTCV 5 UTR is an IRES. To estimate the efficiency of translation mediated by the RTCV IRES, we compared it with the efficiency of type 4 HCV and type 5 AV IRESs in similar dicistronic mRNAs ( Figure  5B, lanes 5 and 7). IRES activity was compared by assaying incorporation of 35 S-Met during in vitro translation into ORF2 products, taking into consideration the methionine content of ORF2 in dicistronic RTCV, HCV and AV mR-NAs, and assuming that the initiating methionine of translated proteins is cleaved off. Initiation by the RTCV IRES (defined as 100%) was similar to the AV IRES (∼90%) and substantially stronger that the HCV IRES (∼15%), consistent with reports that the HCV IRES is weaker than other type 4 IRESs (e.g. from classical swine fever virus (32)).
A defining characteristic of type 4 IRESs is that an essential G-rich loop in subdomain IIId engages with ES7 of 18S rRNA to promote and stabilize factor-independent binding of the IRES to the 40S subunit (e.g. 28,29,82,83). The strong loss of IRES activity resulting from GGG 451-3 →CCC substitutions in this motif ( Figure 5B, lanes 2 and 3, and Figure  5C, compare lanes 1 and 4 with lanes 2 and 5) support the classification of the RTCV IRES as type 4. A second characteristic of type 4 IRESs is that, unlike type 1, type 2 and type 5 IRESs, their activity is independent of eIF4A and eIF4F (e.g. 32,34,82). We therefore compared the influence of the negative trans-dominant eIF4A R362Q mutant on translation of the RTCV IRES with its influence on translation of type 4 HCV and type 5 AV IRESs in similar dicistronic mR-NAs ( Figure 5A). Like the HCV IRES ( Figure 5B, lanes 5-6), translation promoted by the RTCV IRES ( Figure  5B, lanes 2 and 4) was strongly resistant to inhibition by eIF4A R362Q , whereas initiation on the type 5 AV IRES was abrogated ( Figure 5B, lanes 7-8) and initiation on the first cistron was strongly inhibited in all cases. Taken together, these functional characteristics of the RTCV IRES are consistent with its structure-based classification as a type 4 IRES.
When inserted into the monocistronic construct downstream of the same stable hairpin ( G = -32.4 kcal/mol) (MC-Stem-RTCV; Figure 5A), the RTCV IRES promoted translation in RRL as efficiently as in dicistronic DC RTCV mRNA ( Figure 5C, lane 4). Deletion of nt. 1-209 of the 5 UTR in monocistronic constructs with or without the 5terminal stem, leaving only those sequences that are homologous to type 4 IRESs (MC-Stem-RTCV( nt 1-209) and MC-RTCV( nt 1-209); Figure 5A), did not impair IRES activity ( Figure 5C, lanes 1 and 3). As in the case of the full-length RTCV IRES ( Figure 5B, lane 3 and Figure  5C Further characterization of the mechanism of initiation on the RTCV IRES was done by in vitro reconstitution. In this approach, ribosomal complexes are assembled from individual translational components (mRNA, ribosomal subunits, translation factors and aa-tRNAs), after which the ribosomal position on mRNA is determined by toe-printing. Ribosomal 48S/80S complexes with an established codonanticodon interaction yield characteristic toe-prints ∼15-17 nt downstream of the P-site codon.
The RTCV IRES bound directly to 40S subunits, yielding stable complexes that induced RT stops at nt. 548-550 ( + 15-17 relative to A ( + 1) of the initiation codon AUG 534 ; Figure 6A, lane 2). This result indicates that like in other Type 4 IRESs, the coding region of the RTCV mRNA is correctly fixed in the mRNA-binding cleft of the 40S subunit to position AUG 534 for base-pairing with initiator tRNA in the ribosomal P site. The RTCV IRES also bound directly to eIF3, leading to a reverse transcriptase (RT) stop   at C 436 between the IIIc and IIId subdomains ( Figure 6A, lane 3; Figure 4B). The toe-print at this position is analogous to those induced by binding of eIF3 to HCV and other type 4 IRESs (32)(33)(34)82). Strikingly, binding of eIF3 to the RTCV IRES also strongly enhanced endogenous stops at AG 520-1 in PK stem 2 ( Figure 6A, lane 3; Figure 4B), indicating that eIF3 globally stabilizes the structure of this IRES. eIF3 also strongly enhanced formation of IRES/40S com-plexes. Thus, inclusion of eIF3 with 40S subunits intensified toe-prints +16-17 nt downstream from AUG 534 and led to the appearance of toe-prints at nt. 522-523 in addition to those at nt. 520-521 induced by eIF3 alone ( Figure 6A, lane 4; Figure 4B). The nt. 522-523 toe-prints map to PK stem 2 ( Figure 4B), which interacts with ribosomal protein rpS28 in ribosomal complexes assembled on the CFSV and HCV IRESs (35,84). The appearance of these toe-prints would be  Inclusion of eIF2 and Met-tRNA i Met in reaction mixtures containing 40S subunits (with or without eIF3) led to a small shift forward of toe-prints from UUC 548-550 ( + 15-+ 17) to UCA 549-551 ( + 16-+ 18) ( Figure 6A, lanes 5-7), which is characteristic of 48S complex formation on type 4 IRESs and reflects localized adjustments of mRNA and the Met-tRNA i Met anticodon in the mRNA-binding cleft (e.g. 32,34). It also yielded an additional strong toe-print at U 543 , which most likely resulted from 48S complex formation at the upstream near-cognate AUU 525 codon ( Figure  6A, lanes 5-7). 48S complex formation was more efficient in the presence of eIF3 ( Figure 6A, compare lane 5 with lanes 6-7) and, unlike on some other IRESs (85), was not sensitive to replacement of native initiator tRNA by its in vitro transcribed version ( Figure 6A, compare lanes 6 and  7). To our surprise, the relative efficiency of 48S complex formation on cognate AUG 534 and upstream near-cognate AUU 525 was not affected by inclusion of eIF1 alone ( Figure  6B, compare lanes 2 and 3), whereas eIF1A alone or with eIF1 weakened the toe-print at AUU 525 and enhanced 48S complex formation on AUG 534 ( Figure 6B, compare lane 2 with lanes 4, 5). In sucrose density gradient centrifugation experiments, eIF3 stimulated association of the IRES with 40S subunits ∼2-fold, but we did not observe further enhancement of 40S/IRES complex formation by inclusion of eIF1 and eIF1A over that promoted by eIF3 alone, implying that the role of eIF1 and eIF1A in initiation on this IRES is likely limited to ensuring the fidelity of initiation codon selection ( Figure 6C).
Binding of type 4 IRESs to the 40S subunit depends on the initial establishment of base-pairing between the Grich apical loop of subdomain IIId and ES7 of 18S rRNA (28,29,82,83). The substitution of the apical GGG motif in the IIId loop of the RTCV IRES by a CCC triplet abolished its ability to promote translation in vitro ( Figure 5C) and, as expected, abrogated the appearance of toe-prints that are characteristic of 40S subunit association and 48S complex formation on the IRES ( Figure 6D, lane 2). The apical loop of subdomain IIId is thus a critical determinant of ribosomal recruitment to this IRES. In contrast, this apical GGG loop does not influence binding of eIF3 to CSFV and other type 4 IRESs (28), and consistently, its substitution by a CCC triplet did not affect the eIF3-induced toe-prints (Figure 6D).
Viral infection activates innate immune responses, including phosphorylation of eIF2 and consequent impairment of translation (16). However, Type 4 CSFV and HCV IRESs retain initiation activity in these circumstances, at least in part due to their ability to utilize an alternative initiation mechanism in which eIF5B promotes binding of Met-tRNA i Met to the IRES/40S subunit complex (37,38,86). We therefore investigated whether eIF5B can replace eIF2 in initiation on the RTCV IRES. In reaction mixtures containing 40S subunits, eIF3 and Met-tRNA i Met , eIF5B was able to promote 48S complex formation on AUG 534 , albeit at a lower level than with eIF2 ( Figure 6E). In contrast to eIF2, eIF5B did not promote strengthening of toe-prints at U 543 that likely corresponds to 48S complex formation on the upstream near-cognate codon AUU 525 ( Figure 6E). In-clusion into reaction mixtures of individual eIF1 and particularly of eIF1A slightly stimulated 48S complex formation on AUG 534 , whereas together, they substantially weakened toe-prints corresponding to 48S complexes formed on AUG 534 and induced strong + 15-+ 17 nt toe-prints that are indicative of the formation of binary 40S/IRES complexes ( Figure 6F). Thus, similarly to CSFV and SPV9 IRESs (37,82), eIF5B-mediated initiation on the RTCV IRES was sensitive to inhibition by eIF1 and eIF1A.
To confirm that 40S ribosomal complexes formed on the RTCV IRES in the presence of Met-tRNA i Met and either eIF2 or eIF5B are bona fide 48S initiation complexes, we tested their ability to join 60S subunits to form elongationcompetent 80S ribosomes. For this, we employed RTCV-MAC-STOP mRNA, in which a UAA stop codon was introduced as the third codon downstream of AUG 534 . Addition of 60S subunits, eIF5, eIF5B, elongation factor (eEF) 1H, eEF2, and total aminoacylated tRNAs ( aa-tRNA) to 48S complexes that had been assembled with eIF2 and eIF3 (with/without eIF1 and eIF1A) led to the appearance of a toe-print at U 556 , six nucleotides downstream of the toe-prints corresponding to 48S complexes at AUG 534 , and to a concomitant decrease in the intensity of 48S toeprints ( Figure 7A, lanes 3 and 5). The appearance of the U 556 toe-print is consistent with the expected occurrence of two programmed elongation events leading to formation of pre-termination complexes (pre-TCs). The higher efficiency of 48S complex formation in the presence of eIF1 and eIF1A correlated with the higher intensity of toe-prints corresponding to pre-TCs assembled in their presence. 40S ribosomal complexes assembled with Met-tRNA i Met , eIF5B, eIF3 and eIF1A also underwent elongation and formation of pre-TCs upon addition of 60S subunits, elongation factors and aa-tRNA, albeit with substantially lower efficiency ( Figure 7A, lane 7).
Next, we assayed the elongation competency of 40S ribosomal complexes that presumably formed on the nearcognate AUU 525 codon (particularly in the absence of eIF1 and eIF1A) and were characterized by the strong U 543 toeprint ( Figure 6A, B). For this, AUG 534 , which is the fourth in-frame codon after AUU 525 , was replaced by a UGA stop codon to allow synthesis of a tripeptide after initiation on AUU 525 . However, analysis of 48S complexes assembled on this mRNA in reaction mixtures containing 40S subunits, Met-tRNA i Met , eIF2 and eIF3 revealed not only the U 543 toe-print + 18nt downstream of AUU 525 , but also strong stops at UUC 548-550 and a weaker stop at U 556 , which are suggestive of 48S complex formation at the near-cognate codons CUG 533 and UUG 539 , respectively ( Figure 7B, lane 2). Addition of 60S subunits, eIF5, eIF5B, eEF1H, eEF2 and aa-tRNA did not substantially reduce the intensity of toe-prints corresponding to 40S complexes formed on AUU 525 and the concomitant appearance/ strengthening of toe-prints indicating assembly of post-TCs on UGA 534 ( Figure 7B, lane 3). However, it led to weakening of the toe-prints at UUC 548-550 and U 556 corresponding to 48S complexes formed on CUG 533 and UUG 539 , and to the appearance of toe-prints at A 552 and U 576 ( Figure 7B unfractionated aa-tRNA mixture (87). We conclude that in the absence of eIF1 and eIF1A, elongation-competent initiation complexes can form on the RTCV IRES at nearcognate initiation codons in the immediate vicinity of the initiation codon AUG 534 . Taken together, these data confirm that the RTCV 5 UTR contains a fully functional type 4 IRES.

Horizontal gene transfer (HGT) of IRES elements
We report that several avian calicivirus genomes contain 5 UTR elements that can confidently be assigned to established classes of viral IRES. They share a high level of sequence identity with IRESs from specific picornaviruses and may therefore have a common evolutionary origin. The calicivirus type 2 and type 5 IRESs constitute the first examples of these types of IRES in viral genomes outside the Picornaviridae, and the identification of the RTCV IRES is evidence of the co-option of type 4 IRESs by a third virus family in addition to Flaviviridae and Picornaviridae. These findings provide further evidence that IRESs can be exchanged between viral families by HGT (15). These observations were unexpected because FCV genomic RNAs that were engineered to contain a 5 -terminal EMCV IRES were not infectious, and equivalent hybrid MNV RNAs were infectious but yielded progeny in which the IRES had been lost and the 5 -end of the genome had been precisely regenerated (88). Avian calicivirus genomes therefore likely have properties that permit retention of type 2 IRESs, as discussed below. Recombination is an established feature of calicivirus evolution and occurs most commonly at the junc-Nucleic Acids Research, 2022, Vol. 50, No. 2 1065 tion of ORF1 (nonstructural proteins) and ORF2 (structural proteins) (89)(90)(91). The present report suggests that an additional important breakpoint maps to the vicinity of the junction of the 5 UTR and ORF1.
The presence of type 4 IRESs in the genomes of members of Caliciviridae, Flaviviridae and Picornaviridae is indicative of their ability to function in different environments and genomic contexts, which likely reflects their strong activity, their modular, self-contained nature and their exploitation of highly conserved binding targets on components of the translation apparatus that occur in a wide range of organisms. For example, the UCCC loop of ES7 of 18S rRNA, which base-pairs with the GGG motif at the apex of IRES domain IIId, occurs in mammals, birds, reptiles, amphibians and fish (13,35). Interestingly, this element of 18S rRNA is also exploited by the termination-reinitiation process that leads to translation of the minor capsid protein from calicivirus subgenomic mRNA (42,43).
HGT involving type 2 IRESs has been detected less frequently, but it has been implicated in the formation of the genomes of members of the Rabovirus genus of Picornaviridae (92,93). The identification of type 2 IRESs in seven distinct avian caliciviruses suggests that these elements can readily be exchanged between unrelated viral genomes. HGT of type 2 and type 4 IRESs likely have the same requirements, namely the ability of the IRES to function as a self-contained unit and the presence of conserved IRES-binding surfaces on components of the translation apparatus in different species. Initiation on mammalian type 2 IRESs depends on their interaction with eIF4G (19)(20)(21)(22), and type 2 IRESs from avian viruses likely interact analogously with avian eIF4G. The central IRES-binding domain of human eIF4G is closely related to the equivalent domain in eIF4G from the Gruidiae (i.e. cranes) and Anatidae (ducks, geese and swans) (∼75-95% amino acid identity, including all basic and aromatic residues that have been implicated in this interaction (21,22)).
The presence of type 2 IRESs in numerous avian calicivirus genomes contrasts with the incompatibility of the (type 2) EMCV IRES with FCV and MNV genomes, and its precise elimination from chimeric EMCV-MNV genomes (88). An appealling hypothesis is that this incompatibility is due to deleterious interference between the translation initiation processes mediated by the EMCV IRES and by FCV and MNV VPgs, respectively. These processes both depend on specific interactions with eIF4F: type 2 IRESs bind eIF4G/eIF4A, the MNV VPg promotes initiation via interaction with eIF4G, whereas the FCV VPg interacts with eIF4E (45)(46)(47). A notable feature of avian IRES-containing caliciviruses is that they encode a VPg protein (74-84 a.a. long) that is considerably shorter than FCV and MNV VPgs (111 a.a. and 124 a.a., respectively). Whereas the eIF4Ebinding determinants in the former have not been established, interaction of eIF4G with the latter involves Cterminal elements (45,46) that are absent from the VPgs of IRES-containing and related caliciviruses (Supplementary Figure S3). The 'short' calicivirus VPgs may thus not compete with type 2 and type 5 IRESs for binding to eIF4G. It is currently not possible to distinguish between scenarios in which the presence of a 'short' VPg either provides an environment that is permissive for IRES acquisition by HGT or reflects evolutionary loss of initiation factor-binding determinants that are not needed for or even interfere with IRES function.

Consequences of horizontal gene transfer of IRESs into calicivirus genomes
Type 2, type 4 and type 5 IRESs have well-characterized functions, and their acquisition by HGT would likely alter the gene expression strategy of recombinant calicivirus progeny relative to the parental strain. Calicivirus infection leads to a shut-off of cellular translation and to multiple changes to the cellular translation apparatus, including phosphorylation of eIF2␣, viral protease-mediated cleavage of the poly(A)-binding protein PABP, eIF4E phosphorylation, induced caspase-mediated cleavage of eIF4G and translocation of PTB from the nucleus to the cytoplasm (47,(94)(95)(96). Adoption by a calicivirus of an alternative mechanism for translation initiation, such as that mediated by type 2 IRESs, which is independent of eIF4E (19) or by type 4 IRESs, which is independent of eIF4F (32,34) might therefore alter viral replication kinetics and virus yield. Calicivirus replication kinetics might also be affected by the acquisition of a type 2 or a type 5 IRES because whereas their function is commonly PTB-dependent (11,18,20,23), translation of FCV mRNA and thus potentially of other caliciviruses is inhibited by PTB (93).

The structure of the RTCV type 4 IRES
The RTCV genome is the first from a virus outside the Flaviviridae and Picornaviridae in which a type 4 IRES has been identified. It contains all but one of the characteristic structural elements and sequence motifs of conventional type 4 IRES, including a sub-apical 'loop E' motif in domain II, a pseudoknot at the base of domain III and a series of stem-loops, designated IIIa to IIIf. Subdomain IIId has a functionally important apical GGG motif that is critical for binding of the IRES to the 40S subunit ( Figures 5B, 5C, 6D) and that, by analogy with type 4 CSFV and HCV IRESs, engages with ES7 of 18S rRNA (29,35). Subdomain IIIa lacks the 'AGUA' loop that occurs in the HCV IRES, and instead contains a 'UUUUU' loop like that in the type 4 IRESs in members of the avian Colbovirus, Megrivirus and Mesivirus genera of Picornaviridae (13). eIF3 binds to the junction region of domain III (33,35), but whether this Urich loop constitutes an adaptation to the avian translation apparatus remains to be determined.

The mechanism of initiation on the RTCV type 4 IRES
The resistance of RTCV IRES-mediated translation to inhibition by eIF4A R362Q (Figure 5B) is characteristic of type 4 IRES (32,34,41,82) and is consistent with the mechanism of initiation that was elucidated here by in vitro reconstitution. The RTCV IRES bound directly and stably to 40S subunits and to eIF3, and could support recruitment of Met-tRNA i Met either as part of the eIF2-TC (in which case subunit joining mediated by eIF5 and eIF5B yielded an elongation-competent 80S ribosome) or via eIF5B. The RTCV IRES can therefore initiate translation without the involvement of group 4 eIFs, using a mechanism that is typical of type 4 IRESs.
Nevertheless, some aspects of the initiation process characterized here are notable and may be generally relevant to this class of IRES. Although eIF3 binds to the apical region of domain III, yielding toeprints at C 436 that are directly comparable to those that appear on binding of eIF3 to HCV, CSFV, BVDV and Sapelovirus A IRESs (32)(33)(34)82), it nevertheless influenced distant elements of the IRES, stabilizing PK Stem 2 and its interaction with the 40S subunit ( Figure 6A). This stem directs the initiation codon and ORF into the mRNA binding cleft of the 40S subunit (31), and eIF3 therefore indirectly promotes this interaction. This activity may therefore contribute to eIF3 s stimulatory effect on initiation on type 4 IRESs.
On the wt RTCV IRES, 48S complexes could presumably form at AUU 525 , upstream of the initiation codon AUG 534 ( Figure 6A, B), and on the [AUG 534 UGA] mutant IRES, 48S complexes also assembled at CUG 533 and UUG 539 ( Figure 7B). These observations suggest that binding of IRES sequences downstream of PK stem 2 in the mRNA channel of the 40S subunit is followed by a onedimensional search for the initiation codon, i.e. scanning. We note that the length of the spacer between the PK and the initiation codon varies from 8 to 17 nt in different type 4 IRESs (10,13) and that initiation codon location and selection on them therefore likely involves limited localized scanning and is not simply enforced by a molecular ruler mechanism as a function of distance from the PK. Thus, final adjustments of the positioning of the spacer in this and other IRESs in the mRNA channel should occur upon establishment of base-pairing between the Met-tRNA i Met anticodon and the initiation codon. Notably, appearance of toe-printing stops corresponding to 48S complex formation on the near-by upstream AUG was observed on a variant of the CSFV IRES lacking domain II (37). Thus, CSFV domain II functions to fix the spacer and initiation codon in the mRNA-binding channel, influencing initiation codon selection. Domain II of the RTCV IRES may be deficient in this function, potentially allowing initiation to occur in alternate sites around AUG 534 .

DATA AVAILABILITY
All data are available in the main text or the supplementary materials.

SUPPLEMENTARY DATA
Supplementary Data are available at NAR Online.