Functional interaction of translation initiation factor eIF4G with the foot-and-mouth disease virus internal ribosome entry site

A novel picornavirus identified in wild Macaca mulatta in China

The discovery of novel viruses in wild animals allows the prediction of their potential threat to the health of humans and other animals. We report a highly divergent picornavirus (tentatively named "mobovirus A"), identified in a fecal sample from Macaca mulatta in Yunnan province, China, using viral metagenomic analysis, with viral loads of 2 × 10⁷ copies/g. The complete genomic sequence of mobovirus A is 8,325 nucleotides in length. Phylogenetic analysis showed that it clustered with Guangxi changeable lizard picornavirus 1 and Guangxi Chinese leopard gecko picornavirus, with less than 38%, 40%, and 40% amino acid identity in the P1, P2, and P3 protein, respectively. The viruses in this cluster were most closely related to members of the genera Harkavirus, Tremovirus and Hepatovirus. Genomic analysis revealed that mobovirus A has the typical genomic organization and motifs of a picornavirus. Additionally, its codon usage bias complements that of M. mulatta, suggesting that this feature is not restricted only to hepatoviruses. Thus, according to the guidelines of the Picornaviridae Study Group of the International Committee on Taxonomy of Viruses, mobovirus A should be considered a member of a new genus (tentatively named for Monkey-borne virus, "Mobovirus") in the family Picornaviridae. These data will facilitate the understanding of the genetic diversity and evolution of picornaviruses. Further studies are needed to understand the epidemiology and potential pathogenicity of the virus in M. mulatta.

A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites

Picornaviral IRES elements are essential for initiating the cap-independent viral translation. However, three-dimensional structures of these elements remain elusive. Here, we report a 2.84-Å resolution crystal structure of hepatitis A virus IRES domain V (dV) in complex with a synthetic antibody fragment-a crystallization chaperone. The RNA adopts a three-way junction structure, topologically organized by an adenine-rich stem-loop motif. Despite no obvious sequence homology, the dV architecture shows a striking similarity to a circularly permuted form of encephalomyocarditis virus J-K domain, suggesting a conserved strategy for organizing the domain architecture. Recurrence of the motif led us to use homology modeling tools to compute a 3-dimensional structure of the corresponding domain of foot-and-mouth disease virus, revealing an analogous domain organizing motif. The topological conservation observed among these IRESs and other viral domains implicates a structured three-way junction as an architectural scaffold to pre-organize helical domains for recruiting the translation initiation machinery.

Ljungan/Sebokele-like picornavirus in birds of prey, common kestrel (Falco tinnunculus) and red-footed falcon (F. vespertinus)

Ljungan and Sebokele viruses are thought to be rodent-borne (picorna)viruses in the genus Parechovirus. Using random amplification and next generation sequencing method a novel Ljungan/Sebokele-like picornavirus was identified in birds of prey. Viral RNA was detected in total of 1 (9%) of the 11 and 2 (28.6%) of the 7 faecal samples from common kestrels and red-footed falcons in Hungary, respectively. High faecal viral RNA load (4.77×10⁶ genomic copies/ml) measured by qPCR. The complete genome of picornavirus strain falcon/HA18_080/2014/HUN (KY645497) is 7964-nucleotide (nt) long including a 867-nt 5'end and a 101-nt 3'end (excluding the poly(A)-tail). Falcon/HA18_080/2014/HUN has type-II IRES related to hunnivirus IRES, encodes a polyprotein lacking a leader protein, a VP0 maturation cleavage site and it predicted to encode three 2A proteins (2A₁^NPG↓P, 2A₂^NPG↓P and 2A₃^H-Box/NC), two of them end with 'ribosome-skipping' sites (DxExNPG^↓P). Sequence analyses indicated that the ORF1 (6996nt) polyprotein (2331 amino acid - aa) of falcon/HA18_080/2014/HUN shares the highest aa identity, 59% and 57%, to the corresponding polyproteins of Ljungan and Sebokele viruses. This study reports the identification and complete genome characterization of a novel Ljungan/Sebokele-like picornavirus in faeces of birds of prey which suggests that the genetic diversity and the potential host species spectrum of Ljungan/Sebokele-like viruses in genus Parechovirus are wider than previously thought.

Biological function of Foot-and-mouth disease virus non-structural proteins and non-coding elements

Foot-and-mouth disease virus (FMDV) represses host translation machinery, blocks protein secretion, and cleaves cellular proteins associated with signal transduction and the innate immune response to infection. Non-structural proteins (NSPs) and non-coding elements (NCEs) of FMDV play a critical role in these biological processes. The FMDV virion consists of capsid and nucleic acid. The virus genome is a positive single stranded RNA and encodes a single long open reading frame (ORF) flanked by a long structured 5ʹ-untranslated region (5ʹ-UTR) and a short 3ʹ-UTR. The ORF is translated into a polypeptide chain and processed into four structural proteins (VP1, VP2, VP3, and VP4), 10 NSPs (L^pro, 2A, 2B, 2C, 3A, 3B_1–3, 3C^pro, and 3D^pol), and some cleavage intermediates. In the past decade, an increasing number of studies have begun to focus on the molecular pathogenesis of FMDV NSPs and NCEs. This review collected recent research progress on the biological functions of these NSPs and NCEs on the replication and host cellular regulation of FMDV to understand the molecular mechanism of host–FMDV interactions and provide perspectives for antiviral strategy and development of novel vaccines.

Rabovirus: a proposed new picornavirus genus that is phylogenetically basal to enteroviruses and sapeloviruses

We have sequenced the genome of a novel picornavirus, rabovirus A (rat-borne virus, RaBoV-A, NC_026314), which was present in the feces of a Norway rat (Rattus norvegicus) from Berlin, Germany. This virus is related to members of the genera Enterovirus and Sapelovirus. RaboV-A contains a type II IRES that is unlike the type I IRES elements of enteroviruses and the type IV elements of sapeloviruses. Its genome is marked by an L protein and a chymotrypsin-like 2A protease. Our analysis of genome organization, pairwise identities, motif, phylogenic and UTR (GIMPU) indicates that RaBoV-A potentially represents a new picornavirus genus, for which we propose the name "Rabovirus". Spread by their rodent hosts and detected in New York and Berlin rats, these viruses may have a wide geographic distribution.

Complete genome characterization of mosavirus (family Picornaviridae) identified in droppings of a European roller (Coracias garrulus) in Hungary

Mosavirus (mosavirus A1, M-7/2010/USA, JF973687), a novel picornavirus, was found in a canyon mouse (Peromyscus crinitus) in the USA in 2010. It represents a novel species (Mosavirus A) in a novel genus (Mosavirus) in the family Picornaviridae. In this study, the first complete genome sequence of another mosavirus, SZAL6-MoV/2011/HUN (KF958461), was determined from one out of 18 fecal samples from an Afro-Palearctic migratory bird, the European roller (Coracias garrulus). The complete genome of SZAL6-MoV/2011/HUN is 8385 nt long (from poly(C) tract to poly(A) tail), contains a 646-nt-long 5'UTR that forms a type II IRES, and encodes a potential 2550-aa-long polyprotein precursor including an aphthovirus-like L(pro)-proteinase, a small aphthovirus-like 2A(NPG↓P), and two 3B(VPg) proteins. SZAL6-MoV/2011/HUN has 67 %, 74 %, and 76 % aa sequence identity in the P1, P2, and P3 region, respectively, to M-7/2010/USA and represents a second mosavirus type, mosavirus A2.

In silico analysis of IRES RNAs of foot-and-mouth disease virus and related picornaviruses

Foot-and-mouth disease virus (FMDV) uses an internal ribosome entry site (IRES), a highly structured segment of its genomic RNA, to hijack the translational apparatus of an infected host. Computational analysis of 162 type II picornavirus IRES RNA sequences yielded secondary structures that included only base pairs supported by comparative or experimental evidence. The deduced helical sections provided the foundation for a hypothetical three-dimensional model of FMDV IRES RNA. The model was further constrained by incorporation of data derived from chemical modification and enzymatic probing of IRES RNAs as well as high-resolution information about IRES RNA-bound proteins.

Common conformational changes induced in type 2 picornavirus IRESs by cognate trans-acting factors

Type 2 internal ribosomal entry sites (IRESs) of encephalomyocarditis virus (EMCV), foot-and-mouth disease virus (FMDV) and other picornaviruses comprise five major domains H-L. Initiation of translation on these IRESs begins with specific binding of the central domain of initiation factor, eIF4G to the J-K domains, which is stimulated by eIF4A. eIF4G/eIF4A then restructure the region of ribosomal attachment on the IRES and promote recruitment of ribosomal 43S pre-initiation complexes. In addition to canonical translation factors, type 2 IRESs also require IRES trans-acting factors (ITAFs) that are hypothesized to stabilize the optimal IRES conformation that supports efficient ribosomal recruitment: the EMCV IRES is stimulated by pyrimidine tract binding protein (PTB), whereas the FMDV IRES requires PTB and ITAF₄₅. To test this hypothesis, we assessed the effect of ITAFs on the conformations of EMCV and FMDV IRESs by comparing their influence on hydroxyl radical cleavage of these IRESs from the central domain of eIF4G. The observed changes in cleavage patterns suggest that cognate ITAFs promote similar conformational changes that are consistent with adoption by the IRESs of comparable, more compact structures, in which domain J undergoes local conformational changes and is brought into closer proximity to the base of domain I.

Comparative analysis of the large fragment of the 5' untranslated region (LF-5' UTR) of serotype A foot-and-mouth disease virus field isolates from India

India is endemic for foot-and-mouth disease (FMD) and in recent years a unique group within serotype A, carrying a codon deletion at an antigenically critical site in capsid protein VP3 has emerged (VP3(59)-deletion group). This tempted us to analyze the noncoding region, which is an under represented area, though critically associated with virus biology and pathogenesis. Analysis of the large fragment of 5' untranslated region (LF-5' UTR) of type A FMD virus revealed discrepancy in the overall tree topology between LF-5' UTR and 1D region possibly due to independent evolution of coding and noncoding regions. The VP3(59)-deletion group maintained its phylogenetic distinctness even at the LF-5' UTR. Eighteen lineage specific signatures detected here support independent evolutionary paths for the lineages. Extensive deletions of 45 and 89 nucleotides corresponding to the pseudoknot region were noticed. Conservation pattern in the 'A(253)AACA' motif in the cre/bus stem-loop indicates the importance of first three 'A' residues in VPg uridylylation. Of the three polypyrimidine tract binding protein (PTB) binding sites mapped on the internal ribosome entry site (IRES), the pyrimidine tract (Py tract) in the loop of domain 2 was found to be maximally conserved and it might be the major PTB binding site. Strikingly, a deletion group lineage specific transversion was noticed in the Py tract at the 3' end of IRES without significantly affecting its in vitro infectious titer. Hence, we presume that for efficient cap-independent viral translation, either a minimum number of pyrimidine residues rather than a complete Py tract or a Py tract tolerating transversions only at specific locations and a core motif 'CUUU' within the Py tract is essential.

Internal translation initiation of picornaviruses and hepatitis C virus

Picornaviruses and other positive-strand RNA viruses like hepatitis C virus (HCV) enter the cell with a single RNA genome that directly serves as the template for translation. Accordingly, the viral RNA genome needs to recruit the cellular translation machinery for viral protein synthesis. By the use of internal ribosome entry site (IRES) elements in their genomic RNAs, these viruses bypass translation competition with the bulk of capped cellular mRNAs and, moreover, establish the option to largely shut-down cellular protein synthesis. In this review, I discuss the structure and function of viral IRES elements, focusing on the recruitment of the cellular translation machinery by the IRES and on factors that may contribute to viral tissue tropism on the level of translation.

Toward a structural understanding of IRES RNA function

Protein synthesis of an RNA template can start by two different known mechanisms: cap-dependent translation initiation and cap-independent translation initiation. The latter is driven by RNA sequences called internal ribosome entry sites (IRESs) that are found in both viral RNAs and cellular mRNAs. The diverse mechanisms used by IRESs are reflected in their structural diversity, and this structural diversity challenges us to develop a cohesive model linking IRES function to structure. With more direct structural information available for the viral IRESs, data suggest an inverse correlation between the degree to which an IRES RNA can form a stable structure on its own and the number of factors that it requires to function. Lessons learned from the viral IRESs may help understand the cellular IRESs, although more structural data are needed before any strong links can be made.

Molecular and phylogenetic analyses of bovine rhinovirus type 2 shows it is closely related to foot-and-mouth disease virus

Bovine rhinovirus 2 (BRV2), a causative agent of respiratory disease in cattle, is tentatively assigned to the genus Rhinovirus in the family Picornaviridae. A nearly full-length cDNA of the BRV2 genome was cloned and the nucleotide sequence determined. BRV2 possesses a putative leader proteinase, a small 2A protein and a poly(C) tract, which are characteristic of aphthoviruses. Alignment of BRV-2 and FMDV polyproteins showed that 41% of amino acids were identical within the P1 region. Furthermore, 2A, 2C, 3B(3), 3C and 3D proteins are as much as 67%, 52%, 52%, 50%, and 64% identical, respectively. BRV2 leader protein is rapidly released from the viral polyprotein and cleaves eIF4G at a rate similar to FMDV leader proteinase, suggesting a functional relationship between the leader protein in these viruses. The results suggest that BRV2 is closely related to FMDV and should therefore be considered as a new species within the genus Aphthovirus.

Picornavirus internal ribosome entry site elements can stimulate translation of upstream genes

Certain viral and cellular mRNAs initiate translation cap-independently at internal ribosome entry site (IRES) elements. Picornavirus IRES elements are widely used in dicistronic or multicistronic vectors in gene therapy, virus replicon systems, and analysis of IRES function. In such vectors, expression of the upstream gene often serves as internal control to standardize the readings of IRES-driven downstream reporter activity. Picornaviral IRES elements translate optimally at up to 120 mM K(+) concentration, whereas genes used as upstream reporters usually have lower salt optima when present in monocistronic mRNAs. However, here we show that such reporter genes are efficiently translated at higher K(+) concentrations when placed upstream of a functional picornavirus IRES. This translation enhancement occurs in cis, is independent of the nature of the first reporter and of second reporter translation, and is conferred by the IRESs of picornaviruses but not of hepatitis C virus. A defective picornavirus IRES with a deletion killing IRES activity but leaving the binding site for initiation factor eIF4G intact retains translation enhancement activity. Translation enhancement on a capped mRNA is disabled by m(7)GDP. In addition, the C-terminal fragment of eIF4G can confer translation enhancement also on uncapped mRNA. We conclude that whenever eIF4F has been captured to a dicistronic mRNA by binding to a picornavirus IRES via its eIF4G moiety, it can be provided in cis to the 5'-end of the RNA and there stimulate translation initiation, either by binding to the cap nucleotide using its eIF4E moiety or by binding to the RNA cap-independently using its eIF4G moiety.

Internal initiation: IRES elements of picornaviruses and hepatitis c virus

The scanning hypothesis provides an explanation for events preceding the first peptide bond formation during the translation of the vast majority of eukaryotic mRNAs. However, this hypothesis does not explain the translation of eukaryotic mRNAs lacking the cap structure required for scanning. The existence of a group of positive sense RNA viruses lacking cap structures (e.g. picornaviruses) indicates that host cells also contain a 5' cap-independent translation mechanism. This review discusses the translation mechanisms of atypical viral mRNAs such as picornaviruses and hepatitis c virus, and uses these mechanisms to propose a general theme for all translation, including that of both eukaryotic and prokaryotic mRNAs.

Evidence for an RNA chaperone function of polypyrimidine tract-binding protein in picornavirus translation

The cellular polypyrimidine tract-binding protein (PTB) is recruited by the genomic RNAs of picornaviruses to stimulate translation initiation at their internal ribosome entry site (IRES) elements. We investigated the contribution of the individual RNA recognition motif (RRM) domains of PTB to its interaction with the IRES of foot-and-mouth disease virus (FMDV). Using a native gel system, we found that PTB is a monomer, confirming recent reports that challenged the previous view that PTB is a dimer. Mapping the spatial orientation of PTB relative to the bound IRES RNA, we found that the two C-terminal RRM domains III and IV of PTB bind in an oriented way to the IRES. Domain III contacts the IRES stem-loop 2, while domain IV contacts the separate IRES 3' region. PTB domain I appears not to be involved directly in RNA binding, but domain II stabilizes the RNA binding conferred by domains III and IV. A PTB protein containing only these two C-terminal PTB domains is sufficient to enhance the entry of initiation factor eIF4G to the IRES and stimulate IRES activity, and the long-lived PTB-IRES interaction stabilized by domain II is not a prerequisite for this function. Thus, PTB most likely acts as an RNA chaperone to stabilize IRES structure and, in that way, augment IRES activity.

Genetic comparison of large fragment of the 5'untranslated region among foot-and-mouth disease viruses with special reference to serotype Asia1

Foot-and-mouth disease (FMD), the most economically important disease of cloven-hoofed animals, is endemic in India. Sequence analysis revealed that phylogenetic grouping of type Asia1 field isolates on the basis of the large fragment of the 5'untranslated region (5'LF-UTR) was quite similar to that based on the sequences of the capsid-coding (VP1) region of the same viruses. The existence of two distinct lineages of type Asia1 suggested by the study on the VP1 region was further supported by the detection of a difference in length and predicted secondary structure of the 5'LF-UTR between the two lineages. Sequence variability between the isolates of the two lineages was also observed within the different domains of the internal ribosome entry site (IRES) around conserved motifs like the GNRA,- RAAA,- and the polypyrimidine tract. Certain group and lineage-specific signature nucleotides pertaining to FMDV type Asia1 in the 5'LF-UTR have been identified. The present study shows that the 5'LF-UTR of FMDV serotype Asia1 field isolates are variable in relation to the length and probable secondary structure of the IRES.

Comparative genomics of foot-and-mouth disease virus

Here we present complete genome sequences, including a comparative analysis, of 103 isolates of foot-and-mouth disease virus (FMDV) representing all seven serotypes and including the first complete sequences of the SAT1 and SAT3 genomes. The data reveal novel highly conserved genomic regions, indicating functional constraints for variability as well as novel viral genomic motifs with likely biological relevance. Previously undescribed invariant motifs were identified in the 5' and 3' untranslated regions (UTR), as was tolerance for insertions/deletions in the 5' UTR. Fifty-eight percent of the amino acids encoded by FMDV isolates are invariant, suggesting that these residues are critical for virus biology. Novel, conserved sequence motifs with likely functional significance were identified within proteins L(pro), 1B, 1D, and 3C. An analysis of the complete FMDV genomes indicated phylogenetic incongruities between different genomic regions which were suggestive of interserotypic recombination. Additionally, a novel SAT virus lineage containing nonstructural protein-encoding regions distinct from other SAT and Euroasiatic lineages was identified. Insights into viral RNA sequence conservation and variability and genetic diversity in nature will likely impact our understanding of FMDV infections, host range, and transmission.

Sequence and secondary structure requirements in a highly conserved element for foot-and-mouth disease virus internal ribosome entry site activity and eIF4G binding

Foot-and-mouth disease virus (FMDV) and other picornaviruses initiate translation of their positive-strand RNA genomes at the highly structured internal ribosome entry site (IRES), which mediates ribosome recruitment to an internal site of the virus RNA. This process is facilitated by eukaryotic translation initiation factors (eIFs), such as eIF4G and eIF4B. In the eIF4G-binding site, a characteristic, discontinuous sequence element is highly conserved within the cardio- and aphthovirus subgroup (including FMDV) of the picornaviruses. This conserved element was mutated in order to investigate its primary sequence and secondary structure requirements for IRES function. Both binding of eIF4G to the IRES and IRES-directed translation are seriously impaired by mutations in two unpaired dinucleotide stretches that are exposed from the double-stranded (ds)RNA. In the base-paired regions of the conserved element, maintenance of the double-stranded secondary structure is essential, whilst in some cases, the primary sequence within the dsRNA regions is also important for IRES function. Extra eIF4F added to the translation reaction does not restore full IRES activity or eIF4G binding, indicating that disturbances in the structure of this conserved element cannot be overcome by increased initiation factor concentrations.

Foot-and-mouth disease

Foot-and-mouth disease (FMD) is a highly contagious disease of cloven-hoofed animals. The disease was initially described in the 16th century and was the first animal pathogen identified as a virus. Recent FMD outbreaks in developed countries and their significant economic impact have increased the concern of governments worldwide. This review describes the reemergence of FMD in developed countries that had been disease free for many years and the effect that this has had on disease control strategies. The etiologic agent, FMD virus (FMDV), a member of the Picornaviridae family, is examined in detail at the genetic, structural, and biochemical levels and in terms of its antigenic diversity. The virus replication cycle, including virus-receptor interactions as well as unique aspects of virus translation and shutoff of host macromolecular synthesis, is discussed. This information has been the basis for the development of improved protocols to rapidly identify disease outbreaks, to differentiate vaccinated from infected animals, and to begin to identify and test novel vaccine candidates. Furthermore, this knowledge, coupled with the ability to manipulate FMDV genomes at the molecular level, has provided the framework for examination of disease pathogenesis and the development of a more complete understanding of the virus and host factors involved.

Alternative ways to think about mRNA sequences and proteins that appear to promote internal initiation of translation

Translation of some mRNAs is postulated to occur via an internal initiation mechanism which is said to be augmented by a variety of RNA-binding proteins. A pervasive problem is that the RNA sequences to which the proteins bind were not rigorously proven to function as internal ribosome entry sites (IRESs). Critical examination of the evidence reveals flaws that leave room for alternative interpretations, such as the possibility that IRES elements might function as cryptic promoters, splice sites, or sequences that modulate cleavage by RNases. The growing emphasis on IRES-binding proteins diverts attention from these fundamental unresolved issues. Many of the putative IRES-binding proteins are heterogeneous nuclear ribonucleoproteins that have recognized roles in RNA processing or stability and no recognized role in translation. Thus the mechanism whereby they promote internal initiation, if indeed they do, is not obvious. Some recent experiments were said to support the idea that IRES-binding proteins cause functionally important changes in folding of the RNA, but the evidence is not convincing when examined closely. The proteins that bind to some (not all) viral IRES elements include a subset of authentic initiation factors. This has not been demonstrated with any candidate IRES of cellular origin, however; and even with viral RNAs, the required chase experiment has not been done to prove that a pre-bound initiation factor actually mediates subsequent entry of ribosomes. In short, the focus on IRES-binding proteins has gotten us no closer to understanding the mechanism of internal initiation. Given the aforementioned uncertainty about whether other mechanisms (splicing, cryptic promoters) might underlie what-appears-to-be internal initiation, a temporary solution might be to redefine IRES to mean "internal regulatory expression sequence." This compromise would allow the sequences to be used for gene expression studies, for which they sometimes work, without asserting more than has been proven about the mechanism.

Effects of potassium and chloride on ribosome association with the RNA of foot-and-mouth disease virus

Foot-and-mouth disease virus (FMDV) and other picornaviruses initiate translation of their polyprotein cap-independently at an internal site of the positive-strand viral RNA. This process is mediated by the internal ribosome entry site (IRES), a highly structured cis-acting RNA element that binds translation initiation factors and ribosomal subunits. During their life cycle, picornaviruses induce proliferation of membrane structures involved in viral replication and an increase in membrane permeability probably facilitating virus progeny release. Here, I analyze the efficiency of association of the ribosomal subunits with the FMDV IRES RNA at elevated salt concentrations. Potassium stimulates FMDV translation, whereas sodium chloride concentrations up to 150 mM neither stimulate nor interfere with FMDV translation. Even high potassium concentrations allow binding of the viral RNA to ribosomes. Chloride stimulates binding of ribosomes to the viral RNA at the stage of 48S initiation complex formation and FMDV translation at concentrations up to 150 mM. Only at elevated concentrations, binding of ribosomal subunits and translation are inhibited by chloride. However, FMDV start site selection is not influenced by potassium salts. These results indicate that the association of the viral RNA with ribosomal subunits is well adapted to high salt conditions that are induced during picornavirus infection.

Characterization of a novel RNA-binding region of eIF4GI critical for ribosomal scanning

The eukaryotic translation initiation factor eIF4GI binds several proteins and acts as a scaffold to promote preinitiation complex formation on the mRNA molecule (48S). Following mRNA attachment this complex scans along the messenger in a 5' to 3' direction until it locates and recognizes the initiation start codon. By using a combination of retroviral and picornaviral proteases (HIV-2 and L respectively) in the reticulocyte lysate system, we have characterized a 40 amino acid (aa) region of eIF4GI (aa 642-681) that exhibits general RNA-binding properties. Removal of this domain by proteolytic processing followed by translational assays showed virtually no inhibition of internal ribosome entry on the encephalomyocarditis virus, but resulted in drastic impairment of ribosome scanning as demonstrated by studying poliovirus and foot-and-mouth disease virus translation. Based on these findings, we propose that this 40 aa motif of eIF4GI is critical for ribosome scanning.

N/A

N/A

Molecular basis of pathogenesis of FMDV

Current understanding of the molecular basis of pathogenesis of foot-and-mouth disease (FMD) has been achieved through over 100 years of study into the biology of the etiologic agent, FMDV. Over the last 40 years, classical biochemical and physical analyses of FMDV grown in cell culture have helped to reveal the structure and function of the viral proteins, while knowledge gained by the study of the virus' genetic diversity has helped define structures that are essential for replication and production of disease. More recently, the availability of genetic engineering methodology has permitted the direct testing of hypotheses formulated concerning the role of individual RNA structures, coding regions and polypeptides in viral replication and disease. All of these approaches have been aided by the simultaneous study of other picornavirus pathogens of animals and man, most notably poliovirus. Although many questions of how FMDV causes its devastating disease remain, the following review provides a summary of the current state of knowledge into the molecular basis of the virus' interaction with its host that produces one of the most contagious and frightening diseases of animals or man.

Impaired binding of standard initiation factors mediates poliovirus translation attenuation

In the oral poliovirus vaccine, three attenuated virus strains generated by Albert Sabin are used. However, insufficient genetic stability of these strains causes major problems in poliovirus eradication. In infected cells, translation of the plus-strand poliovirus RNA genome is directed by the internal ribosome entry site (IRES), a cis-acting RNA element that facilitates the cap-independent binding of ribosomes to an internal site of the viral RNA. In each Sabin vaccine strain, a single point mutation in the IRES secondary-structure domain V is a major determinant of neurovirulence attenuation. Here we report how these decisive mutations in the IRES confer a reduction in poliovirus translation efficiency. These single-nucleotide exchanges impair the interaction of the standard translation initiation factor eIF4G with the IRES domain V. Moreover, binding of eIF4B and the polypyrimidine tract-binding protein and the association of ribosomes with the viral RNA are affected by these mutations. However, the negative effects of the IRES mutations are completely relieved by addition of purified eIF4F. This indicates that eIF4G is the crucial factor that initially binds to the poliovirus IRES and recruits the IRES to the other components of the translational apparatus, while impaired binding of eIF4G plays a key role in attenuation of poliovirus neurovirulence.

Eukaryotic initiation factors 4G and 4A mediate conformational changes downstream of the initiation codon of the encephalomyocarditis virus internal ribosomal entry site

Initiation of translation of encephalomyocarditis virus mRNA is mediated by an internal ribosome entry site (IRES) comprising structural domains H, I, J-K, and L immediately upstream of the initiation codon AUG at nucleotide 834 (AUG834). Assembly of 48S ribosomal complexes on the IRES requires eukaryotic initiation factor 2 (eIF2), eIF3, eIF4A, and the central domain of eIF4G to which eIF4A binds. Footprinting experiments confirmed that eIF4G binds a three-way helical junction in the J-K domain and showed that it interacts extensively with RNA duplexes in the J-K and L domains. Deletion of apical hairpins in the J and K domains synergistically impaired the binding of eIF4G and IRES function. Directed hydroxyl radical probing, done by using Fe(II) tethered to surface residues in eIF4G's central domain, indicated that it is oriented with its N terminus towards the base of domain J and its C terminus towards the apex. eIF4G recruits eIF4A to a defined location on the IRES, and the eIF4G/eIF4A complex caused localized ATP-independent conformational changes in the eIF4G-binding region of the IRES. This complex also induced more extensive conformational rearrangements at the 3' border of the ribosome binding site that required ATP and active eIF4A. We propose that these conformational changes prepare the region flanking AUG834 for productive binding of the ribosome.

Interaction of translation initiation factor eIF4B with the poliovirus internal ribosome entry site

Poliovirus translation is initiated at the internal ribosome entry site (IRES). Most likely involving the action of standard initiation factors, this highly structured cis element in the 5" noncoding region of the viral RNA guides the ribosome to an internal silent AUG. The actual start codon for viral protein synthesis further downstream is then reached by ribosomal scanning. In this study we show that two of the secondary structure elements of the poliovirus IRES, domain V and, to a minor extent, domain VI, are the determinants for binding of the eukaryotic initiation factor eIF4B. Several mutations in domain V which are known to greatly affect poliovirus growth also seriously impair the binding of eIF4B. The interaction of eIF4B with the IRES is not dependent on the presence of the polypyrimidine tract-binding protein, which also binds to the poliovirus IRES. In contrast to its weak interaction with cellular mRNAs, eIF4B remains tightly associated with the poliovirus IRES during the formation of complete 80S ribosomes. Binding of eIF4B to the IRES is energy dependent, and binding of the small ribosomal subunit to the IRES requires the previous energy-dependent association of initiation factors with the IRES. These results indicate that the interaction of eIF4B with the 3" region of the poliovirus IRES may be directly involved in translation initiation.