Elsevier

Current Opinion in Virology

Volume 12, June 2015, Pages 113-120
Current Opinion in Virology

Structural insights into viral IRES-dependent translation mechanisms

https://doi.org/10.1016/j.coviro.2015.04.008Get rights and content

Highlights

  • Viral IRESs adopt diverse three-dimensional structures.

  • Evolutionary conserved motifs preserve RNA structure and RNA-protein interactions.

  • Picornavirus IRESs differ in RNA structure and RNA-binding proteins requirement.

A diverse group of viruses subvert the host translational machinery to promote viral genome translation. This process often involves altering canonical translation initiation factors to repress cellular protein synthesis while viral proteins are efficiently synthesized. The discovery of this strategy in picornaviruses, which is based on the use of internal ribosome entry site (IRES) elements, opened new avenues to study alternative translational control mechanisms evolved in different groups of RNA viruses. IRESs are cis-acting RNA sequences that adopt three-dimensional structures and recruit the translation machinery assisted by a subset of translation initiation factors and various RNA binding proteins. However, IRESs present in the genome of different RNA viruses perform the same function despite lacking conservation of primary sequence and secondary RNA structure, and differing in host factor requirement to recruit the translation machinery. Evolutionary conserved motifs tend to preserve sequences impacting on RNA structure and RNA–protein interactions important for IRES function. While some motifs are found in various picornavirus IRESs, others occur only in one type reflecting specialized factor requirements. This review is focused to describe recent advances on the principles and RNA structure features of picornavirus IRESs.

Introduction

Initiation of translation in a diverse group of RNA viruses differs from the bulk of cellular mRNAs in many ways [1, 2]. Most cellular mRNAs initiate translation by a mechanism that depends on the recognition of the m7G(5′)ppp(5′)N structure (termed cap) located at the 5′ end of mRNAs. In this mechanism, the 5′ cap structure is recognized by a translation initiation factor (eIF) composed of the cap-binding protein eIF4E, the scaffolding protein eIF4G, and the RNA helicase eIF4A. In turn, the 43S complex that comprises the ternary complex (consisting of the initiator methionyl-tRNAi and eIF2-GTP) bound to the 40S ribosomal subunit is recruited to the mRNA along with eIF1A, eIF1, eIF3, and eIF5. The 43S complex scans the 5′ untranslated region of the mRNA until the first initiation codon in the proper context is encountered, leading to the formation of the 48S initiation complex. Base pairing between the start codon and the tRNA anticodon triggers a conformational change in the 43S complex, leading to 48S scanning-incompetent conformation. eIF5 promotes GTP hydrolysis by eIF2 in the 48S complex, followed by phosphate release and displacement of eIF1 from its binding site on the 40S subunit. GTP hydrolysis lowers the affinity of eIF2 for the Met-tRNAi, eIF2-GDP dissociates and eIF5B replaces it on the Met-tRNAi. Then, eIF5B and eIF1A promotes the recruitment of the 60S subunit. Finally, ribosomal subunit joining promotes GTP hydrolysis by eIF5B, leaving a competent 80S ribosome with a Met-tRNAi in the P-site ready for translation elongation (reviewed in [1]).

In contrast to this mechanism used by the vast majority of cellular mRNAs, various viral RNAs have evolved alternative mechanisms to initiate translation [2, 3, 4]. A paradigmatic example is provided by picornaviruses, which subvert the host translational machinery to promote translation of the viral genome using a cap-independent mechanism. Recruitment of the ribosomal subunits to initiate translation of the viral RNA is governed by a cis-acting region designated internal ribosome entry site (IRES) element [5, 6]. Indeed, the picornavirus genomic RNA does not contain a cap structure at the 5′ end. Instead, a viral protein (VPg) is covalently linked to the 5′ end of the viral genome. Moreover, cleavage of host factors by viral-encoded proteases profoundly alter several processes critical for cell viability, including transcription, nucleo-cytoplasmic transport, RNA granules composition, and global protein synthesis [7]. Specifically, cellular mRNA translation is inhibited by the proteolysis of eIF4G, eIF3a, eIF5B, or PABP, dephosphorylation of 4E-BPs and phosphorylation of eIF2α [1, 7].

Section snippets

Dicistrovirus and hepatitis C IRESs

In addition to picornaviruses, IRESs have been found to drive translation initiation in various groups of viral RNAs, including dicistroviruses, hepatitis C virus (HCV) and pestiviruses [3, 8]. While all IRESs perform the same function, they posses different structural organization and promote internal initiation by using distinct mechanisms. Regarding factor requirement, the intergenic region (IGR) of dicistroviruses appears to use the simplest mechanism, assembling a 48S complex in the

Picornavirus IRESs

Picornaviruses induce a shutdown of cap-dependent translation in infected cells [7]. Furthermore, these RNA viruses highjack the translation machinery and evade translation inhibition taking advantage of IRES elements [5, 6]. These RNAs recruit the 40S ribosomal subunit internally by a process guided jointly by RNA structural motifs, a subset of eIFs and a number of RNA-binding proteins (RBPs). Translation of picornavirus RNA is, therefore, resistant to cap-dependent inhibition.

IRESs, initially

Host factors critical for picornavirus IRES activity

Picornavirus IRES-dependent protein synthesis rely on the recognition of the IRES element by specific eIFs, which however, depend upon the type of IRES (Table 1). One of these factors is the proteolytic C-terminal fragment of eIF4G that, despite being unable to direct cap-dependent translation, it is fully efficient in type I and II IRES-driven translation initiation. Reconstitution assays have shown that assembly of 48S initiation complexes into IRESs belonging to types I and II require eIF4A,

RNA motifs critical for picornavirus IRES activity

As mentioned above, IRESs govern initiation of translation of all picornavirus RNAs. Despite a similar general genome organization, the untranslated regions of picornavirus genomes differ in length, sequences and structural elements. These differences also apply to the IRES element, which in most picornavirus genomes precede the single open reading frame encoding the viral polyprotein. Only in the case of cadicivirus A structural and nonstructural proteins are encoded by different open reading

Concluding remarks

IRES elements consist of a modular organization with a distribution of functions among the different domains. Deciphering the RNA structure organization of two groups of viral IRESs, the dicistrovirus intergenic region and the HCV-like IRES, has made great progress in recent years [11••, 14••, 66•]. However, the three-dimensional structure of picornavirus IRESs is still unknown, likely due to their long RNA sequence, and high RNA flexibility [8, 15]. Given the diversity of primary sequences and

References and recommended reading

Papers of particular interest, published within the period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgements

We are grateful to current and former laboratory members for their insightful contributions. This work was supported by grants BFU2011-25437 and CSD2009-00080 from MINECO, and by an Institutional grant from Fundación Ramón Areces.

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