tRNA-mimicry in IRES-mediated translation and recoding

Abstract

Viruses maintain compact genomes that must be packaged within capsids typically less than 200 nanometers in diameter. Therefore, instead of coding for a full set of genes needed for replication, viruses have evolved remarkable strategies for co-opting the host cellular machinery. Additionally, viruses often increase the coding capacity of their own genomes by employing overlapping open reading frames (ORFs). Some overlapping viral ORFs involve recoding events that are programmed by the viral RNA. During these programmed recoding events, the ribosome is directed to translate in an alternative reading frame. Here we describe how the Dicistroviridae family of viruses utilize an internal ribosome entry site (IRES) in order to recruit ribosomes to initiate translation at a non-AUG codon. The IRES accomplishes this in part by mimicking the structure of a tRNA. Recently, we showed that the Israeli Acute Paralysis Virus (IAPV) member of the Dicistroviridae family utilizes its IRES to initiate translation in 2 different reading frames. Thus, IAPV has evolved an apparently novel recoding mechanism that reveals important insights into translation. Finally, we compare the IAPV structure to other systems that utilize tRNA mimicry in translation.

Keywords: Frameshifting; IRES; ribosome; translation; virus.

Figure 1.

(A) Location of the dicistrovirus IGR IRES between ORF1 and 2, which code for the non-structural and structural proteins, respectively. VPg is viral protein, which is covalently linked to the 5′ end of the viral RNA. The expanded region shows the secondary structure of the IGR IRES, color-coded to emphasize the 3 different pseudoknot (PK) regions, the loop region L1.1, and the stem-loops SLIII, SLIV and SLV. VLR, variable linker region. (C) Diagram of the proposed IGR IRES factorless translation mechanism. The IGR IRES first extends the PKI domain into the A site of the ribosome. After eukaryotic elongation factor 2 (eEF2)-assisted pseudotranslocation of PKI into the P site, an amino-acyl tRNA^Gly is delivered by eEF1A (thick black arrows). Figure adapted from Journal of Virology.

Figure 2.

(A) Cryo-EM structure of the CrPV IGR IRES bound to the 80S ribosome (PDB ID 4V91)(Figure republished from Cell licensed under CC by 3.0. (B) Zoom-in view of the IRES (colored as in Fig. 1). The positions of the A, P and E site tRNAs (light gray) are superimposed.

Figure 3.

(A) Secondary structure of the IAPV IRES. (B) NMR/SAXS structure of the IAPV IRES PKI domain (PDB ID 2N8V) superimposed over tRNA^Phe (PDB ID 4TNA, light gray spheres). (C) Secondary structure of tmRNA showing the tRNA-like domain (TLD), mRNA-like domain (MLD), Helices (H), and Pseudoknots (PK). (D) Structure of the tmRNA (PDB ID 4V6T, ref.⁵⁴). Reproduced from Frontiers in Microbiology licensed under CC. (E) Secondary structure of Turnip yellow mosaic virus tRNA-like structure (TYMV TLS). F. Structure of the TYMV TLS (PDB ID 4P5J,⁵¹). Reproduced from Nature with permission.