Initiation of translation on nedicistrovirus and related intergenic region IRESs by their factor-independent binding to the P site of 80S ribosomes

Initiation of translation on many viral mRNAs occurs by noncanonical mechanisms that involve 5' end-independent binding of ribosomes to an internal ribosome entry site (IRES). The similar to 190-nt-long intergenic region (IGR) IRES of dicistroviruses such as cricket paralysis virus (CrPV) initiates translation without Met-tRNAiMet or initiation factors. Advances in metagenomics have revealed numerous dicistrovirus-like genomes with shorter, structurally distinct IGRs, such as nedicistrovirus (NediV) and Antarctic picorna-like virus 1 (APLV1). Like canonical IGR IRESs, the similar to 165-nt-long NediV-like IGRs comprise three domains, but they lack key canonical motifs, including L1.1a/L1.1b loops (which bind to the L1 stalk of the ribosomal 60S subunit) and the apex of stem-loop V (SLV) (which binds to the head of the 40S subunit). Domain 2 consists of a compact, highly conserved pseudoknot (PKIII) that contains a UACUA loop motif and a protruding CrPV-like stem-loop SLIV. In vitro reconstitution experiments showed that NediV-like IRESs initiate translation from a non-AUG codon and form elongation-competent 80S ribosomal complexes in the absence of initiation factors and Met-tRNAiMet. Unlike canonical IGR IRESs, NediVlike IRESs bind directly to the peptidyl (P) site of ribosomes leaving the aminoacyl (A) site accessible for decoding. The related structures of NediV-like IRESs and their common mechanism of action indicate that they exemplify a distinct class of IGR IRES.

Automated summary

Translation initiation on viral mRNAs can occur through noncanonical mechanisms involving ribosome binding to an internal ribosome entry site (IRES). Dicistroviruses, such as cricket paralysis virus (CrPV), have long IRESs that initiate translation without conventional initiation factors. Recent discoveries have identified shorter IRESs in dicistrovirus-like genomes, like nedicistrovirus (NediV) and Antarctic picorna-like virus 1 (APLV1), which initiate translation from non-AUG codons. These NediV-like IRESs bind directly to the ribosomal peptidyl (P) site and form functional ribosomal complexes without initiation factors.