The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs

Abstract

Colony collapse disorder (CCD) is a multi‐faceted syndrome decimating bee populations worldwide, and a group of viruses of the widely distributed Dicistroviridae family have been identified as a causing agent of CCD. This family of viruses employs non‐coding RNA sequences, called internal ribosomal entry sites (IRESs), to precisely exploit the host machinery for viral protein production. Using single‐particle cryo‐electron microscopy (cryo‐EM), we have characterized how the IRES of Israeli acute paralysis virus (IAPV) intergenic region captures and redirects translating ribosomes toward viral RNA messages. We reconstituted two in vitro reactions targeting a pre‐translocation and a post‐translocation state of the IAPV‐IRES in the ribosome, allowing us to identify six structures using image processing classification methods. From these, we reconstructed the trajectory of IAPV‐IRES from the early small subunit recruitment to the final post‐translocated state in the ribosome. An early commitment of IRES/ribosome complexes for global pre‐translocation mimicry explains the high efficiency observed for this IRES. Efforts directed toward fighting CCD by targeting the IAPV‐IRES using RNA‐interference technology are underway, and the structural framework presented here may assist in further refining these approaches.

Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation

“…As previously noted from the yeast 80S structure 21 , eL41 is more strongly associated to the small ribosomal subunit than to the large one. Consistent with this observation, eL41 was indeed found in the structures of several 40S 17,22 . In the present archaeal structure, eL41 is also found in the small ribosomal subunit, as in 12 .…”

Negative charge in the RACK1 loop broadens the translational capacity of the human ribosome

“…Intriguingly, the type III or IV IRES elements of RNA viruses such as hepatitis C virus (HCV), Israeli acute paralysis virus (IAPV), or cricket paralysis virus (CrPV) manipulate 40S head rotation to enable cap- and scanning-independent initiation ( Acosta-Reyes et al, 2019 ; Murray et al, 2016 ; Quade et al, 2015 ; Spahn et al, 2001 ; Yamamoto et al, 2015 ). These IRESs also interact with RACK1 and require RACK1 for their translation ( Jackson, 2013 ; Johnson et al, 2019 ; LaFontaine et al, 2020 ; Majzoub et al, 2014 ; Qin and Sarnow, 2004 ).…”

“…Viruses often evolve strategies to dysregulate tightly controlled processes, and in this case, negative charge in the human RACK1 loop appears to dysregulate and broaden the functionality of the human ribosome to support the noncanonical modes of translation that many RNA viruses use. More directly related to effects on 40S head swivel, S 278 E RACK1 mimics the 40S remodeling induced by structurally complex HCV, CrPV, and IAPV IRES elements that drive 80S assembly with minimal dependence on eIFs ( Acosta-Reyes et al, 2019 ; Neupane et al, 2020 ; Quade et al, 2015 ; Spahn et al, 2001 ; Yamamoto et al, 2015 ). By contrast, poxviruses are DNA viruses that generate mRNAs with very short 5′ poly(A) leaders ( Meade et al, 2019a ).…”

Minding the message: tactics controlling RNA decay, modification, and translation in virus-infected cells

“…While CrPV IRES codon–anticodon mimicking PK initially occupies the ribosome A-site, 40S rotation and eEF2-dependent translocation into the P-site are required to expose the A-site for elongation to commence ( Costantino et al 2008 ). By imitating an intermediate ribosomal state with hybrid tRNAs, IRES PK I from Israeli acute paralysis virus (IAPV) within the A-site blocks eIF1/eIF1A binding and promotes 60S joining followed by codon translocation to the P-site in a related elongation factor recruitment strategy ( Costantino et al 2008 ; Acosta-Reyes et al 2019 ). A simpler mechanism used by Halastavi árva virus positions the IRES PK into the P-site, averting the need for eEF2-mediated translocation prior to commencing decoding ( Abaeva et al 2020 ).…”