title: An RNA trapping mechanism in Alphavirus mRNA promotes ribosome stalling and translation initiation.
abstract: During translation initiation, eukaryotic initiation factor 2 (eIF2) delivers the Met-tRNA to the 40S ribosomal subunit to locate the initiation codon (AUGi) of mRNA during the scanning process. Stress-induced eIF2 phosphorylation leads to a general blockade of translation initiation and represents a key antiviral pathway in mammals. However, some viral mRNAs can initiate translation in the presence of phosphorylated eIF2 via stable RNA stem-loop structures (DLP; Downstream LooP) located in their coding sequence (CDS), which promote 43S preinitiation complex stalling on the initiation codon. We show here that during the scanning process, DLPs of Alphavirus mRNA become trapped in ES6S region (680-914 nt) of 18S rRNA that are projected from the solvent side of 40S subunit. This trapping can lock the progress of the 40S subunit on the mRNA in a way that places the upstream initiator AUGi on the P site of 40S subunit, obviating the participation of eIF2. Notably, the DLP structure is released from 18S rRNA upon 60S ribosomal subunit joining, suggesting conformational changes in ES6Ss during the initiation process. These novel findings illustrate how viral mRNA is threaded into the 40S subunit during the scanning process, exploiting the topology of the 40S subunit solvent side to enhance its translation in vertebrate hosts.
authors.affiliation: Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM) and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain.
authors.forename: René
authors.initials: R
authors.lastname: Toribio
authors.affiliation: Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM) and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain.
authors.forename: Irene
authors.initials: I
authors.lastname: Díaz-López
authors.affiliation: Structural Biology and Biocomputing Programme, Electron Microscopy Unit, Spanish Nacional Cancer Research Center (CNIO), 28029 Madrid, Spain.
authors.forename: Jasminka
authors.initials: J
authors.lastname: Boskovic
authors.affiliation: Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM) and Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain iventoso@cbm.csic.es.
authors.forename: Iván
authors.initials: I
authors.lastname: Ventoso
mesh_terms: D000330:Aedes; D000524:Alphavirus / Q000235:genetics* / Q000378:metabolism; D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D018387:Codon, Initiator; D006224:Cricetinae; D015967:Gene Expression Regulation, Viral; D055029:Inverted Repeat Sequences; D008958:Models, Molecular; D010442:Peptide Chain Initiation, Translational; D020871:RNA Stability; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012337:RNA, Ribosomal, 18S / Q000737:chemistry / Q000502:physiology; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012270:Ribosomes / Q000502:physiology
chemical_list: D018387:Codon, Initiator; D012333:RNA, Messenger; D012337:RNA, Ribosomal, 18S; D012367:RNA, Viral