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To determine the codon-anticodon pairs that are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the intergenic region (IGR) of the Cricket Paralysis Virus. It contains an essential pseudoknot PKI that structurally and functionally mimics a codon-anticodon helix. We screened the entire set of 4096 possible combinations using ultrahigh-throughput screenings combining coupled transcription\/translation and droplet-based microfluidics. Only 97 combinations are efficiently accepted and accommodated for translocation and further elongation: 38 combinations involve cognate recognition with Watson-Crick pairs and 59 involve near-cognate recognition pairs with at least one mismatch. More than half of the near-cognate combinations (36\/59) contain a G at the first position of the anticodon (numbered 34 of tRNA). G34-containing tRNAs decoding 4-codon boxes are almost absent from eukaryotic genomes in contrast to bacterial genomes. We reconstructed these missing tRNAs and could demonstrate that these tRNAs are toxic to cells due to their miscoding capacity in eukaryotic translation systems. We also show that the nature of the purine at position 34 is correlated with the nucleotides present at 32 and 38.<\/jats:p>","DOI":"10.1093\/nar\/gkaa221","type":"journal-article","created":{"date-parts":[[2020,3,25]],"date-time":"2020-03-25T20:10:54Z","timestamp":1585167054000},"page":"6170-6183","source":"Crossref","is-referenced-by-count":23,"title":["The nature of the purine at position 34 in tRNAs of 4-codon boxes is correlated with nucleotides at positions 32 and 38 to maintain decoding fidelity"],"prefix":"10.1093","volume":"48","author":[{"given":"Ketty","family":"Pernod","sequence":"first","affiliation":[{"name":"Institut de Biologie Mol\u00e9culaire et Cellulaire, \u2018Architecture et R\u00e9activit\u00e9 de l\u2019ARN\u2019 CNRS UPR9002, Universit\u00e9 de Strasbourg, 2, all\u00e9e Konrad Roentgen, F-67084 Strasbourg, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laure","family":"Schaeffer","sequence":"first","affiliation":[{"name":"Institut de Biologie Mol\u00e9culaire et Cellulaire, \u2018Architecture et R\u00e9activit\u00e9 de l\u2019ARN\u2019 CNRS UPR9002, Universit\u00e9 de Strasbourg, 2, all\u00e9e Konrad Roentgen, F-67084 Strasbourg, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johana","family":"Chicher","sequence":"first","affiliation":[{"name":"Institut de Biologie Mol\u00e9culaire et Cellulaire, Plateforme Prot\u00e9omique Strasbourg \u2013 Esplanade, CNRS FRC1589, Universit\u00e9 de Strasbourg, 2, all\u00e9e Konrad Roentgen Descartes, F-67084 Strasbourg, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eveline","family":"Hok","sequence":"first","affiliation":[{"name":"Laboratory of tRNA Biology, Department of Biology, Rita Liddy Hollings Science Center, 58 Coming Street, Charleston, SC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian","family":"Rick","sequence":"first","affiliation":[{"name":"Institut de Biologie Mol\u00e9culaire et Cellulaire, \u2018Architecture et R\u00e9activit\u00e9 de l\u2019ARN\u2019 CNRS UPR9002, Universit\u00e9 de Strasbourg, 2, all\u00e9e Konrad Roentgen, F-67084 Strasbourg, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Renaud","family":"Geslain","sequence":"first","affiliation":[{"name":"Laboratory of tRNA Biology, Department of Biology, Rita Liddy Hollings Science Center, 58 Coming Street, Charleston, SC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gilbert","family":"Eriani","sequence":"first","affiliation":[{"name":"Institut de Biologie Mol\u00e9culaire et Cellulaire, \u2018Architecture et R\u00e9activit\u00e9 de l\u2019ARN\u2019 CNRS UPR9002, Universit\u00e9 de Strasbourg, 2, all\u00e9e Konrad Roentgen, F-67084 Strasbourg, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6172-5422","authenticated-orcid":false,"given":"Eric","family":"Westhof","sequence":"first","affiliation":[{"name":"Institut de Biologie Mol\u00e9culaire et Cellulaire, \u2018Architecture et R\u00e9activit\u00e9 de l\u2019ARN\u2019 CNRS UPR9002, Universit\u00e9 de Strasbourg, 2, all\u00e9e Konrad Roentgen, F-67084 Strasbourg, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2225-3733","authenticated-orcid":false,"given":"Michael","family":"Ryckelynck","sequence":"first","affiliation":[{"name":"Institut de Biologie Mol\u00e9culaire et Cellulaire, \u2018Architecture et R\u00e9activit\u00e9 de l\u2019ARN\u2019 CNRS UPR9002, Universit\u00e9 de Strasbourg, 2, all\u00e9e Konrad Roentgen, F-67084 Strasbourg, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9724-4025","authenticated-orcid":false,"given":"Franck","family":"Martin","sequence":"first","affiliation":[{"name":"Institut de Biologie Mol\u00e9culaire et Cellulaire, \u2018Architecture et R\u00e9activit\u00e9 de l\u2019ARN\u2019 CNRS UPR9002, Universit\u00e9 de Strasbourg, 2, all\u00e9e Konrad Roentgen, F-67084 Strasbourg, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,4,8]]},"reference":[{"key":"2020061304432115200_B1","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1016\/j.cell.2008.05.042","article-title":"Mistranslation-Induced protein misfolding as a dominant constraint on Coding-Sequence evolution","volume":"134","author":"Drummond","year":"2008","journal-title":"Cell"},{"key":"2020061304432115200_B2","doi-asserted-by":"crossref","first-page":"16502","DOI":"10.1073\/pnas.0809179105","article-title":"Quality control despite mistranslation caused by an ambiguous genetic code","volume":"105","author":"Ruan","year":"2008","journal-title":"Proc. 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