{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,19]],"date-time":"2026-09-19T07:17:35Z","timestamp":1789802255121,"version":"4.0.1"},"reference-count":224,"publisher":"Elsevier BV","issue":"6","license":[{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T00:00:00Z","timestamp":1775088000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01 AI150493"],"award-info":[{"award-number":["R01 AI150493"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35 GM141880"],"award-info":[{"award-number":["R35 GM141880"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["GM128836"],"award-info":[{"award-number":["GM128836"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["jbc.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Biological Chemistry"],"published-print":{"date-parts":[[2026,6]]},"DOI":"10.1016\/j.jbc.2026.111430","type":"journal-article","created":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T16:18:32Z","timestamp":1775578712000},"page":"111430","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":1,"title":["tRNA modifications in viral replication"],"prefix":"10.1016","volume":"302","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1527-0882","authenticated-orcid":false,"given":"Chathuri","family":"Pathirage","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7763-9262","authenticated-orcid":false,"given":"Kristin S.","family":"Koutmou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0354-4172","authenticated-orcid":false,"given":"Karin","family":"Musier-Forsyth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jbc.2026.111430_bib1","series-title":"Encylopedia of Cell Biology","first-page":"309","article-title":"Transfer RNA","author":"Doherty","year":"2016"},{"key":"10.1016\/j.jbc.2026.111430_bib2","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1038\/nrg3861","article-title":"Emerging roles of tRNA in adaptive translation, signalling dynamics and disease","volume":"16","author":"Kirchner","year":"2015","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.jbc.2026.111430_bib3","first-page":"16","article-title":"Multiple layers of stress-induced regulation in tRNA biology","volume":"6","author":"Huang","year":"2016","journal-title":"Life (Basel)"},{"key":"10.1016\/j.jbc.2026.111430_bib4","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.chembiol.2023.12.008","article-title":"Recognition of the tRNA structure: everything everywhere but not all at once","volume":"31","author":"Zhang","year":"2024","journal-title":"Cell Chem. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib5","doi-asserted-by":"crossref","first-page":"898","DOI":"10.1261\/rna.079620.123","article-title":"The life and times of a tRNA","volume":"29","author":"Phizicky","year":"2023","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2026.111430_bib6","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1080\/15476286.2017.1356562","article-title":"Celebrating wobble decoding: half a century and still much is new","volume":"15","author":"Agris","year":"2018","journal-title":"RNA Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib7","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1016\/S0022-2836(66)80022-0","article-title":"Codon-anticodon pairing: the wobble hypothesis","volume":"19","author":"Crick","year":"1966","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib8","doi-asserted-by":"crossref","DOI":"10.3389\/fviro.2022.1073619","article-title":"The host tRNA epitranscriptome: A new player in RNA virus infections","volume":"2","author":"Tall\u00f3-Parra","year":"2022","journal-title":"Front. Virol."},{"key":"10.1016\/j.jbc.2026.111430_bib9","doi-asserted-by":"crossref","first-page":"1146","DOI":"10.7150\/ijbs.80233","article-title":"tRNA modifications and modifying enzymes in disease, the potential therapeutic targets","volume":"19","author":"Cui","year":"2023","journal-title":"Int. J. Biol. Sci."},{"key":"10.1016\/j.jbc.2026.111430_bib10","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2025.1642370","article-title":"Decoding tRNA dynamics in neuroimmune disorders: mechanistic insights, diagnostic innovations, and therapeutic opportunities","volume":"16","author":"Liang","year":"2025","journal-title":"Front. Immunol."},{"key":"10.1016\/j.jbc.2026.111430_bib11","doi-asserted-by":"crossref","first-page":"4287","DOI":"10.1016\/j.febslet.2014.09.038","article-title":"tRNA modifications regulate translation during cellular stress","volume":"588","author":"Gu","year":"2014","journal-title":"FEBS Lett."},{"key":"10.1016\/j.jbc.2026.111430_bib12","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1038\/s41580-021-00342-0","article-title":"The expanding world of tRNA modifications and their disease relevance","volume":"22","author":"Suzuki","year":"2021","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib13","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1016\/j.jgg.2022.10.002","article-title":"Emerging functions of tRNA modifications in mRNA translation and diseases","volume":"50","author":"Wang","year":"2023","journal-title":"J. Genet. Genomics."},{"key":"10.1016\/j.jbc.2026.111430_bib14","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1038\/s41419-021-03838-x","article-title":"Roles of tRNA metabolism in aging and lifespan","volume":"12","author":"Zhou","year":"2021","journal-title":"Cell Death Dis."},{"key":"10.1016\/j.jbc.2026.111430_bib15","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/j.semcdb.2023.06.003","article-title":"Anticodon stem-loop tRNA modifications influence codon decoding and frame maintenance during translation","volume":"154","author":"Smith","year":"2023","journal-title":"Semin. Cell Dev. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib16","doi-asserted-by":"crossref","first-page":"374","DOI":"10.3390\/genes15030374","article-title":"Beyond the anticodon: tRNA core modifications and their impact on structure, translation and stress adaptation","volume":"15","author":"Yared","year":"2024","journal-title":"Genes (Basel)"},{"key":"10.1016\/j.jbc.2026.111430_bib17","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1016\/j.molcel.2021.12.007","article-title":"tRNA modification dynamics from individual organisms to metaepitranscriptomics of microbiomes","volume":"82","author":"Zhang","year":"2022","journal-title":"Mol. Cell"},{"key":"10.1016\/j.jbc.2026.111430_bib18","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1038\/s41586-022-04677-2","article-title":"Reversible RNA phosphorylation stabilizes tRNA for cellular thermotolerance","volume":"605","author":"Ohira","year":"2022","journal-title":"Nature"},{"key":"10.1016\/j.jbc.2026.111430_bib19","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.58461","article-title":"Manipulation of the human tRNA pool reveals distinct tRNA sets that act in cellular proliferation or cell cycle arrest","volume":"9","author":"Aharon-Hefetz","year":"2020","journal-title":"Elife"},{"key":"10.1016\/j.jbc.2026.111430_bib20","doi-asserted-by":"crossref","DOI":"10.1016\/j.jbc.2024.107488","article-title":"RNA modifying enzymes shape tRNA biogenesis and function","volume":"300","author":"Schultz","year":"2024","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jbc.2026.111430_bib21","doi-asserted-by":"crossref","first-page":"3504","DOI":"10.1021\/acs.accounts.3c00572","article-title":"Molecular coping mechanisms: reprogramming tRNAs to regulate codon-biased translation of stress response proteins","volume":"56","author":"Mitchener","year":"2023","journal-title":"Acc. Chem. Res."},{"key":"10.1016\/j.jbc.2026.111430_bib22","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkaf594","article-title":"Key RNA-binding domains in the La protein establish tRNA modification levels in Trypanosoma brucei","volume":"53","author":"Gunaratne","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.111430_bib23","doi-asserted-by":"crossref","first-page":"706","DOI":"10.3390\/ijms26020706","article-title":"Decoding codon bias: the role of tRNA modifications in tissue-specific translation","volume":"26","author":"Ando","year":"2025","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.jbc.2026.111430_bib24","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1021\/acs.biochem.8b01035","article-title":"Can protein expression be regulated by modulation of tRNA modification profiles?","volume":"58","author":"Pollo-Oliveira","year":"2019","journal-title":"Biochemistry"},{"key":"10.1016\/j.jbc.2026.111430_bib25","doi-asserted-by":"crossref","DOI":"10.1126\/scisignal.aat6409","article-title":"Cells alter their tRNA abundance to selectively regulate protein synthesis during stress conditions","volume":"11","author":"Torrent","year":"2018","journal-title":"Sci. Signal."},{"key":"10.1016\/j.jbc.2026.111430_bib26","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1001247","article-title":"A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress","volume":"6","author":"Chan","year":"2010","journal-title":"PLoS Genet."},{"key":"10.1016\/j.jbc.2026.111430_bib27","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1038\/nrg.2016.169","article-title":"Detecting RNA modifications in the epitranscriptome: predict and validate","volume":"18","author":"Helm","year":"2017","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.jbc.2026.111430_bib28","doi-asserted-by":"crossref","DOI":"10.1002\/wrna.1367","article-title":"Going global: the new era of mapping modifications in RNA","volume":"8","author":"Limbach","year":"2017","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"10.1016\/j.jbc.2026.111430_bib29","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1039\/C9AN02111F","article-title":"Improved RNA modification mapping of cellular non-coding RNAs using C- and U-specific RNases","volume":"145","author":"Thakur","year":"2020","journal-title":"Analyst"},{"key":"10.1016\/j.jbc.2026.111430_bib30","doi-asserted-by":"crossref","first-page":"1124","DOI":"10.1080\/15476286.2016.1251543","article-title":"Next-generation sequencing technologies for detection of modified nucleotides in RNAs","volume":"14","author":"Schwartz","year":"2017","journal-title":"RNA Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib31","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1016\/j.tig.2023.11.001","article-title":"Advances in methods for tRNA sequencing and quantification","volume":"40","author":"Padhiar","year":"2024","journal-title":"Trends Genet."},{"key":"10.1016\/j.jbc.2026.111430_bib32","doi-asserted-by":"crossref","first-page":"1819","DOI":"10.3390\/v13091819","article-title":"Interplay between host tRNAs and HIV-1: A structural perspective","volume":"13","author":"Zhang","year":"2021","journal-title":"Viruses"},{"key":"10.1016\/j.jbc.2026.111430_bib33","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1042\/BJ20070024","article-title":"Signalling to translation: how signal transduction pathways control the protein synthetic machinery","volume":"403","author":"Proud","year":"2007","journal-title":"Biochem. J."},{"key":"10.1016\/j.jbc.2026.111430_bib34","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.cell.2014.03.005","article-title":"Remote control of gene function by local translation","volume":"157","author":"Jung","year":"2014","journal-title":"Cell"},{"key":"10.1016\/j.jbc.2026.111430_bib35","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1006\/excr.1999.4683","article-title":"Ribosome S6 kinase signaling and the control of translation","volume":"253","author":"Dufner","year":"1999","journal-title":"Exp. Cell Res."},{"key":"10.1016\/j.jbc.2026.111430_bib36","doi-asserted-by":"crossref","first-page":"20823","DOI":"10.1016\/S0021-9258(19)30005-5","article-title":"Protein phosphorylation controls translation rates","volume":"264","author":"Hershey","year":"1989","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jbc.2026.111430_bib37","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1016\/S0079-6603(08)60883-1","article-title":"Growth control of translation in mammalian cells","volume":"51","author":"Morris","year":"1995","journal-title":"Prog. Nucleic Acid Res. Mol. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib38","doi-asserted-by":"crossref","DOI":"10.1016\/j.jbc.2023.105163","article-title":"Coping with stress: how bacteria fine-tune protein synthesis and protein transport","volume":"299","author":"Njenga","year":"2023","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jbc.2026.111430_bib39","doi-asserted-by":"crossref","first-page":"5102","DOI":"10.1111\/febs.17076","article-title":"Translation regulation in response to stress","volume":"291","author":"Williams","year":"2024","journal-title":"FEBS J."},{"key":"10.1016\/j.jbc.2026.111430_bib40","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a032870","article-title":"Role of eIF2alpha kinases in translational control and adaptation to cellular stress","volume":"10","author":"Wek","year":"2018","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib41","doi-asserted-by":"crossref","first-page":"1719","DOI":"10.1261\/rna.058180.116","article-title":"Codon optimality controls differential mRNA translation during amino acid starvation","volume":"22","author":"Saikia","year":"2016","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2026.111430_bib42","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1146\/annurev-virology-100114-055014","article-title":"A cap-to-tail guide to mRNA translation strategies in virus-infected cells","volume":"3","author":"Jan","year":"2016","journal-title":"Annu. Rev. Virol."},{"key":"10.1016\/j.jbc.2026.111430_bib43","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a012351","article-title":"Tinkering with translation: protein synthesis in virus-infected cells","volume":"5","author":"Walsh","year":"2013","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib44","doi-asserted-by":"crossref","DOI":"10.1002\/wrna.1619","article-title":"Emerging translation strategies during virus-host interaction","volume":"12","author":"Hoang","year":"2021","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"10.1016\/j.jbc.2026.111430_bib45","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a033001","article-title":"Translational control in virus-infected cells","volume":"11","author":"Stern-Ginossar","year":"2019","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib46","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1038\/nature11433","article-title":"Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11","volume":"491","author":"Li","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.jbc.2026.111430_bib47","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1007\/s11033-021-06749-4","article-title":"Codon usage bias","volume":"49","author":"Parvathy","year":"2022","journal-title":"Mol. Biol. Rep."},{"key":"10.1016\/j.jbc.2026.111430_bib48","doi-asserted-by":"crossref","first-page":"2279","DOI":"10.1101\/gr.2896904","article-title":"Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization","volume":"14","author":"Rocha","year":"2004","journal-title":"Genome Res."},{"key":"10.1016\/j.jbc.2026.111430_bib49","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1007\/s00239-008-9068-6","article-title":"Codon bias is a major factor explaining phage evolution in translationally biased hosts","volume":"66","author":"Carbone","year":"2008","journal-title":"J. Mol. Evol."},{"key":"10.1016\/j.jbc.2026.111430_bib50","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1000001","article-title":"Genome landscapes and bacteriophage codon usage","volume":"4","author":"Lucks","year":"2008","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib51","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1038\/msb.2009.71","article-title":"Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences","volume":"5","author":"Bahir","year":"2009","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib52","doi-asserted-by":"crossref","first-page":"1580","DOI":"10.3390\/v15071580","article-title":"Different patterns of codon usage and amino acid composition across primate lentiviruses","volume":"15","author":"Pavesi","year":"2023","journal-title":"Viruses"},{"key":"10.1016\/j.jbc.2026.111430_bib53","doi-asserted-by":"crossref","first-page":"1827","DOI":"10.1093\/molbev\/msr005","article-title":"HIV-1 modulates the tRNA pool to improve translation efficiency","volume":"28","author":"van Weringh","year":"2011","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.jbc.2026.111430_bib54","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1186\/s13059-018-1611-1","article-title":"Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses","volume":"19","author":"Chan","year":"2018","journal-title":"Genome Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib55","doi-asserted-by":"crossref","first-page":"4725","DOI":"10.1038\/s41467-022-31835-x","article-title":"CHIKV infection reprograms codon optimality to favor viral RNA translation by altering the tRNA epitranscriptome","volume":"13","author":"Jungfleisch","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jbc.2026.111430_bib56","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0168-1702(02)00309-X","article-title":"The extent of codon usage bias in human RNA viruses and its evolutionary origin","volume":"92","author":"Jenkins","year":"2003","journal-title":"Virus. Res."},{"key":"10.1016\/j.jbc.2026.111430_bib57","doi-asserted-by":"crossref","DOI":"10.3390\/ijms252111614","article-title":"SARS-CoV-2 displays a suboptimal codon usage bias for efficient translation in human cells diverted by hijacking the tRNA epitranscriptome","volume":"25","author":"Eldin","year":"2024","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.jbc.2026.111430_bib58","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1186\/1742-4690-9-92","article-title":"The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus","volume":"9","author":"van der Kuyl","year":"2012","journal-title":"Retrovirology"},{"key":"10.1016\/j.jbc.2026.111430_bib59","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1089\/08892220252779674","article-title":"Codon and amino acid usage in retroviral genomes is consistent with virus-specific nucleotide pressure","volume":"18","author":"Berkhout","year":"2002","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"10.1016\/j.jbc.2026.111430_bib60","doi-asserted-by":"crossref","first-page":"2944","DOI":"10.1038\/s41467-026-69700-w","article-title":"Coronaviruses reprogram the tRNA epitranscriptome to favor viral protein expression","volume":"17","author":"Muscolino","year":"2026","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jbc.2026.111430_bib61","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1038\/s44320-024-00052-7","article-title":"Dengue virus preferentially uses human and mosquito non-optimal codons","volume":"20","author":"Castellano","year":"2024","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib62","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1186\/s12985-025-02838-z","article-title":"Respiratory syncytial virus (RSV) enhances translation of virus-resembling AU-rich host transcripts","volume":"22","author":"Kerkhofs","year":"2025","journal-title":"Virol. J."},{"key":"10.1016\/j.jbc.2026.111430_bib63","doi-asserted-by":"crossref","first-page":"355","DOI":"10.3390\/microorganisms11020355","article-title":"Bacteriophage infection of the marine bacterium Shewanella glacialimarina induces dynamic changes in tRNA modifications","volume":"11","author":"Lampi","year":"2023","journal-title":"Microorganisms"},{"key":"10.1016\/j.jbc.2026.111430_bib64","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/j.semcdb.2023.01.011","article-title":"\"Transfer\" of power: the intersection of DNA virus infection and tRNA biology","volume":"146","author":"Dremel","year":"2023","journal-title":"Semin Cell Dev. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib65","doi-asserted-by":"crossref","DOI":"10.1080\/21505594.2025.2580129","article-title":"Coronaviruses remodel the mature human tRNAome to modulate infection","volume":"16","author":"Wang","year":"2025","journal-title":"Virulence"},{"key":"10.1016\/j.jbc.2026.111430_bib66","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1038\/s41467-022-28144-8","article-title":"Manipulation of RNA polymerase III by Herpes Simplex Virus-1","volume":"13","author":"Dremel","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jbc.2026.111430_bib67","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.02664-20","article-title":"Alteration of the premature tRNA landscape by gammaherpesvirus infection","volume":"11","author":"Tucker","year":"2020","journal-title":"mBio"},{"key":"10.1016\/j.jbc.2026.111430_bib68","doi-asserted-by":"crossref","first-page":"1914","DOI":"10.1093\/nar\/gks986","article-title":"Vaccinia and influenza A viruses select rather than adjust tRNAs to optimize translation","volume":"41","author":"Pavon-Eternod","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.111430_bib69","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2021.108872","article-title":"Translational adaptation of human viruses to the tissues they infect","volume":"34","author":"Hernandez-Alias","year":"2021","journal-title":"Cell Rep."},{"key":"10.1016\/j.jbc.2026.111430_bib70","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1016\/j.molmed.2019.05.011","article-title":"tRNA deregulation and its consequences in cancer","volume":"25","author":"Santos","year":"2019","journal-title":"Trends Mol. Med."},{"key":"10.1016\/j.jbc.2026.111430_bib71","article-title":"Hepatitis E virus infection remodels the mature tRNAome in macrophages to orchestrate NLRP3 inflammasome response","volume":"120","author":"Li","year":"2023","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jbc.2026.111430_bib72","doi-asserted-by":"crossref","first-page":"502","DOI":"10.3390\/v16040502","article-title":"Schlafen14 impairs HIV-1 expression in a codon usage-dependent manner","volume":"16","author":"Valenzuela","year":"2024","journal-title":"Viruses"},{"key":"10.1016\/j.jbc.2026.111430_bib73","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1038\/s42003-023-04841-y","article-title":"Schlafen 12 restricts HIV-1 latency reversal by a codon-usage dependent post-transcriptional block in CD4+ T cells","volume":"6","author":"Kobayashi-Ishihara","year":"2023","journal-title":"Commun. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib74","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1038\/s41594-018-0142-5","article-title":"DNA damage-induced cell death relies on SLFN11-dependent cleavage of distinct type II tRNAs","volume":"25","author":"Li","year":"2018","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib75","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1038\/s41589-022-01170-9","article-title":"Velcrin-induced selective cleavage of tRNA(Leu)(TAA) by SLFN12 causes cancer cell death","volume":"19","author":"Lee","year":"2023","journal-title":"Nat. Chem. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib76","doi-asserted-by":"crossref","first-page":"5464","DOI":"10.1038\/s41467-022-33123-0","article-title":"Mechanistic understanding of human SLFN11","volume":"13","author":"Metzner","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jbc.2026.111430_bib77","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.1038\/s41467-018-03544-x","article-title":"Structure of Schlafen13 reveals a new class of tRNA\/rRNA- targeting RNase engaged in translational control","volume":"9","author":"Yang","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jbc.2026.111430_bib78","doi-asserted-by":"crossref","first-page":"5776","DOI":"10.1093\/nar\/gky029","article-title":"Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection","volume":"46","author":"McIntyre","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.111430_bib79","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1038\/nprot.2014.047","article-title":"Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry","volume":"9","author":"Su","year":"2014","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.jbc.2026.111430_bib80","doi-asserted-by":"crossref","first-page":"43950","DOI":"10.1074\/jbc.M112.409300","article-title":"Characterization and structure of the Aquifex aeolicus protein DUF752: a bacterial tRNA-methyltransferase (MnmC2) functioning without the usually fused oxidase domain (MnmC1)","volume":"287","author":"Kitamura","year":"2012","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jbc.2026.111430_bib81","article-title":"Dengue Virus exploits the host tRNA epitranscriptome to promote viral replication","author":"Chan","year":"2023","journal-title":"bioRxiv"},{"key":"10.1016\/j.jbc.2026.111430_bib82","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/s44320-025-00181-7","article-title":"Essentiality and dynamic expression of the human tRNA pool during viral infection","volume":"22","author":"Aharon-Hefetz","year":"2026","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib83","doi-asserted-by":"crossref","first-page":"1233","DOI":"10.3390\/biom12091233","article-title":"t(6)A and ms(2)t(6)A modified nucleosides in serum and urine as strong candidate biomarkers of COVID-19 infection and severity","volume":"12","author":"Nagayoshi","year":"2022","journal-title":"Biomolecules"},{"key":"10.1016\/j.jbc.2026.111430_bib84","doi-asserted-by":"crossref","DOI":"10.1016\/j.jmb.2025.169091","article-title":"The biology of tRNA t(6)A modification and hypermodifications-biogenesis and disease relevance","volume":"437","author":"Zhang","year":"2025","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib85","doi-asserted-by":"crossref","DOI":"10.3389\/fcell.2022.999351","article-title":"tRNA abundance, modification and fragmentation in nasopharyngeal swabs as biomarkers for COVID-19 severity","volume":"10","author":"Katanski","year":"2022","journal-title":"Front. Cell Dev. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib86","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2106556118","article-title":"Dynamic changes in tRNA modifications and abundance during T cell activation","volume":"118","author":"Rak","year":"2021","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jbc.2026.111430_bib87","doi-asserted-by":"crossref","first-page":"1209","DOI":"10.1080\/15476286.2017.1295204","article-title":"Wobble uridine modifications-a reason to live, a reason to die?","volume":"14","author":"Schaffrath","year":"2017","journal-title":"RNA Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib88","doi-asserted-by":"crossref","DOI":"10.1016\/j.heliyon.2020.e03915","article-title":"Codon usage similarity between viral and some host genes suggests a codon-specific translational regulation","volume":"6","author":"Jitobaom","year":"2020","journal-title":"Heliyon"},{"key":"10.1016\/j.jbc.2026.111430_bib89","doi-asserted-by":"crossref","first-page":"1433","DOI":"10.1038\/s41590-022-01301-3","article-title":"tRNA-m(1)A modification promotes T cell expansion via efficient MYC protein synthesis","volume":"23","author":"Liu","year":"2022","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.jbc.2026.111430_bib90","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1016\/j.cell.2015.05.022","article-title":"Optimization of codon translation rates via tRNA modifications maintains proteome integrity","volume":"161","author":"Nedialkova","year":"2015","journal-title":"Cell"},{"key":"10.1016\/j.jbc.2026.111430_bib91","doi-asserted-by":"crossref","first-page":"12289","DOI":"10.1073\/pnas.1300781110","article-title":"tRNA tKUUU, tQUUG, and tEUUC wobble position modifications fine-tune protein translation by promoting ribosome A-site binding","volume":"110","author":"Rezgui","year":"2013","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jbc.2026.111430_bib92","doi-asserted-by":"crossref","first-page":"13390","DOI":"10.1021\/bi001302g","article-title":"Modified nucleoside dependent Watson-Crick and wobble codon binding by tRNALys UUU species","volume":"39","author":"Yarian","year":"2000","journal-title":"Biochemistry"},{"key":"10.1016\/j.jbc.2026.111430_bib93","doi-asserted-by":"crossref","DOI":"10.15252\/embr.202356808","article-title":"Expanded tRNA methyltransferase family member TRMT9B regulates synaptic growth and function","volume":"24","author":"Hogan","year":"2023","journal-title":"EMBO Rep."},{"key":"10.1016\/j.jbc.2026.111430_bib94","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.aas9184","article-title":"Phosphorylation of human TRM9L integrates multiple stress-signaling pathways for tumor growth suppression","volume":"4","author":"Gu","year":"2018","journal-title":"Sci. Adv."},{"key":"10.1016\/j.jbc.2026.111430_bib95","first-page":"366","article-title":"A human tRNA methyltransferase 9-like protein prevents tumour growth by regulating LIN9 and HIF1-alpha EMBO","volume":"5","author":"Begley","year":"2013","journal-title":"Mol. Med."},{"key":"10.1016\/j.jbc.2026.111430_bib96","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1016\/j.molcel.2007.09.021","article-title":"Trm9-catalyzed tRNA modifications link translation to the DNA damage response","volume":"28","author":"Begley","year":"2007","journal-title":"Mol. Cell"},{"key":"10.1016\/j.jbc.2026.111430_bib97","article-title":"Zika Virus Reprograms the Host tRNA Epitranscriptome to Adapt Translation to A-ending Codon Bias","author":"Eldin","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.jbc.2026.111430_bib98","doi-asserted-by":"crossref","first-page":"7479","DOI":"10.3390\/ijms26157479","article-title":"tRNA modifications: a tale of two viruses-SARS-CoV-2 and ZIKV","volume":"26","author":"Eldin","year":"2025","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.jbc.2026.111430_bib99","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1146\/annurev-virology-111821-120646","article-title":"Structural and functional insights into viral programmed ribosomal frameshifting","volume":"10","author":"Hill","year":"2023","journal-title":"Annu. Rev. Virol."},{"key":"10.1016\/j.jbc.2026.111430_bib100","doi-asserted-by":"crossref","first-page":"1123","DOI":"10.1016\/j.tig.2022.05.009","article-title":"Slippy-sloppy translation: a tale of programmed and induced-ribosomal frameshifting","volume":"38","author":"Champagne","year":"2022","journal-title":"Trends Genet."},{"key":"10.1016\/j.jbc.2026.111430_bib101","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1006\/jmbi.1997.1134","article-title":"Expression of a coronavirus ribosomal frameshift signal in Escherichia coli: influence of tRNA anticodon modification on frameshifting","volume":"270","author":"Brierley","year":"1997","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib102","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.virusres.2005.10.008","article-title":"Programmed ribosomal frameshifting in HIV-1 and the SARS-CoV","volume":"119","author":"Brierley","year":"2006","journal-title":"Virus. Res."},{"key":"10.1016\/j.jbc.2026.111430_bib103","doi-asserted-by":"crossref","DOI":"10.3389\/fmolb.2022.842261","article-title":"Thinking outside the frame: impacting genomes capacity by programmed ribosomal frameshifting","volume":"9","author":"Riegger","year":"2022","journal-title":"Front. Mol. Biosci."},{"key":"10.1016\/j.jbc.2026.111430_bib104","series-title":"Modification and Editing of RNA","first-page":"517","article-title":"Importance of modified nucleotides in replication of retroviruses, plant pararetroviruses, and retrotransposons","volume":"28","author":"Marquet","year":"1998"},{"key":"10.1016\/j.jbc.2026.111430_bib105","doi-asserted-by":"crossref","first-page":"1834","DOI":"10.1128\/JVI.75.4.1834-1841.2001","article-title":"Maintenance of the Gag\/gag-Pol ratio is important for human immunodeficiency virus type 1 RNA dimerization and viral infectivity","volume":"75","author":"Shehu-Xhilaga","year":"2001","journal-title":"J. Virol."},{"key":"10.1016\/j.jbc.2026.111430_bib106","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/j.virol.2005.08.048","article-title":"Decreasing the frameshift efficiency translates into an equivalent reduction of the replication of the human immunodeficiency virus type 1","volume":"345","author":"Dulude","year":"2006","journal-title":"Virology"},{"key":"10.1016\/j.jbc.2026.111430_bib107","doi-asserted-by":"crossref","first-page":"1619","DOI":"10.1016\/j.cell.2014.04.041","article-title":"Programmed -1 frameshifting by kinetic partitioning during impeded translocation","volume":"157","author":"Caliskan","year":"2014","journal-title":"Cell"},{"key":"10.1016\/j.jbc.2026.111430_bib108","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1038\/nature13428","article-title":"Dynamic pathways of -1 translational frameshifting","volume":"512","author":"Chen","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.jbc.2026.111430_bib109","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1016\/0042-6822(89)90589-8","article-title":"Chromatographic analysis of the aminoacyl-tRNAs which are required for translation of codons at and around the ribosomal frameshift sites of HIV, HTLV-1, and BLV","volume":"173","author":"Hatfield","year":"1989","journal-title":"Virology"},{"key":"10.1016\/j.jbc.2026.111430_bib110","doi-asserted-by":"crossref","first-page":"4863","DOI":"10.1093\/emboj\/20.17.4863","article-title":"Improvement of reading frame maintenance is a common function for several tRNA modifications","volume":"20","author":"Urbonavicius","year":"2001","journal-title":"EMBO J."},{"key":"10.1016\/j.jbc.2026.111430_bib111","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1006\/viro.1998.9569","article-title":"Transfer RNA modification status influences retroviral ribosomal frameshifting","volume":"255","author":"Carlson","year":"1999","journal-title":"Virology"},{"key":"10.1016\/j.jbc.2026.111430_bib112","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1007\/s10059-000-0113-6","article-title":"Yeast asparagine (Asn) tRNA without Q base promotes eukaryotic frameshifting more efficiently than mammalian Asn tRNAs with or without Q base","volume":"10","author":"Carlson","year":"2000","journal-title":"Mol. Cells"},{"key":"10.1016\/j.jbc.2026.111430_bib113","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1016\/j.bbrc.2008.07.118","article-title":"Ribosomal frameshifting in response to hypomodified tRNAs in Xenopus oocytes","volume":"375","author":"Carlson","year":"2008","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"10.1016\/j.jbc.2026.111430_bib114","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1006\/jmbi.1999.3361","article-title":"The Q-base of asparaginyl-tRNA is dispensable for efficient -1 ribosomal frameshifting in eukaryotes","volume":"295","author":"Marczinke","year":"2000","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib115","doi-asserted-by":"crossref","first-page":"26026","DOI":"10.1074\/jbc.M703391200","article-title":"Role of a tRNA base modification and its precursors in frameshifting in eukaryotes","volume":"282","author":"Waas","year":"2007","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jbc.2026.111430_bib116","doi-asserted-by":"crossref","first-page":"20785","DOI":"10.1073\/pnas.2003358117","article-title":"Epigenetic loss of the transfer RNA-modifying enzyme TYW2 induces ribosome frameshifts in colon cancer","volume":"117","author":"Rossello-Tortella","year":"2020","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jbc.2026.111430_bib117","doi-asserted-by":"crossref","first-page":"5210","DOI":"10.1093\/nar\/gkz202","article-title":"Modulation of HIV-1 Gag\/gag-pol frameshifting by tRNA abundance","volume":"47","author":"Korniy","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.111430_bib118","doi-asserted-by":"crossref","first-page":"986","DOI":"10.1126\/science.2471265","article-title":"Prevention of translational frameshifting by the modified nucleoside 1-methylguanosine","volume":"244","author":"Bjork","year":"1989","journal-title":"Science"},{"key":"10.1016\/j.jbc.2026.111430_bib119","doi-asserted-by":"crossref","DOI":"10.1016\/j.jmb.2025.169095","article-title":"Connecting tRNA charging and decoding through the axis of nucleotide modifications at position 37","volume":"437","author":"Masuda","year":"2025","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib120","doi-asserted-by":"crossref","first-page":"7392","DOI":"10.1038\/s41467-025-62342-4","article-title":"An RNA modification prevents extended codon-anticodon interactions from facilitating +1 frameshifting","volume":"16","author":"Kimbrough","year":"2025","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jbc.2026.111430_bib121","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1006\/viro.2000.0692","article-title":"1-Methylguanosine in place of Y base at position 37 in phenylalanine tRNA is responsible for its shiftiness in retroviral ribosomal frameshifting","volume":"279","author":"Carlson","year":"2001","journal-title":"Virology"},{"key":"10.1016\/j.jbc.2026.111430_bib122","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1038\/msb.2011.101","article-title":"Competing pathways control host resistance to virus via tRNA modification and programmed ribosomal frameshifting","volume":"8","author":"Maynard","year":"2012","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib123","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1006\/jmbi.1993.1568","article-title":"A programmed translational frameshift is required for the synthesis of a bacteriophage \u03bb tail assembly protein","volume":"234","author":"Levin","year":"1993","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib124","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.02025-15","article-title":"Host RNA packaging by retroviruses: a newly synthesized story","volume":"7","author":"Eckwahl","year":"2016","journal-title":"mBio"},{"key":"10.1016\/j.jbc.2026.111430_bib125","doi-asserted-by":"crossref","DOI":"10.3389\/fcell.2022.768356","article-title":"Profiling selective packaging of host RNA and viral RNA modification in SARS-CoV-2 viral preparations","volume":"10","author":"Pena","year":"2022","journal-title":"Front. Cell Dev. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib126","doi-asserted-by":"crossref","first-page":"8697","DOI":"10.1038\/s41598-019-45079-1","article-title":"LC\/MS analysis and deep sequencing reveal the accurate RNA composition in the HIV-1 virion","volume":"9","author":"Simonova","year":"2019","journal-title":"Sci. Rep."},{"key":"10.1016\/j.jbc.2026.111430_bib127","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1261\/rna.1928110","article-title":"Profiling non-lysyl tRNAs in HIV-1","volume":"16","author":"Pavon-Eternod","year":"2010","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2026.111430_bib128","doi-asserted-by":"crossref","first-page":"5352","DOI":"10.1074\/jbc.REV118.002957","article-title":"Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication","volume":"294","author":"Jin","year":"2019","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jbc.2026.111430_bib129","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkaf114","article-title":"Structural basis for aminoacylation of cellular modified tRNALys3 by human lysyl-tRNA synthetase","volume":"53","author":"Devarkar","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.111430_bib130","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1093\/nar\/18.4.703","article-title":"Heterogeneities in vertebrate tRNAsTrp avian retroviruses package only as a primer the tRNATrp lacking modified m2G in positon 7","volume":"18","author":"Keith","year":"1990","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.111430_bib131","doi-asserted-by":"crossref","first-page":"92","DOI":"10.3390\/genes10020092","article-title":"RNA modifications modulate activation of innate toll-like receptors","volume":"10","author":"Freund","year":"2019","journal-title":"Genes (Basel)"},{"key":"10.1016\/j.jbc.2026.111430_bib132","doi-asserted-by":"crossref","first-page":"E4780","DOI":"10.1073\/pnas.1315996110","article-title":"Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes","volume":"110","author":"Burdick","year":"2013","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jbc.2026.111430_bib133","doi-asserted-by":"crossref","first-page":"5486","DOI":"10.1073\/pnas.1920631117","article-title":"HIV-1 uncoats in the nucleus near sites of integration","volume":"117","author":"Burdick","year":"2020","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jbc.2026.111430_bib134","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.64776","article-title":"HIV-1 Uncoating by release of viral cDNA from capsid-like structures in the nucleus of infected cells","volume":"10","author":"Muller","year":"2021","journal-title":"Elife"},{"key":"10.1016\/j.jbc.2026.111430_bib135","doi-asserted-by":"crossref","first-page":"2928","DOI":"10.1021\/acsnano.3c07678","article-title":"HIV-1 capsid uncoating is a multistep process that proceeds through defect formation followed by disassembly of the capsid lattice","volume":"18","author":"Gifford","year":"2024","journal-title":"ACS Nano"},{"key":"10.1016\/j.jbc.2026.111430_bib136","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.immuni.2005.06.008","article-title":"Suppression of RNA recognition by Toll-like receptors: the impact of nucleoside modification and the evolutionary origin of RNA","volume":"23","author":"Kariko","year":"2005","journal-title":"Immunity"},{"key":"10.1016\/j.jbc.2026.111430_bib137","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1084\/jem.20111044","article-title":"Identification of modifications in microbial, native tRNA that suppress immunostimulatory activity","volume":"209","author":"Gehrig","year":"2012","journal-title":"J. Exp. Med."},{"key":"10.1016\/j.jbc.2026.111430_bib138","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1084\/jem.20111075","article-title":"The 2'-O-methylation status of a single guanosine controls transfer RNA-mediated toll-like receptor 7 activation or inhibition","volume":"209","author":"Jockel","year":"2012","journal-title":"J. Exp. Med."},{"key":"10.1016\/j.jbc.2026.111430_bib139","doi-asserted-by":"crossref","first-page":"9764","DOI":"10.1093\/nar\/gky644","article-title":"Double methylation of tRNA-U54 to 2'-O-methylthymidine (Tm) synergistically decreases immune response by toll-like receptor 7","volume":"46","author":"Keller","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.111430_bib140","doi-asserted-by":"crossref","DOI":"10.1002\/cbic.202200281","article-title":"Honeybee Iflaviruses pack specific tRNA fragments from host cells in their virions","volume":"23","author":"Simonova","year":"2022","journal-title":"Chembiochem"},{"key":"10.1016\/j.jbc.2026.111430_bib141","doi-asserted-by":"crossref","first-page":"2349","DOI":"10.1038\/s41594-025-01653-y","article-title":"tRNA as an assembly chaperone for a macromolecular transcription-processing complex","volume":"32","author":"Bartuli","year":"2025","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib142","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.1016\/j.cell.2019.11.024","article-title":"Structural basis of poxvirus transcription: vaccinia RNA polymerase complexes","volume":"179","author":"Grimm","year":"2019","journal-title":"Cell"},{"key":"10.1016\/j.jbc.2026.111430_bib143","doi-asserted-by":"crossref","first-page":"8087","DOI":"10.1128\/jvi.71.11.8087-8095.1997","article-title":"Primer tRNAs for reverse transcription","volume":"71","author":"Mak","year":"1997","journal-title":"J. Virol."},{"key":"10.1016\/j.jbc.2026.111430_bib144","doi-asserted-by":"crossref","first-page":"213","DOI":"10.3390\/v2010213","article-title":"Initiation of HIV reverse transcription","volume":"2","author":"Isel","year":"2010","journal-title":"Viruses"},{"key":"10.1016\/j.jbc.2026.111430_bib145","doi-asserted-by":"crossref","first-page":"4251","DOI":"10.1128\/JVI.73.5.4251-4256.1999","article-title":"The human immunodeficiency virus type 1 gag polyprotein has nucleic acid chaperone activity: possible role in dimerization of genomic RNA and placement of tRNA on the primer binding site","volume":"73","author":"Feng","year":"1999","journal-title":"J. Virol."},{"key":"10.1016\/j.jbc.2026.111430_bib146","doi-asserted-by":"crossref","first-page":"17488","DOI":"10.1074\/jbc.M501310200","article-title":"A HIV-1 minimal gag protein is superior to nucleocapsid at in vitro annealing and exhibits multimerization-induced inhibition of reverse transcription","volume":"280","author":"Roldan","year":"2005","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jbc.2026.111430_bib147","doi-asserted-by":"crossref","first-page":"1594","DOI":"10.1128\/JVI.01809-10","article-title":"Matrix domain modulates HIV-1 Gag's nucleic acid chaperone activity via inositol phosphate binding","volume":"85","author":"Jones","year":"2011","journal-title":"J. Virol."},{"key":"10.1016\/j.jbc.2026.111430_bib148","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1016\/j.virusres.2012.06.006","article-title":"Initiation of HIV-1 reverse transcription and functional role of nucleocapsid-mediated tRNA\/viral genome interactions","volume":"169","author":"Sleiman","year":"2012","journal-title":"Virus. Res."},{"key":"10.1016\/j.jbc.2026.111430_bib149","series-title":"Fine-Tuning of RNA Functions by Modification and Editing","first-page":"401","article-title":"Transfer RNA modifications and DNA editing in HIV-1 reverse transcription","volume":"59","author":"Marquet","year":"2005"},{"key":"10.1016\/j.jbc.2026.111430_bib150","doi-asserted-by":"crossref","first-page":"2464","DOI":"10.1128\/jvi.66.4.2464-2472.1992","article-title":"Interaction between retroviral U5 RNA and the T4C loop of the tRNATrP primer is required for efficient initiation of reverse transcription","volume":"66","author":"Aiyar","year":"1992","journal-title":"J. Virol."},{"key":"10.1016\/j.jbc.2026.111430_bib151","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1038\/s41586-018-0055-9","article-title":"Architecture of an HIV-1 reverse transcriptase initiation complex","volume":"557","author":"Larsen","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.jbc.2026.111430_bib152","doi-asserted-by":"crossref","first-page":"1818","DOI":"10.1128\/JVI.73.3.1818-1827.1999","article-title":"Genetic analysis of a unique human immunodeficiency virus type 1 (HIV-1) with a primer binding site complementary to tRNAMet supports a role for U5-PBS stem-loop RNA structures in initiation of HIV-1 reverse transcription","volume":"73","author":"Kang","year":"1999","journal-title":"J. Virol."},{"key":"10.1016\/j.jbc.2026.111430_bib153","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1002\/j.1460-2075.1996.tb00426.x","article-title":"Specific initiation and switch to elongation of human immunodeficiency virus type 1 reverse transcription require the post-transcriptional modifications of primer tRNA3Lys","volume":"15","author":"Isel","year":"1996","journal-title":"EMBO J."},{"key":"10.1016\/j.jbc.2026.111430_bib154","doi-asserted-by":"crossref","first-page":"25269","DOI":"10.1016\/S0021-9258(19)74387-7","article-title":"Modified nucleotides of tRNALys3 modulate primer\/template loop-loop interaction in the initiation complex of HIV-1 reverse transcription","volume":"268","author":"Isel","year":"1993","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jbc.2026.111430_bib155","doi-asserted-by":"crossref","first-page":"4700","DOI":"10.1128\/jvi.70.7.4700-4706.1996","article-title":"Effects of modifying the tRNA3Lys anticodon on the initiation of human immunodeficiency virus type 1 reverse transcription","volume":"70","author":"Huang","year":"1996","journal-title":"J. Virol."},{"key":"10.1016\/j.jbc.2026.111430_bib156","doi-asserted-by":"crossref","first-page":"21309","DOI":"10.1074\/jbc.273.33.21309","article-title":"Mechanistic studies of early pausing events during initiation of HIV-1 reverse transcription","volume":"273","author":"Liang","year":"1998","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jbc.2026.111430_bib157","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1128\/jvi.70.2.966-975.1996","article-title":"Construction of a type 1 human immunodeficiency virus that maintains a primer binding site complementary to tRNAHis","volume":"70","author":"Wakefield","year":"1996","journal-title":"J. Virol."},{"key":"10.1016\/j.jbc.2026.111430_bib158","doi-asserted-by":"crossref","first-page":"14302","DOI":"10.1021\/ja028015f","article-title":"An RNA complex of the HIV-1 A-loop and tRNA(Lys,3) is stabilized by nucleoside modifications","volume":"124","author":"Bajji","year":"2002","journal-title":"J. Am. Chem. Soc."},{"key":"10.1016\/j.jbc.2026.111430_bib159","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1017\/S1355838200000947","article-title":"NMR and biochemical characterization of recombinant human tRNA3Lys expressed in Escherichia coli: identification of posttranscriptional nucleotide modifications required for efficient initiation of HIV-1 reverse transcription","volume":"6","author":"Tisne","year":"2000","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2026.111430_bib160","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1016\/j.jmb.2011.04.025","article-title":"Functional recognition of the modified human tRNALys3(UUU) anticodon domain by HIV's nucleocapsid protein and a peptide mimic","volume":"410","author":"Graham","year":"2011","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib161","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1021\/bi401174h","article-title":"Amino acid signature enables proteins to recognize modified tRNA","volume":"53","author":"Spears","year":"2014","journal-title":"Biochemistry"},{"key":"10.1016\/j.jbc.2026.111430_bib162","doi-asserted-by":"crossref","first-page":"31247","DOI":"10.1074\/jbc.M102441200","article-title":"Initiation of HIV-1 reverse transcription is regulated by a primer activation signal","volume":"276","author":"Beerens","year":"2001","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jbc.2026.111430_bib163","doi-asserted-by":"crossref","first-page":"2227","DOI":"10.1128\/JVI.74.5.2227-2238.2000","article-title":"A structured RNA motif is involved in correct placement of the tRNA3Lys primer onto the human immunodeficiency virus genome","volume":"74","author":"Beerens","year":"2000","journal-title":"J. Virol."},{"key":"10.1016\/j.jbc.2026.111430_bib164","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0064700","article-title":"The interaction between tRNA(Lys) 3 and the primer activation signal deciphered by NMR spectroscopy","volume":"8","author":"Sleiman","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.jbc.2026.111430_bib165","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1038\/nsmb.3270","article-title":"m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of hoogsteen base pairs","volume":"23","author":"Zhou","year":"2016","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib166","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1006\/jmbi.1997.1487","article-title":"Modified nucleotides of tRNAPro restrict interactions in the binary primer\/template complex of M-MuLV","volume":"275","author":"Fosse","year":"1998","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib167","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a006882","article-title":"HIV-1 reverse transcription","volume":"2","author":"Hu","year":"2012","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"10.1016\/j.jbc.2026.111430_bib168","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.virusres.2007.12.017","article-title":"Strand transfer events during HIV-1 reverse transcription","volume":"134","author":"Basu","year":"2008","journal-title":"Virus. Res."},{"key":"10.1016\/j.jbc.2026.111430_bib169","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/0092-8674(79)90357-X","article-title":"A detailed model of reverse transcription and tests of crucial aspects","volume":"18","author":"Gilboa","year":"1979","journal-title":"Cell"},{"key":"10.1016\/j.jbc.2026.111430_bib170","doi-asserted-by":"crossref","first-page":"4412","DOI":"10.1074\/jbc.274.7.4412","article-title":"Role of post-transcriptional modifications of primer tRNALys,3 in the fidelity and efficacy of plus strand DNA transfer during HIV-1 reverse transcription","volume":"274","author":"Auxilien","year":"1999","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jbc.2026.111430_bib171","doi-asserted-by":"crossref","first-page":"3946","DOI":"10.1093\/nar\/gkg448","article-title":"Importance of the reverse hoogsteen base pair 54-58 for tRNA function","volume":"31","author":"Zagryadskaya","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.111430_bib172","doi-asserted-by":"crossref","first-page":"3650","DOI":"10.1101\/gad.12.23.3650","article-title":"The essential Gcd10p\u2013Gcd14p nuclear complex is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA","volume":"12","author":"Anderson","year":"1998","journal-title":"Genes Dev."},{"key":"10.1016\/j.jbc.2026.111430_bib173","doi-asserted-by":"crossref","first-page":"1281","DOI":"10.1261\/rna.5040605","article-title":"The bipartite structure of the tRNA m1A58 methyltransferase from S. cerevisiae is conserved in humans","volume":"11","author":"Ozanick","year":"2005","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2026.111430_bib174","doi-asserted-by":"crossref","first-page":"4794","DOI":"10.1128\/JVI.73.6.4794-4805.1999","article-title":"Molecular requirements for human immunodeficiency virus type 1 plus-strand transfer: analysis in reconstituted and endogenous reverse transcription systems","volume":"73","author":"Wu","year":"1999","journal-title":"J. Virol."},{"key":"10.1016\/j.jbc.2026.111430_bib175","doi-asserted-by":"crossref","first-page":"7210","DOI":"10.1073\/pnas.94.14.7210","article-title":"Posttranscriptional modification of retroviral primers is required for late stages ofDNA replication","volume":"94","author":"Burnett","year":"1997","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jbc.2026.111430_bib176","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1006\/jmbi.2001.5205","article-title":"The HIV plus-strand transfer reaction: determination of replication-competent intermediates and identification of a novel lentiviral element, the primer over-extension sequence","volume":"315","author":"Muthuswami","year":"2002","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib177","doi-asserted-by":"crossref","first-page":"11855","DOI":"10.1093\/nar\/gkab879","article-title":"Cooperative methylation of human tRNA3Lys at positions A58 and U54 drives the early and late steps of HIV-1 replication","volume":"49","author":"Fukuda","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.111430_bib178","doi-asserted-by":"crossref","first-page":"9671","DOI":"10.1128\/JVI.75.20.9671-9678.2001","article-title":"Mutation of the methylated tRNA(Lys)(3) residue A58 disrupts reverse transcription and inhibits replication of human immunodeficiency virus type 1","volume":"75","author":"Renda","year":"2001","journal-title":"J. Virol."},{"key":"10.1016\/j.jbc.2026.111430_bib179","first-page":"429","article-title":"Advances in the structural and functional understanding of m(1)A RNA modification","volume":"57","author":"Smoczynski","year":"2024","journal-title":"Acc. Chem. Res."},{"key":"10.1016\/j.jbc.2026.111430_bib180","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2401743121","article-title":"Conserved 5-methyluridine tRNA modification modulates ribosome translocation","volume":"121","author":"Jones","year":"2024","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jbc.2026.111430_bib181","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.91168.3","article-title":"Recognition and cleavage of human tRNA methyltransferase TRMT1 by the SARS-CoV-2 main protease","volume":"12","author":"D'Oliviera","year":"2025","journal-title":"eLife"},{"key":"10.1016\/j.jbc.2026.111430_bib182","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.90316.3","article-title":"Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease","volume":"12","author":"Zhang","year":"2024","journal-title":"elife"},{"key":"10.1016\/j.jbc.2026.111430_bib183","doi-asserted-by":"crossref","DOI":"10.1093\/jmcb\/mjad024","article-title":"SARS-CoV-2 main protease Nsp5 cleaves and inactivates human tRNA methyltransferase TRMT1","volume":"15","author":"Lu","year":"2023","journal-title":"J. Mol. Cell Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib184","doi-asserted-by":"crossref","first-page":"9523","DOI":"10.3390\/ijms21249523","article-title":"Identification of host cellular protein substrates of SARS-COV-2 Main Protease","volume":"21","author":"Miczi","year":"2020","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.jbc.2026.111430_bib185","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1016\/j.chom.2008.10.004","article-title":"Genome-scale RNAi screen for host factors required for HIV replication","volume":"4","author":"Zhou","year":"2008","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.jbc.2026.111430_bib186","doi-asserted-by":"crossref","first-page":"2238","DOI":"10.1099\/vir.0.022210-0","article-title":"Comparison of U2OS and Huh-7 cells for identifying host factors that affect hepatitis C virus RNA replication","volume":"91","author":"Jones","year":"2010","journal-title":"J. Gen. Virol."},{"key":"10.1016\/j.jbc.2026.111430_bib187","doi-asserted-by":"crossref","first-page":"57","DOI":"10.3390\/v15010057","article-title":"Parent tRNA modification status determines the induction of functional tRNA-Derived RNA by respiratory syncytial virus infection","volume":"15","author":"Choi","year":"2022","journal-title":"Viruses"},{"key":"10.1016\/j.jbc.2026.111430_bib188","doi-asserted-by":"crossref","first-page":"1622","DOI":"10.1038\/mt.2015.124","article-title":"Respiratory syncytial virus utilizes a tRNA fragment to suppress antiviral responses through a novel targeting mechanism","volume":"23","author":"Deng","year":"2015","journal-title":"Mol. Ther."},{"key":"10.1016\/j.jbc.2026.111430_bib189","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1038\/mt.2012.237","article-title":"Identification and functional characterization of tRNA-derived RNA fragments (tRFs) in respiratory syncytial virus infection","volume":"21","author":"Wang","year":"2013","journal-title":"Mol. Ther."},{"key":"10.1016\/j.jbc.2026.111430_bib190","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1099\/jgv.0.000852","article-title":"Identification of two novel functional tRNA-derived fragments induced in response to respiratory syncytial virus infection","volume":"98","author":"Zhou","year":"2017","journal-title":"J. Gen. Virol."},{"key":"10.1016\/j.jbc.2026.111430_bib191","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1038\/s41580-023-00690-z","article-title":"Roles and regulation of tRNA-derived small RNAs in animals","volume":"25","author":"Muthukumar","year":"2024","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib192","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1002\/wrna.42","article-title":"Viral tRNAs and tRNA-like structures","volume":"1","author":"Dreher","year":"2010","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"10.1016\/j.jbc.2026.111430_bib193","doi-asserted-by":"crossref","first-page":"180","DOI":"10.3390\/v11020180","article-title":"Global in-silico scenario of tRNA genes and their organization in virus genomes","volume":"11","author":"Morgado","year":"2019","journal-title":"Viruses"},{"key":"10.1016\/j.jbc.2026.111430_bib194","doi-asserted-by":"crossref","first-page":"1486","DOI":"10.1101\/gr.6649807","article-title":"Causes for the intriguing presence of tRNAs in phages","volume":"17","author":"Bailly-Bechet","year":"2007","journal-title":"Genome Res."},{"key":"10.1016\/j.jbc.2026.111430_bib195","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1016\/j.cels.2021.05.019","article-title":"Degradation of host translational machinery drives tRNA acquisition in viruses","volume":"12","author":"Yang","year":"2021","journal-title":"Cell Syst."},{"key":"10.1016\/j.jbc.2026.111430_bib196","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1006\/viro.1999.9949","article-title":"Aminoacylation of tRNAs encoded by chlorella virus CVK2","volume":"263","author":"Nishida","year":"1999","journal-title":"Virology"},{"key":"10.1016\/j.jbc.2026.111430_bib197","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1126\/science.aal4657","article-title":"Giant viruses with an expanded complement of translation system components","volume":"356","author":"Schulz","year":"2017","journal-title":"Science"},{"key":"10.1016\/j.jbc.2026.111430_bib198","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1038\/s41467-018-03168-1","article-title":"Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere","volume":"9","author":"Abrahao","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jbc.2026.111430_bib199","doi-asserted-by":"crossref","first-page":"5089","DOI":"10.1111\/febs.16070","article-title":"tRNA-like structures and their functions","volume":"289","author":"Wu","year":"2022","journal-title":"FEBS J."},{"key":"10.1016\/j.jbc.2026.111430_bib200","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1016\/0005-2787(78)90238-1","article-title":"In vitro methylation of tobacco mosaic virus RNA with ribothymidine-forming tRNA methyltransferase of Escherichia coli","volume":"520","author":"Lesiewicz","year":"1978","journal-title":"Biochim. Biophys. Acta"},{"key":"10.1016\/j.jbc.2026.111430_bib201","doi-asserted-by":"crossref","first-page":"798","DOI":"10.1016\/0006-291X(75)90393-9","article-title":"Methylation of TMV RNA","volume":"62","author":"Marcu","year":"1975","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"10.1016\/j.jbc.2026.111430_bib202","doi-asserted-by":"crossref","first-page":"3991","DOI":"10.1093\/nar\/26.17.3991","article-title":"Pseudouridine and ribothymidine formation in the tRNA-like domain of turnip yellow mosaic virus RNA","volume":"26","author":"Becker","year":"1998","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.111430_bib203","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1111\/j.1432-1033.1977.tb11270.x","article-title":"Studies on the sequence of the 3'-terminal region of turnip-yellow-mosaic-virus RNA","volume":"72","author":"Silberklang","year":"1977","journal-title":"Eur. J. Biochem."},{"key":"10.1016\/j.jbc.2026.111430_bib204","first-page":"1662","article-title":"The brome mosaic virus RNA3 intergenic replication enhancer folds to mimic a tRNA TCC-stem loop and is modified in vivo","volume":"7","author":"Baumstark","year":"2001","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2026.111430_bib205","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1016\/S0968-0004(99)01525-X","article-title":"Anticodon nucleases","volume":"25","author":"Kaufmann","year":"2000","journal-title":"Trends Biochem. Sci."},{"key":"10.1016\/j.jbc.2026.111430_bib206","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1002\/wrna.99","article-title":"RNA toxins: mediators of stress adaptation and pathogen defense","volume":"2","author":"Zhabokritsky","year":"2011","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"10.1016\/j.jbc.2026.111430_bib207","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1007\/s00253-012-4349-9","article-title":"Anticodon nuclease encoding virus-like elements in yeast","volume":"96","author":"Satwika","year":"2012","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"10.1016\/j.jbc.2026.111430_bib208","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1006\/jmbi.2000.4282","article-title":"Specific interaction between anticodon nuclease and the tRNA(Lys) wobble base","volume":"305","author":"Jiang","year":"2001","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib209","doi-asserted-by":"crossref","first-page":"3836","DOI":"10.1074\/jbc.M110072200","article-title":"Structural features of tRNALys favored by anticodon nuclease as inferred from reactivities of anticodon stem and loop substrate analogs","volume":"277","author":"Jiang","year":"2002","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jbc.2026.111430_bib210","article-title":"Human SAMD9 is a poxvirus-activatable anticodon nuclease inhibiting codon-specific protein synthesis","volume":"9","author":"Zhang","year":"2023","journal-title":"Sci. Adv."},{"key":"10.1016\/j.jbc.2026.111430_bib211","doi-asserted-by":"crossref","first-page":"1383","DOI":"10.1002\/j.1460-2075.1990.tb08253.x","article-title":"The optional E.coli prr locus encodes a latent form of phage T4-induced anticodon nuclease","volume":"9","author":"Levitz","year":"1990","journal-title":"EMBO J."},{"key":"10.1016\/j.jbc.2026.111430_bib212","doi-asserted-by":"crossref","first-page":"1660","DOI":"10.1261\/rna.062000.117","article-title":"Rapid RNase L-driven arrest of protein synthesis in the dsRNA response without degradation of translation machinery","volume":"23","author":"Donovan","year":"2017","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2026.111430_bib213","doi-asserted-by":"crossref","first-page":"e02201","DOI":"10.1128\/JVI.02201-16","article-title":"Lineage A Betacoronavirus NS2 proteins and the homologous Torovirus Berne pp1a carboxy-terminal domain are phosphodiesterases that antagonize activation of RNase L","volume":"91","author":"Goldstein","year":"2017","journal-title":"J. Virol."},{"key":"10.1016\/j.jbc.2026.111430_bib214","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1000602","article-title":"RNase L mediated protection from virus induced demyelination","volume":"5","author":"Ireland","year":"2009","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.jbc.2026.111430_bib215","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1261\/rna.080419.125","article-title":"RNase L produces tRNA-derived RNAs that contribute to translation inhibition","volume":"31","author":"Takenaka","year":"2025","journal-title":"RNA"},{"key":"10.1016\/j.jbc.2026.111430_bib216","doi-asserted-by":"crossref","DOI":"10.1016\/j.jmb.2024.168934","article-title":"Studying the function of tRNA modifications: experimental challenges and opportunities","volume":"437","author":"Kompatscher","year":"2025","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib217","doi-asserted-by":"crossref","DOI":"10.3389\/fcell.2022.886642","article-title":"tRNA function and dysregulation in cancer","volume":"10","author":"Gupta","year":"2022","journal-title":"Front. Cell Dev. Biol."},{"key":"10.1016\/j.jbc.2026.111430_bib218","doi-asserted-by":"crossref","first-page":"1397","DOI":"10.1016\/j.neuron.2024.01.028","article-title":"Cell-type-specific expression of tRNAs in the brain regulates cellular homeostasis","volume":"112","author":"Kapur","year":"2024","journal-title":"Neuron"},{"key":"10.1016\/j.jbc.2026.111430_bib219","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1006264","article-title":"Tissue- and time-specific expression of otherwise identical tRNA genes","volume":"12","author":"Sagi","year":"2016","journal-title":"PLoS Genet."},{"key":"10.1016\/j.jbc.2026.111430_bib220","doi-asserted-by":"crossref","first-page":"16642","DOI":"10.1021\/acsnano.1c06488","article-title":"Direct nanopore sequencing of individual full length tRNA strands","volume":"15","author":"Thomas","year":"2021","journal-title":"ACS Nano"},{"key":"10.1016\/j.jbc.2026.111430_bib221","article-title":"Comparative analysis of 43 distinct RNA modifications by nanopore tRNA sequencing","author":"White","year":"2024","journal-title":"bioRxiv"},{"key":"10.1016\/j.jbc.2026.111430_bib222","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1038\/s41587-023-01743-6","article-title":"Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing","volume":"42","author":"Lucas","year":"2024","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.jbc.2026.111430_bib223","doi-asserted-by":"crossref","first-page":"12074","DOI":"10.1093\/nar\/gkae796","article-title":"Combining nanopore direct RNA sequencing with molecular genetics and mass spectrometry for analysis of T-loop base modifications across 42 yeast tRNA isoacceptors","volume":"52","author":"Shaw","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jbc.2026.111430_bib224","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1038\/s41467-025-56348-1","article-title":"Genome-wide profiling of tRNA modifications by Induro-tRNAseq reveals coordinated changes","volume":"16","author":"Nakano","year":"2025","journal-title":"Nat. Commun."}],"container-title":["Journal of Biological Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0021925826003005?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0021925826003005?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T07:31:17Z","timestamp":1787643077000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0021925826003005"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6]]},"references-count":224,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2026,6]]}},"alternative-id":["S0021925826003005"],"URL":"https:\/\/doi.org\/10.1016\/j.jbc.2026.111430","relation":{},"ISSN":["0021-9258"],"issn-type":[{"value":"0021-9258","type":"print"}],"subject":[],"published":{"date-parts":[[2026,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"tRNA modifications in viral replication","name":"articletitle","label":"Article Title"},{"value":"Journal of Biological Chemistry","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jbc.2026.111430","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier Inc on behalf of American Society for Biochemistry and Molecular Biology.","name":"copyright","label":"Copyright"}],"article-number":"111430"}}