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This parasite undergoes drastic changes in its morphology and metabolism between infective and noninfective forms through global remodeling of its proteome. Chemical modification of tRNA (tRNA modification) contributes to the control of protein expression by modulating the codon decoding process. However, knowledge of tRNA modification profiles, the enzymes that create modifications and their regulation in different cellular conditions is largely restricted to relatively few model organisms. Here, we profile tRNA modifications in both infective and noninfective forms of\n                    <jats:italic>T. cruzi<\/jats:italic>\n                    \u00a0to probe their dynamic changes. Genome mining of tRNA modifying enzymes identified 65 putative tRNA-modifying enzymes in\n                    <jats:italic>T. cruzi<\/jats:italic>\n                    for 27 species of tRNA modifications, most of which were detected in\n                    <jats:italic>T. cruzi<\/jats:italic>\n                    tRNA by liquid chromatography mass spectrometry analyses. tRNA sequencing detected reverse transcription-derived signatures at 170 sites in\n                    <jats:italic>T. cruzi<\/jats:italic>\n                    tRNAs that are likely derived from 19 tRNA modifications. tRNA modifications and tRNA modification enzymes are differentially modulated across the life stages of\n                    <jats:italic>T. cruzi.<\/jats:italic>\n                    We found that hydroxywybutosine (OHyW) at position 37 on tRNA\n                    <jats:sup>Phe(GAA)<\/jats:sup>\n                    had a reduced level in the infective form (metacyclic trypomastigote) and the associated modification enzyme Tyw1a exhibited reduced expression in this stage. Knockout of Tyw1a increased the differentiation from epimastigote (noninfective form) to metacyclic trypomastigote, suggesting that changes in OHyW37 modification levels alter the rate of metacyclogenesis. Overall, our findings suggest that tRNA modification changes during the life stages of\n                    <jats:italic>T. cruzi<\/jats:italic>\n                    contribute to the differentiation of this parasite.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1014249","type":"journal-article","created":{"date-parts":[[2026,5,26]],"date-time":"2026-05-26T17:39:28Z","timestamp":1779817168000},"page":"e1014249","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["Remodeling of tRNA modification in Trypanosoma cruzi life forms"],"prefix":"10.1371","volume":"22","author":[{"given":"Herbert Guimaraes de Sousa","family":"Silva","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janaina de Freitas","family":"Nascimento","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marilene Souza","family":"Braga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana Paula de Jesus","family":"Menezes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ariel M.","family":"Silber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew K.","family":"Waldor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia Pinheiro Chagas","family":"da Cunha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3555-5877","authenticated-orcid":true,"given":"Satoshi","family":"Kimura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,5,26]]},"reference":[{"key":"ppat.1014249.ref001","author":"World Health Organization","year":"2024"},{"issue":"1","key":"ppat.1014249.ref002","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1186\/s13071-018-2664-4","article-title":"Revisiting the Trypanosoma cruzi metacyclogenesis: morphological and ultrastructural analyses during cell differentiation","volume":"11","author":"CS Gon\u00e7alves","year":"2018","journal-title":"Parasit Vectors"},{"issue":"1","key":"ppat.1014249.ref003","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/s13072-022-00450-x","article-title":"Open chromatin analysis in Trypanosoma cruzi life forms highlights critical differences in genomic compartments and developmental regulation at tDNA loci","volume":"15","author":"ARJ Lima","year":"2022","journal-title":"Epigenetics Chromatin"},{"key":"ppat.1014249.ref004","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.8947","article-title":"Transcriptomic changes across the life cycle of Trypanosoma cruzi II","volume":"8","author":"L Cruz-Saavedra","year":"2020","journal-title":"PeerJ"},{"key":"ppat.1014249.ref005","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.3017","article-title":"Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition in Trypanosoma cruzi","volume":"5","author":"L Bern\u00e1","year":"2017","journal-title":"PeerJ"},{"issue":"8","key":"ppat.1014249.ref006","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1016\/j.pt.2023.05.010","article-title":"Navigating the boundaries between metabolism and epigenetics in trypanosomes","volume":"39","author":"AP Menezes","year":"2023","journal-title":"Trends Parasitol"},{"issue":"1","key":"ppat.1014249.ref007","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1186\/s12864-015-1563-8","article-title":"Ribosome profiling reveals translation control as a key mechanism generating differential gene expression in Trypanosoma cruzi","volume":"16","author":"P Smircich","year":"2015","journal-title":"BMC Genomics"},{"key":"ppat.1014249.ref008","doi-asserted-by":"crossref","first-page":"27","DOI":"10.3389\/fcimb.2020.00027","article-title":"The influence of environmental cues on the development of Trypanosoma cruzi in Triatominae vector","volume":"10","author":"FP Melo R de","year":"2020","journal-title":"Front Cell Infect Microbiol"},{"issue":"5","key":"ppat.1014249.ref009","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1111\/mmi.14621","article-title":"Signaling pathways involved in environmental sensing in Trypanosoma cruzi","volume":"115","author":"N Lander","year":"2021","journal-title":"Mol Microbiol"},{"issue":"3","key":"ppat.1014249.ref010","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/j.resmic.2014.01.006","article-title":"Dealing with environmental challenges: mechanisms of adaptation in Trypanosoma cruzi","volume":"165","author":"V Jimenez","year":"2014","journal-title":"Res 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Trypanosoma brucei","volume":"278","author":"JS Krog","year":"2011","journal-title":"FEBS J"},{"key":"ppat.1014249.ref030","first-page":"55","article-title":"Discovering RNA modification enzymes using a comparative genomics approach","author":"S Kimura","year":"2023"},{"issue":"19","key":"ppat.1014249.ref031","doi-asserted-by":"crossref","first-page":"3756","DOI":"10.1093\/nar\/24.19.3756","article-title":"Identification of new RNA modifying enzymes by iterative genome search using known modifying enzymes as probes","volume":"24","author":"C Gustafsson","year":"1996","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"ppat.1014249.ref032","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1038\/s41589-020-0558-1","article-title":"Comparative tRNA sequencing and RNA mass spectrometry for surveying tRNA modifications","volume":"16","author":"S Kimura","year":"2020","journal-title":"Nat Chem Biol"},{"issue":"5733","key":"ppat.1014249.ref033","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1126\/science.1112181","article-title":"Comparative genomics of Trypanosomatid parasitic protozoa","volume":"309","author":"NM El-Sayed","year":"2005","journal-title":"Science"},{"issue":"1","key":"ppat.1014249.ref034","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1590\/S1415-47572012005000008","article-title":"Trypanosomatid comparative genomics: contributions to the study of parasite biology and different parasitic diseases","volume":"35","author":"SM Teixeira","year":"2012","journal-title":"Genet Mol Biol"},{"issue":"6","key":"ppat.1014249.ref035","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1101\/gr.115089.110","article-title":"High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome","volume":"21","author":"S Alsford","year":"2011","journal-title":"Genome Res"},{"issue":"2","key":"ppat.1014249.ref036","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.pt.2016.10.009","article-title":"TrypTag.org: a trypanosome genome-wide protein localisation resource","volume":"33","author":"S Dean","year":"2017","journal-title":"Trends Parasitol"},{"key":"ppat.1014249.ref037","article-title":"tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa","author":"J Sun","year":"2024","journal-title":"bioRxiv"},{"key":"ppat.1014249.ref038","article-title":"tModBase: deciphering the landscape of tRNA modifications and their dynamic changes from epitranscriptome data","volume":"51","author":"H-T Lei","year":"2023","journal-title":"Nucleic Acids Res"},{"issue":"17","key":"ppat.1014249.ref039","doi-asserted-by":"crossref","first-page":"4212","DOI":"10.1002\/j.1460-2075.1995.tb00095.x","article-title":"tRNAs are imported into mitochondria of Trypanosoma brucei independently of their genomic context and genetic origin","volume":"14","author":"R Hauser","year":"1995","journal-title":"EMBO J"},{"issue":"8","key":"ppat.1014249.ref040","doi-asserted-by":"crossref","first-page":"2547","DOI":"10.1091\/mbc.10.8.2547","article-title":"tRNAs and proteins are imported into mitochondria of Trypanosoma brucei by two distinct mechanisms","volume":"10","author":"CE Nabholz","year":"1999","journal-title":"Mol Biol Cell"},{"key":"ppat.1014249.ref041","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1080\/15476286.2021.1940445","article-title":"A mitochondrial cytidine deaminase is responsible for C to U editing of tRNATrp to decode the UGA codon in Trypanosoma brucei","volume":"18","author":"Z Paris","year":"2021","journal-title":"RNA Biol"},{"issue":"12","key":"ppat.1014249.ref042","doi-asserted-by":"crossref","first-page":"7401","DOI":"10.1093\/nar\/gkx354","article-title":"ALKBH1 is an RNA dioxygenase responsible for cytoplasmic and mitochondrial tRNA 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Ebhardt","year":"2009","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"ppat.1014249.ref052","article-title":"General principles for the detection of modified nucleotides in RNA by specific reagents","volume":"5","author":"M Helm","year":"2021","journal-title":"Adv Biol"},{"issue":"1","key":"ppat.1014249.ref053","doi-asserted-by":"crossref","DOI":"10.1128\/mra.00579-24","article-title":"The Trypanosoma brucei tRNA methylome","volume":"14","author":"KT Militello","year":"2025","journal-title":"Microbiol Resour Announc"},{"issue":"10","key":"ppat.1014249.ref054","doi-asserted-by":"crossref","first-page":"1559","DOI":"10.1038\/s41587-023-02034-w","article-title":"Ultrafast bisulfite sequencing detection of 5-methylcytosine in DNA and RNA","volume":"42","author":"Q Dai","year":"2024","journal-title":"Nat Biotechnol"},{"key":"ppat.1014249.ref055","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.ymeth.2018.10.011","article-title":"Misincorporation signatures for detecting modifications in mRNA: not as simple as it sounds","volume":"156","author":"A Sas-Chen","year":"2019","journal-title":"Methods"},{"key":"ppat.1014249.ref056","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkad1083","article-title":"MODOMICS: a database of RNA modifications and related information. 2023 update","volume":"52","author":"A Cappannini","year":"2024","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"ppat.1014249.ref057","doi-asserted-by":"crossref","first-page":"2620","DOI":"10.1021\/bi00709a023","article-title":"3-(3-Amino-3-carboxypropyl)uridine: a novel modified nucleoside isolated from Escherichia coli phenylalanine transfer ribonucleic acid","volume":"13","author":"Z Ohashi","year":"1974","journal-title":"Biochemistry"},{"issue":"14","key":"ppat.1014249.ref058","doi-asserted-by":"crossref","first-page":"2932","DOI":"10.1021\/bi00711a024","article-title":"3-(3-amino-3-carboxy-n-propyl)uridine. 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