{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T04:19:22Z","timestamp":1787026762060,"version":"build-2736575974"},"reference-count":85,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,3,13]],"date-time":"2024-03-13T00:00:00Z","timestamp":1710288000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    Transfer RNA (tRNA) modifications play a crucial role in maintaining translational fidelity and efficiency, and they may function as regulatory elements in stress response and virulence. Despite their pivotal roles, a comprehensive mapping of tRNA modifications and their associated synthesis genes is still limited, with a predominant focus on free-living bacteria. In this study, we employed a multidisciplinary approach, incorporating comparative genomics, mass spectrometry, and next-generation sequencing, to predict the set of tRNA modification genes responsible for tRNA maturation in two intracellular pathogens\u2014\n                    <jats:italic>Bartonella henselae<\/jats:italic>\n                    Houston I and\n                    <jats:italic>Bartonella quintana<\/jats:italic>\n                    Toulouse, which are causative agents of cat-scratch disease and trench fever, respectively. This analysis presented challenges, particularly because of host RNA contamination, which served as a potential source of error. However, our approach predicted 26 genes responsible for synthesizing 23 distinct tRNA modifications in\n                    <jats:italic>B. henselae<\/jats:italic>\n                    and 22 genes associated with 23 modifications in\n                    <jats:italic>B. quintana<\/jats:italic>\n                    . Notably, akin to other intracellular and symbiotic bacteria, both Bartonella species have undergone substantial reductions in tRNA modification genes, mostly by simplifying the hypermodifications present at positions 34 and 37.\n                    <jats:italic>Bartonella quintana<\/jats:italic>\n                    exhibited the additional loss of four modifications and these were linked to examples of gene decay, providing snapshots of reductive evolution.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2024.1369018","type":"journal-article","created":{"date-parts":[[2024,3,13]],"date-time":"2024-03-13T00:52:27Z","timestamp":1710291147000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":13,"title":["Mapping the tRNA modification landscape of Bartonella henselae Houston I and Bartonella quintana Toulouse"],"prefix":"10.3389","volume":"15","author":[{"given":"Samia","family":"Quaiyum","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingjing","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Virginie","family":"Marchand","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guangxin","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Colbie J.","family":"Reed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuri","family":"Motorin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter C.","family":"Dedon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael F.","family":"Minnick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Val\u00e9rie","family":"de Cr\u00e9cy-Lagard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2024,3,13]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.1016\/S0040-4039(00)02191-2","article-title":"Facile methods for the synthesis of 5-formylcytidine","volume":"42","author":"Abdel Rahman","year":"2001","journal-title":"Tetrahedron Lett."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"22327","DOI":"10.1074\/jbc.M116.747865","article-title":"Pseudouridine in the anticodon of Escherichia coli tRNATyr(Q\u03a8A) is catalyzed by the dual specificity enzyme RluF","volume":"291","author":"Addepalli","year":"2016","journal-title":"J. Biol. Chem."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1038\/nrg.2016.39","article-title":"Evolution by gene loss","volume":"17","author":"Albalat","year":"2016","journal-title":"Nat. Rev. Genet."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"9716","DOI":"10.1073\/pnas.0305659101","article-title":"The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae","volume":"101","author":"Alsmark","year":"2004","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1016\/S0966-842X(98)01312-2","article-title":"Reductive evolution of resident genomes","volume":"6","author":"Andersson","year":"1998","journal-title":"Trends Microbiol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"1125","DOI":"10.3390\/genes12081125","article-title":"Rna modifications in pathogenic bacteria: impact on host adaptation and virulence","volume":"12","author":"Antoine","year":"2021","journal-title":"Genes"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"1126","DOI":"10.1002\/iub.2041","article-title":"To be or not to be modified: miscellaneous aspects influencing nucleotide modifications in tRNAs","volume":"71","author":"Barraud","year":"2019","journal-title":"IUBMB Life"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"6593","DOI":"10.1016\/j.tetlet.2015.10.023","article-title":"Synthesis of various substituted 5-methyluridines (xm5U) and 2-thiouridines (xm5s2U) via nucleophilic substitution of 5-pivaloyloxymethyluridine\/2-thiouridine","volume":"56","author":"Bartosik","year":"2015","journal-title":"Tetrahedron Lett."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"D523","DOI":"10.1093\/nar\/gkac1052","article-title":"UniProt: the universal protein knowledgebase in 2023","volume":"51","author":"Bateman","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"mc03c01s10","DOI":"10.1002\/9780471729259.mc03c01s10","article-title":"Laboratory maintenance of Bartonella quintana","volume":"3","author":"Battisti","year":"2008","journal-title":"Curr. Protoc. Microbiol."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"408053","DOI":"10.4061\/2011\/408053","article-title":"Use of specific chemical reagents for detection of modified nucleotides in RNA","volume":"2011","author":"Behm-Ansmant","year":"2011","journal-title":"J Nucleic Acids"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"2131","DOI":"10.1261\/rna.2245910","article-title":"YibK is the 2\u2019-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNALeu isoacceptors","volume":"16","author":"Ben\u00edtez-P\u00e1ez","year":"2010","journal-title":"RNA"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1080\/15476286.2020.1809197","article-title":"Transfer RNAs: diversity in form and function","volume":"18","author":"Berg","year":"2021","journal-title":"RNA Biol."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"25090","DOI":"10.1074\/jbc.M203208200","article-title":"Identification of the tRNA-dihydrouridine synthase family","volume":"277","author":"Bishop","year":"2002","journal-title":"J. Biol. Chem."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"D303","DOI":"10.1093\/nar\/gkx1030","article-title":"MODOMICS: a database of RNA modification pathways. 2017 update","volume":"46","author":"Boccaletto","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"1386","DOI":"10.1093\/nar\/gkx1294","article-title":"Unveiling structural and functional divergences of bacterial tRNA dihydrouridine synthases: perspectives on the evolution scenario","volume":"46","author":"Bou-Nader","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1021\/bi00892a005","article-title":"Purine nucleosides. VI. Further methylation studies of naturally occurring purine nucleosides","volume":"3","author":"Broom","year":"1964","journal-title":"Biochemistry"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"e1001247","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":"ref20","doi-asserted-by":"publisher","first-page":"D184","DOI":"10.1093\/nar\/gkv1309","article-title":"GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes","volume":"44","author":"Chan","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"1631","DOI":"10.1016\/S0960-894X(03)00291-9","article-title":"Novel synthesis of 2\u2032-O-methylguanosine","volume":"13","author":"Chow","year":"2003","journal-title":"Bioorg. Med. Chem. Lett."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"6182","DOI":"10.1021\/bi4000832","article-title":"Peroxide-shunt substrate-specificity for the Salmonella typhimurium O 2 -dependent tRNA modifying monooxygenase (MiaE)","volume":"52","author":"Corder","year":"2013","journal-title":"Biochemistry"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"1045","DOI":"10.1016\/j.ajhg.2018.10.026","article-title":"Variants in PUS7 cause intellectual disability with speech delay, microcephaly, short stature, and aggressive behavior","volume":"103","author":"de Brouwer","year":"2018","journal-title":"Am. J. Hum. Genet."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1016\/j.tim.2020.06.010","article-title":"Functions of bacterial tRNA modifications: from ubiquity to diversity","volume":"29","author":"de Cr\u00e9cy-Lagard","year":"2021","journal-title":"Trends Microbiol."},{"key":"ref25","first-page":"11","article-title":"Decoding in Candidatus Riesia pediculicola, close to a minimal tRNA modification set?","volume":"7","author":"de Cr\u00e9cy-Lagard","year":"2012","journal-title":"Trends Cell Mol. Biol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3390\/biom10070977","article-title":"Survey and validation of tRNA modifications and their corresponding genes in Bacillus subtilis sp subtilis strain 168","volume":"10","author":"de Cr\u00e9cy-Lagard","year":"2020","journal-title":"Biomol. Ther."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"1992","DOI":"10.1039\/D0RA09803E","article-title":"Efficient access to 3\u2032-O-phosphoramidite derivatives of tRNA related N6-threonylcarbamoyladenosine (t6A) and 2-methylthio-N6-threonylcarbamoyladenosine (ms2t6A)","volume":"11","author":"Debiec","year":"2021","journal-title":"RSC Adv."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1146\/annurev-genet-110711-155641","article-title":"Biosynthesis and function of posttranscriptional modifications of transfer RNAs","volume":"46","author":"El Yacoubi","year":"2012","journal-title":"Annu. Rev. Genet."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1159\/000235769","article-title":"Genomics of host-restricted pathogens of the genus Bartonella","volume":"6","author":"Engel","year":"2009","journal-title":"Genome Dyn."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"2278","DOI":"10.1080\/15476286.2021.1899653","article-title":"Dihydrouridine synthesis in tRNAs is under reductive evolution in Mollicutes","volume":"18","author":"Faivre","year":"2021","journal-title":"RNA Biol."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"217","DOI":"10.3201\/eid1202.050874","article-title":"Bartonella quintana characteristics and clinical management","volume":"12","author":"Foucault","year":"2006","journal-title":"Emerg. Infect. Dis."},{"key":"ref32","author":"Fruchard","year":"2022"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"1017","DOI":"10.1080\/15257770008033040","article-title":"Synthesis and antiviral activity of C-5 substituted analogues of D4T bearing methylamino- or methyldiamino-linker arms","volume":"19","author":"Gavriliu","year":"2000","journal-title":"Nucleosides Nucleotides Nucleic Acids"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"e1004363","DOI":"10.1371\/journal.pgen.1004363","article-title":"Predicting the minimal translation apparatus: lessons from the reductive evolution of Mollicutes","volume":"10","author":"Grosjean","year":"2014","journal-title":"PLoS Genet."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1016\/j.febslet.2009.11.052","article-title":"Deciphering synonymous codons in the three domains of life: co-evolution with specific tRNA modification enzymes","volume":"584","author":"Grosjean","year":"2010","journal-title":"FEBS Lett."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"8020","DOI":"10.1093\/nar\/gkw608","article-title":"An integrated, structure- and energy-based view of the genetic code","volume":"44","author":"Grosjean","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"1125","DOI":"10.1016\/j.chembiol.2006.09.009","article-title":"Pseudouridine synthases","volume":"13","author":"Hamma","year":"2006","journal-title":"Chem. Biol."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1016\/j.chembiol.2013.10.015","article-title":"Posttranscriptional RNA modifications: playing metabolic games in a cell\u2019s chemical legoland","volume":"21","author":"Helm","year":"2014","journal-title":"Chem. Biol."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"851","DOI":"10.1007\/s00706-003-0592-1","article-title":"The synthesis of 2\u2032-O-[(Triisopropylsilyl)oxy] methyl (TOM) phosphoramidites of pethylated Ribonucleosides (m1G, m2G, m22G, m1I, m3U, m4C, m6A, m62A) for use in automated RNA solid-phase synthesis","volume":"134","author":"H\u00f6bartner","year":"2003","journal-title":"Monatshefte f\u00fcr Chemie"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"1878","DOI":"10.1021\/jm0203276","article-title":"Antiviral amphipathic oligo- and polyribonucleotides: analogue development and biological studies","volume":"46","author":"Hyde","year":"2003","journal-title":"J. Med. Chem."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"750","DOI":"10.1128\/JB.186.3.750-757.2004","article-title":"The conserved Cys-X1-X2-Cys motif present in the TtcA protein is required for the thiolation of cytidine in position 32 of tRNA from Salmonella enterica serovar typhimurium","volume":"186","author":"Jager","year":"2004","journal-title":"J. Bacteriol."},{"key":"ref42","author":"Jaroch","year":"2023"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"D545","DOI":"10.1093\/nar\/gkaa970","article-title":"KEGG: integrating viruses and cellular organisms","volume":"49","author":"Kanehisa","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref44","first-page":"61","article-title":"Conformational characteristics of 4-acetylcytidine found in tRNA","volume":"21","author":"Kawai","year":"1989","journal-title":"Nucleic Acids Symp. Ser."},{"key":"ref45","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":"Kimura","year":"2020","journal-title":"Nat. Chem. Biol."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"809","DOI":"10.1016\/S0223-5234(99)00211-1","article-title":"5-substituted UTP derivatives as P2Y2 receptor agonists","volume":"34","author":"Knoblauch","year":"1999","journal-title":"Eur. J. Med. Chem."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1016\/j.bbagrm.2018.01.015","article-title":"Transfer RNA modification and infection \u2013 implications for pathogenicity and host responses","volume":"1861","author":"Koh","year":"2018","journal-title":"Biochimica et Biophysica Acta Gene Regul Mech"},{"key":"ref48","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1016\/S0040-4020(01)87419-6","article-title":"Syntheses of hypermodified nucleoside q, and its biosynthetic precursors preQ0 and preQ1","volume":"42","author":"Kondo","year":"1986","journal-title":"Tetrahedron"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"e0029422","DOI":"10.1128\/jb.00294-22","article-title":"Landscape of post-transcriptional tRNA modifications in Streptomyces albidoflavus J1074 as portrayed by mass spectrometry and genomic data mining","volume":"205","author":"Koshla","year":"2023","journal-title":"J. Bacteriol."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"ftab052","DOI":"10.1093\/femspd\/ftab052","article-title":"Keeping the host alive\u2014lessons from obligate intracellular bacterial pathogens","volume":"79","author":"Loterio","year":"2021","journal-title":"Pathog Dis"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"9253","DOI":"10.1016\/j.tetlet.2006.10.150","article-title":"Selective fluorescence-based detection of dihydrouridine with boronic acids","volume":"47","author":"Luvino","year":"2006","journal-title":"Tetrahedron Lett."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"16785","DOI":"10.1002\/anie.201810946","article-title":"AlkAniline-Seq: profiling of m7G and m3C RNA modifications at single nucleotide resolution","volume":"57","author":"Marchand","year":"2018","journal-title":"Angewandte Chemie"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"e135","DOI":"10.1093\/nar\/gkw547","article-title":"Illumina-based RiboMethSeq approach for mapping of 2\u2019-O-me residues in RNA","volume":"44","author":"Marchand","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/bs.mie.2021.06.001","article-title":"Mapping of 7-methylguanosine (m7G), 3-methylcytidine (m3C), dihydrouridine (D) and 5-hydroxycytidine (ho5C) RNA modifications by AlkAniline-Seq","author":"Marchand","year":"2021","journal-title":"Methods Enzymol."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"13","DOI":"10.3390\/biom7010013","article-title":"Next-generation sequencing-based ribomethseq protocol for analysis of tRNA 2\u2019-O-methylation","volume":"7","author":"Marchand","year":"2017","journal-title":"Biomol. Ther."},{"key":"ref57","doi-asserted-by":"publisher","first-page":"544","DOI":"10.1038\/nrmicro.2017.59","article-title":"Engineering of obligate intracellular bacteria: Progress, challenges and paradigms","volume":"15","author":"McClure","year":"2017","journal-title":"Nat. Rev. Microbiol."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"E11505","DOI":"10.1073\/pnas.1815992115","article-title":"Loss of protein synthesis quality control in host-restricted organisms","volume":"115","author":"Melnikov","year":"2018","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"5951","DOI":"10.1021\/ja00127a007","article-title":"Nucleic acid related compounds. 86. Nucleophilic functionalization of adenine, adenosine, tubercidin, and formycin derivatives via elaboration of the heterocyclic amino group into a readily displaced 1,2,4-triazol-4-yl substituent","volume":"117","author":"Miles","year":"1995","journal-title":"J. Am. Chem. Soc."},{"key":"ref60","doi-asserted-by":"publisher","first-page":"642","DOI":"10.3390\/genes9120642","article-title":"Detection and analysis of RNA ribose 2\u2019-O-methylations: challenges and solutions","volume":"9","author":"Motorin","year":"2018","journal-title":"Genes"},{"key":"ref61","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1016\/S0076-6879(07)25002-5","article-title":"Identification of modified residues in RNAs by reverse transcription-based methods","volume":"425","author":"Motorin","year":"2007","journal-title":"Methods Enzymol."},{"key":"ref62","doi-asserted-by":"publisher","first-page":"918","DOI":"10.3389\/fmicb.2018.00918","article-title":"Unique features and anti-microbial targeting of folate- and flavin-dependent methyltransferases required for accurate maintenance of genetic information","volume":"9","author":"Myllykallio","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref63","doi-asserted-by":"publisher","first-page":"D7","DOI":"10.1093\/nar\/gkv1290","article-title":"Database resources of the National Center for biotechnology information","volume":"44","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref64","doi-asserted-by":"publisher","first-page":"826","DOI":"10.3891\/acta.chem.scand.40b-0826","article-title":"Synthesis of O2\u2032-methyluridine, O2\u2019-methylcytidine, N4,O2\u2019-dimethylcytidine and N4,N4,O2\u2019-trimethylcytidine from a common intermediate","author":"Nyilas","year":"1986","journal-title":"Acta Chem. Scand."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"D678","DOI":"10.1093\/nar\/gkac1003","article-title":"Introducing the bacterial and viral bioinformatics resource center (BV-BRC): a resource combining PATRIC, IRD and ViPR","volume":"51","author":"Olson","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"11669","DOI":"10.1021\/ja00152a006","article-title":"Syntheses of [6,7-15N]-adenosine, [6,7-15N]-2\u2019-deoxyadenosine, and [7-15N]-hypoxanthine","volume":"117","author":"Pagano","year":"1995","journal-title":"J. Am. Chem. Soc."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"1011","DOI":"10.1111\/j.1365-2958.1993.tb01645.x","article-title":"Modification of tRNA as a regulatory device","volume":"8","author":"Persson","year":"1993","journal-title":"Mol. Microbiol."},{"key":"ref68","author":"Quaiyum","year":"2023"},{"key":"ref69","doi-asserted-by":"publisher","first-page":"1541","DOI":"10.1086\/523716","article-title":"From cat scratch disease to Bartonella henselae infection","volume":"45","author":"Raoult","year":"2007","journal-title":"Clin. Infect. Dis."},{"key":"ref70","doi-asserted-by":"publisher","first-page":"634","DOI":"10.1002\/ejoc.200500556","article-title":"Straightforward pyrimidine ring construction: a versatile tool for the synthesis of nucleobase and nucleoside analogues","volume":"2006","author":"Robin","year":"2006","journal-title":"European J Org Chem"},{"key":"ref71","unstructured":"Rovid SpicklerA.\n          2005"},{"key":"ref72","doi-asserted-by":"publisher","first-page":"2515","DOI":"10.1246\/bcsj.57.2515","article-title":"A stereocontrolled total synthesis of C -nucleosides","volume":"57","author":"Sato","year":"1984","journal-title":"Bull. Chem. Soc. Jpn."},{"key":"ref73","doi-asserted-by":"publisher","first-page":"e12","DOI":"10.1093\/nar\/gkn954","article-title":"RNA cytosine methylation analysis by bisulfite sequencing","volume":"37","author":"Schaefer","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"ref74","doi-asserted-by":"publisher","first-page":"1232","DOI":"10.1038\/ismej.2016.201","article-title":"Genomic changes associated with the evolutionary transition of an insect gut symbiont into a blood-borne pathogen","volume":"11","author":"Segers","year":"2017","journal-title":"ISME J."},{"key":"ref75","doi-asserted-by":"publisher","first-page":"1905","DOI":"10.1021\/bi00706a020","article-title":"Reaction of cytidine with ethylating agents","volume":"13","author":"Sun","year":"1974","journal-title":"Biochemistry"},{"key":"ref76","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"Thorvaldsd\u00f3ttir","year":"2012","journal-title":"Brief. Bioinform."},{"key":"ref77","doi-asserted-by":"publisher","first-page":"RP87146","DOI":"10.7554\/eLife.87146","article-title":"A tRNA modification in Mycobacterium tuberculosis facilitates optimal intracellular growth","volume":"12","author":"Tomasi","year":"2023","journal-title":"eLife"},{"key":"ref78","doi-asserted-by":"publisher","first-page":"2938","DOI":"10.1021\/jm00072a013","article-title":"Antiviral activity of C-alkylated purine nucleosides obtained by cross-coupling with tetraalkyltin reagents","volume":"36","author":"Van Aerschot","year":"1993","journal-title":"J. Med. Chem."},{"key":"ref79","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1002\/bscb.19680770307","article-title":"Preparation of cytidine, cytidylic acids and ribonucleic acid specifically acetylated in the exocyclic amino group of cytosine","volume":"77","author":"van Montagu","year":"1968","journal-title":"Bull Soc Chim Belges"},{"key":"ref80","doi-asserted-by":"publisher","first-page":"913","DOI":"10.1016\/j.jmb.2019.12.016","article-title":"A structural basis for restricted codon recognition mediated by 2-thiocytidine in tRNA containing a wobble position inosine","volume":"432","author":"Vangaveti","year":"2020","journal-title":"J. Mol. Biol."},{"key":"ref81","doi-asserted-by":"publisher","first-page":"4.72.1-4.72.13","DOI":"10.1002\/cpnc.22","article-title":"Synthesis of geranyl-2-thiouridine-modified RNA","volume":"68","author":"Wang","year":"2017","journal-title":"Curr. Protoc. Nucleic Acid Chem."},{"key":"ref82","doi-asserted-by":"publisher","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":"ref83","doi-asserted-by":"publisher","first-page":"3734","DOI":"10.1093\/nar\/gkaa113","article-title":"Machine learning of reverse transcription signatures of variegated polymerases allows mapping and discrimination of methylated purines in limited transcriptomes","volume":"48","author":"Werner","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref84","doi-asserted-by":"publisher","first-page":"14482","DOI":"10.1021\/jacs.1c07403","article-title":"Prebiotic photochemical coproduction of purine ribo- and deoxyribonucleosides","volume":"143","author":"Xu","year":"2021","journal-title":"J. Am. Chem. Soc."},{"key":"ref85","doi-asserted-by":"publisher","first-page":"746","DOI":"10.1016\/j.cell.2009.01.036","article-title":"Fidelity at the molecular level: lessons from protein synthesis","volume":"136","author":"Zaher","year":"2009","journal-title":"Cell"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1369018\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,13]],"date-time":"2024-03-13T00:52:33Z","timestamp":1710291153000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1369018\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,3,13]]},"references-count":85,"alternative-id":["10.3389\/fmicb.2024.1369018"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2024.1369018","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,3,13]]},"article-number":"1369018"}}