{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T04:40:06Z","timestamp":1790484006826,"version":"4.1.0"},"reference-count":141,"publisher":"The Royal Society","issue":"4","license":[{"start":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T00:00:00Z","timestamp":1776211200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T00:00:00Z","timestamp":1776211200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>tRNA modifications are central to bacterial translational control. Here, we integrated genetics, mass spectrometry, epitranscriptomics and comparative genomics to map the tRNA modification genes of the Gram-positive pathogens Streptococcus mutans and Streptococcus pneumoniae. Both species show a marked loss of modifications dependent on Fe\u2013S enzymes, consistent with a broader trend of Fe\u2013S enzyme reduction in Streptococcus central metabolism. In addition, the D, m1A, m7G, t6A and i6A modifications were mapped in S. pneumoniae tRNAs, and we confirmed that a unique DusB1 enzyme is responsible for the insertion of all the detectable D modifications. We uncovered differences in queuosine (Q) metabolism: while S. mutans synthesizes Q de novo, S. pneumoniae instead salvages preQ\u2081 and accumulates the epoxy-Q precursor, a strategy shared with multiple other streptococci as revealed by analysis of Q pathways in 1599 sequenced streptococcal genomes. Comparative essentiality profiling of modification genes revealed notable differences, including the essentiality of the N\u2076-threonylcarbamoyladenosine (t\u2076A) synthesis enzyme TsaE in S. pneumoniae but not in S. mutans, which was confirmed by genetic studies. We found that suppressor mutations in asnS encoding asparaginyl-tRNA synthetase (AsnRS) restored viability to \u2206tsaE mutants, albeit with reduced growth. Our finding highlights the functional importance of modifications in the recognition of tRNAs by aminoacyl-tRNA synthetases.<\/jats:p>","DOI":"10.1098\/rsob.250445","type":"journal-article","created":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T00:17:01Z","timestamp":1776212221000},"source":"Crossref","is-referenced-by-count":3,"title":["tRNA modification landscapes in streptococci: shared losses and clade-specific adaptations"],"prefix":"10.1098","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0849-874X","authenticated-orcid":false,"given":"Ho-Ching Tiffany","family":"Tsui","sequence":"first","affiliation":[{"name":"Indiana University Bloomington 1 , , ,","place":["Bloomington, IN, USA"],"department":["Department of Biology"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7963-8725","authenticated-orcid":false,"given":"Chi-Kong","family":"Chan","sequence":"additional","affiliation":[{"name":"Massachusetts 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USA"],"department":["Department of Chemistry"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Grazyna","family":"Leszczynska","sequence":"additional","affiliation":[{"name":"Lodz University of Technology 8 , ,","place":["\u0141\u00f3d\u017a, Poland"],"department":["Institute of Organic Chemistry"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kinda","family":"Seaton","sequence":"additional","affiliation":[{"name":"University of Florida 4 , , ,","place":["Gainesville, FL, USA"],"department":["Department of Microbiology and Cell Science"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8018-334X","authenticated-orcid":false,"given":"Yuri","family":"Motorin","sequence":"additional","affiliation":[{"name":"University of Lorraine 5 , ,","place":["Nancy, France"],"department":["Epitranscriptomics and RNA Sequencing Core 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Evol."},{"key":"2026052805163389200_R59","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res."},{"key":"2026052805163389200_R60","doi-asserted-by":"crossref","first-page":"4169","DOI":"10.1021\/acs.biochem.9b00735","article-title":"The EFI web resource for genomic enzymology tools: leveraging protein, genome, and metagenome databases to discover novel enzymes and metabolic pathways","volume":"58","author":"Zallot","year":"2019","journal-title":"Biochemistry"},{"key":"2026052805163389200_R61","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"2026052805163389200_R62","doi-asserted-by":"crossref","first-page":"1406","DOI":"10.1093\/bioinformatics\/btx793","article-title":"Gene graphics: a genomic neighborhood data visualization web application","volume":"34","author":"Harrison","year":"2018","journal-title":"Bioinformatics"},{"key":"2026052805163389200_R63","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/s13059-016-0997-x","article-title":"Mash: fast genome and metagenome distance estimation using MinHash","volume":"17","author":"Ondov","year":"2016","journal-title":"Genome Biol."},{"key":"2026052805163389200_R64","article-title":"In press. 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Microbiol."},{"key":"2026052805163389200_R71","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1039\/C0MT00050G","article-title":"Interplay between manganese and zinc homeostasis in the human pathogen Streptococcus pneumoniae","volume":"3","author":"Jacobsen","year":"2011","journal-title":"Metallomics"},{"key":"2026052805163389200_R72","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1111\/mmi.13613","article-title":"Suppression and synthetic-lethal genetic relationships of \u0394gpsB mutations indicate that GpsB mediates protein phosphorylation and penicillin-binding protein interactions in Streptococcus pneumoniae D39","volume":"103","author":"Rued","year":"2017","journal-title":"Mol. 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Chem."},{"key":"2026052805163389200_R75","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1111\/mmi.15122","article-title":"Negative regulation of MurZ and MurA underlies the essentiality of GpsB- and StkP-mediated protein phosphorylation in Streptococcus pneumoniae D39","volume":"120","author":"Tsui","year":"2023","journal-title":"Mol. Microbiol."},{"key":"2026052805163389200_R76","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1007\/978-1-4939-0554-6_12","article-title":"Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq","volume":"1151","author":"Deatherage","year":"2014","journal-title":"Methods Mol. 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Chem."},{"key":"2026052805163389200_R91","doi-asserted-by":"crossref","first-page":"30560","DOI":"10.1074\/jbc.M112.388538","article-title":"Structural basis of biological nitrile reduction","volume":"287","author":"Chikwana","year":"2012","journal-title":"J. Biol. Chem."},{"key":"2026052805163389200_R92","doi-asserted-by":"crossref","first-page":"1369018","DOI":"10.3389\/fmicb.2024.1369018","article-title":"Mapping the tRNA modification landscape of Bartonella henselae Houston I and Bartonella quintana Toulouse","volume":"15","author":"Quaiyum","year":"2024","journal-title":"Front. Microbiol."},{"key":"2026052805163389200_R93","doi-asserted-by":"crossref","first-page":"1926","DOI":"10.1002\/cbic.200500063","article-title":"Mechanism and substrate specificity of tRNA-guanine transglycosylases (TGTs): tRNA-modifying enzymes from the three different kingdoms of life share a common catalytic mechanism","volume":"6","author":"Stengl","year":"2005","journal-title":"ChemBioChem"},{"key":"2026052805163389200_R94","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00766-20","article-title":"Codon usage optimization in the prokaryotic tree of life: how synonymous codons are differentially selected in sequence domains with different expression levels and degrees of conservation","volume":"11","author":"L\u00f3pez","year":"2020","journal-title":"mBio"},{"key":"2026052805163389200_R95","doi-asserted-by":"crossref","DOI":"10.1128\/mSphere.00031-18","article-title":"Genomewide identification of essential genes and fitness determinants of Streptococcus mutans UA159","volume":"3","author":"Shields","year":"2018","journal-title":"mSphere"},{"key":"2026052805163389200_R96","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1008344","article-title":"Repurposing the Streptococcus mutans CRISPR-Cas9 system to understand essential gene function","volume":"16","author":"Shields","year":"2020","journal-title":"PLoS Pathog."},{"key":"2026052805163389200_R97","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1111\/omi.12107","article-title":"Functional profiling in Streptococcus mutans: construction and examination of a genomic collection of gene deletion mutants","volume":"30","author":"Quivey","year":"2015","journal-title":"Mol. Oral Microbiol."},{"key":"2026052805163389200_R98","doi-asserted-by":"crossref","first-page":"D839","DOI":"10.1093\/nar\/gkae923","article-title":"PneumoBrowse 2: an integrated visual platform for curated genome annotation and multiomics data analysis of Streptococcus pneumoniae","volume":"53","author":"Janssen","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"2026052805163389200_R99","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.03149-23","article-title":"Construction of an arrayed CRISPRi library as a resource for essential gene function studies in Streptococcus mutans","volume":"12","author":"St. Pierre","year":"2024","journal-title":"Microbiol. Spectr."},{"key":"2026052805163389200_R100","doi-asserted-by":"crossref","first-page":"1952","DOI":"10.1128\/JB.02625-14","article-title":"Abbreviated pathway for biosynthesis of 2-thiouridine in Bacillus subtilis","volume":"197","author":"Black","year":"2015","journal-title":"J. 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Microbiol."},{"key":"2026052805163389200_R106","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1007\/s42995-024-00220-6","article-title":"Spontaneous mutations and mutational responses to penicillin treatment in the bacterial pathogen Streptococcus pneumoniae D39","volume":"6","author":"Jiang","year":"2024","journal-title":"Mar. Life Sci. Technol."},{"key":"2026052805163389200_R107","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1111\/mmi.13847","article-title":"Absence of the KhpA and KhpB (JAG\/EloR) RNA-binding proteins suppresses the requirement for PBP2b by overproduction of FtsA in Streptococcus pneumoniae D39","volume":"106","author":"Zheng","year":"2017","journal-title":"Mol. Microbiol."},{"key":"2026052805163389200_R108","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1261\/rna.1381309","article-title":"Initiation of ribosome degradation during starvation in Escherichia coli","volume":"15","author":"Zundel","year":"2009","journal-title":"RNA"},{"key":"2026052805163389200_R109","doi-asserted-by":"crossref","DOI":"10.1186\/s12915-020-0763-0","article-title":"Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner","volume":"18","author":"Cherlin","year":"2020","journal-title":"BMC Biol."},{"key":"2026052805163389200_R110","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1073\/pnas.1423314112","article-title":"Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis","volume":"112","author":"Suzuki","year":"2015","journal-title":"Proc. Natl Acad. Sci. 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Biol."},{"key":"2026052805163389200_R114","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1016\/j.jmb.2010.11.049","article-title":"A hybrid structural model of the complete Brugia malayi cytoplasmic asparaginyl-tRNA synthetase","volume":"405","author":"Crepin","year":"2011","journal-title":"J. Mol. Biol."},{"key":"2026052805163389200_R115","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1038\/s41467-024-45224-z","article-title":"Reaction hijacking inhibition of Plasmodium falciparum asparagine tRNA synthetase","volume":"15","author":"Xie","year":"2024","journal-title":"Nat. Commun."},{"key":"2026052805163389200_R116","doi-asserted-by":"crossref","first-page":"1632","DOI":"10.1093\/emboj\/cdg148","article-title":"Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain","volume":"22","author":"Charron","year":"2003","journal-title":"EMBO J."},{"key":"2026052805163389200_R117","doi-asserted-by":"crossref","first-page":"1313","DOI":"10.1006\/jmbi.2000.3791","article-title":"The free yeast aspartyl-tRNA synthetase differs from the tRNAAsp-complexed enzyme by structural changes in the catalytic site, hinge region, and anticodon-binding domain","volume":"299","author":"Sauter","year":"2000","journal-title":"J. Mol. Biol."},{"key":"2026052805163389200_R118","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1006\/jmbi.2000.3819","article-title":"An intermediate step in the recognition of tRNA Asp by aspartyl-tRNA synthetase 1","volume":"299","author":"Briand","year":"2000","journal-title":"J. Mol. Biol."},{"key":"2026052805163389200_R119","doi-asserted-by":"crossref","first-page":"936","DOI":"10.1016\/j.tree.2017.09.006","article-title":"Why might bacterial pathogens have small genomes?","volume":"32","author":"Weinert","year":"2017","journal-title":"Trends Ecol. Evol."},{"key":"2026052805163389200_R120","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1515\/9783110479850-005","volume-title":"Biochemistry, biosynthesis and human diseases","author":"Dos Santos","year":"2017"},{"key":"2026052805163389200_R121","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2021.671533","article-title":"Streptococcus mutans lacking sufCDSUB is viable, but displays major defects in growth, stress tolerance responses and biofilm formation","volume":"12","author":"Ellepola","year":"2021","journal-title":"Front. Microbiol."},{"key":"2026052805163389200_R122","doi-asserted-by":"crossref","first-page":"1074","DOI":"10.1038\/s41396-020-0592-8","article-title":"Pyruvate secretion by oral streptococci modulates hydrogen peroxide dependent antagonism","volume":"14","author":"Redanz","year":"2020","journal-title":"ISME J."},{"key":"2026052805163389200_R123","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1159\/000479091","article-title":"Diversity in antagonistic interactions between commensal oral streptococci and Streptococcus mutans","volume":"52","author":"Huang","year":"2018","journal-title":"Caries Res."},{"key":"2026052805163389200_R124","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2021.627328","article-title":"Interactions between neutrophils and periodontal pathogens in late-onset periodontitis","volume":"11","author":"Jiang","year":"2021","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"2026052805163389200_R125","doi-asserted-by":"crossref","DOI":"10.1007\/s12275-018-7545-1","article-title":"Antimicrobial actions of dual oxidases and lactoperoxidase","volume":"56","author":"Sarr","year":"2018","journal-title":"J. Microbiol."},{"key":"2026052805163389200_R126","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1038\/nchembio.1426","article-title":"Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism","volume":"10","author":"Dowling","year":"2014","journal-title":"Nat. Chem. Biol."},{"key":"2026052805163389200_R127","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1002\/wrna.60","article-title":"Antibiotics that target protein synthesis","volume":"2","author":"McCoy","year":"2011","journal-title":"Wiley Interdiscip. Rev. 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Biotechnol."},{"key":"2026052805163389200_R131","doi-asserted-by":"crossref","first-page":"4732","DOI":"10.1128\/JB.00136-09","article-title":"Conserved network of proteins essential for bacterial viability","volume":"191","author":"Handford","year":"2009","journal-title":"J. Bacteriol."},{"key":"2026052805163389200_R132","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1042\/BJ20041082","article-title":"Probing the active site of YjeE: a vital Escherichia coli protein of unknown function","volume":"384","author":"Allali-hassani","year":"2004","journal-title":"Biochem. J."},{"key":"2026052805163389200_R133","doi-asserted-by":"crossref","first-page":"3318","DOI":"10.1128\/JB.00131-06","article-title":"Isolation of the rstA gene as a multicopy suppressor of YjeE, an essential ATPase of unknown function in Escherichia coli","volume":"189","author":"Campbell","year":"2007","journal-title":"J. Bacteriol."},{"key":"2026052805163389200_R134","first-page":"483","article-title":"Identification of novel essential Escherichia coli genes conserved among pathogenic bacteria","volume":"3","author":"Freiberg","year":"2001","journal-title":"J. Mol. Microbiol. Biotechnol."},{"key":"2026052805163389200_R135","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1111\/j.1747-0285.2007.00521.x","article-title":"From bacterial genomes to novel antibacterial agents: discovery, characterization, and antibacterial activity of compounds that bind to HI0065 (YjeE) from Haemophilus influenzae","volume":"69","author":"Lerner","year":"2007","journal-title":"Chem. Biol. Drug Des."},{"key":"2026052805163389200_R136","doi-asserted-by":"crossref","first-page":"12467","DOI":"10.1093\/nar\/gkab1067","article-title":"Evolutionary repair reveals an unexpected role of the tRNA modification m1G37 in aminoacylation","volume":"49","author":"Clifton","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2026052805163389200_R137","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkaf696","article-title":"tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa","volume":"53","author":"Sun","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"2026052805163389200_R138","article-title":"The landscape of tRNA modifications in archaea","author":"Leavitt","year":"2025","journal-title":"bioRxiv."},{"key":"2026052805163389200_R139","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1011937","article-title":"The tRNA epitranscriptomic landscape and RNA modification enzymes in Vibrio cholerae","volume":"21","author":"Hardy","year":"2025","journal-title":"PLoS Genet."},{"key":"2026052805163389200_R140","article-title":"This is the archived source code for version 0.9.0 of the private repository \u2018tRNA_mod_in_Streptococci\u2019. 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