{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T20:32:12Z","timestamp":1768509132257,"version":"3.49.0"},"posted":{"date-parts":[[2024,1,9]]},"group-title":"Microbiology","reference-count":66,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2024,1,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <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\n                  <jats:italic>Bartonella<\/jats:italic>\n                  species have undergone substantial reductions in tRNA modification genes, mostly by simplifying the hypermodifications present at positions 34 and 37.\n                  <jats:italic>B. 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":"10.1101\/2024.01.08.574729","type":"posted-content","created":{"date-parts":[[2024,1,10]],"date-time":"2024-01-10T02:38:48Z","timestamp":1704854328000},"source":"Crossref","is-referenced-by-count":0,"title":["Mapping the tRNA Modification Landscape of\n                  <i>Bartonella henselae<\/i>\n                  Houston I and\n                  <i>Bartonella quintana<\/i>\n                  Toulouse"],"prefix":"10.64898","author":[{"given":"Samia","family":"Quaiyum","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jingjing","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Virginie","family":"Marchand","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guangxin","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Colbie J.","family":"Reed","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuri","family":"Motorin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0011-3067","authenticated-orcid":false,"given":"Peter C.","family":"Dedon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael F.","family":"Minnick","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Val\u00e9rie","family":"de Cr\u00e9cy-Lagard","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2024011103101270000_2024.01.08.574729v1.1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2009.01.036"},{"issue":"3","key":"2024011103101270000_2024.01.08.574729v1.2","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1080\/15476286.2020.1809197","article-title":"Transfer RNAs: Diversity in form and function","volume":"18","year":"2021","journal-title":"RNA Biology"},{"key":"2024011103101270000_2024.01.08.574729v1.3","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-genet-110711-155641"},{"key":"2024011103101270000_2024.01.08.574729v1.4","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000901"},{"key":"2024011103101270000_2024.01.08.574729v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2020.06.010"},{"issue":"4","key":"2024011103101270000_2024.01.08.574729v1.6","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","year":"2023","journal-title":"J Genet Genomics"},{"key":"2024011103101270000_2024.01.08.574729v1.7","doi-asserted-by":"publisher","DOI":"10.1016\/j.chembiol.2013.10.015"},{"key":"2024011103101270000_2024.01.08.574729v1.8","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.1993.tb01645.x"},{"issue":"4","key":"2024011103101270000_2024.01.08.574729v1.9","doi-asserted-by":"crossref","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","year":"2018","journal-title":"Biochim Biophys Acta - Gene Regul Mech"},{"key":"2024011103101270000_2024.01.08.574729v1.10","unstructured":"Fruchard L , Babosan A , Carvalho A , Lang M , Li B , Duchateau M , Giai-Gianetto Q , Matondo M , Bonhomme F , Fabret C , Namy O , de Cr\u00e9cy-Lagard V , Mazel D , Baharoglu Z . 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