{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T14:18:11Z","timestamp":1790000291281,"version":"4.0.1"},"reference-count":63,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["MicrobiologyOpen"],"published-print":{"date-parts":[[2026,10]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Epitranscriptomics has recently gained significant momentum due to technological advances and translational applications; however, studies on bacterial RNA modifications remain limited. Bacterial RNA is notoriously prone to degradation, and methodologies to investigate the epitranscriptome are challenging. Prior research has shown RNA modifications modulate antimicrobial resistance, virulence and pathogenicity. This research employed CRISPR interference to knock down five known\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    rRNA modification genes (\n                    <jats:italic>rlmF<\/jats:italic>\n                    ,\n                    <jats:italic>rlmJ<\/jats:italic>\n                    ,\n                    <jats:italic>rluD<\/jats:italic>\n                    ,\n                    <jats:italic>rsmF<\/jats:italic>\n                    and\n                    <jats:italic>rsmG<\/jats:italic>\n                    ) in three\n                    <jats:italic>E. coli<\/jats:italic>\n                    strains. These isolates were investigated for growth delays, changes in the proteome and the influence on mRNA modifications via native RNA sequencing.\n                  <\/jats:p>\n                  <jats:p>\n                    CRISPRi adequately silenced the majority of RNA modification genes in\n                    <jats:italic>E. coli<\/jats:italic>\n                    (&gt;\u200980% reduction). Significant growth delays were associated with\n                    <jats:italic>rlmF<\/jats:italic>\n                    ,\n                    <jats:italic>rluD<\/jats:italic>\n                    and\n                    <jats:italic>rsmF<\/jats:italic>\n                    repression. Unique protein pathways corresponding with RNA modification loss were found for\n                    <jats:italic>rlmJ<\/jats:italic>\n                    (TreB, XylF),\n                    <jats:italic>rluD<\/jats:italic>\n                    (CysH, HycB, PutP, TrpB),\n                    <jats:italic>rsmF<\/jats:italic>\n                    (EvgA) and\n                    <jats:italic>rsmG<\/jats:italic>\n                    (OppC). Known rRNA modification sites for\n                    <jats:italic>rluD<\/jats:italic>\n                    (\u03a8) and\n                    <jats:italic>rsmG<\/jats:italic>\n                    (m7G) were detected from analysis of nanopore electrical signal; however, only a weak signal was apparent for m6A (\n                    <jats:italic>rlmF, rlmJ<\/jats:italic>\n                    ) and m5C (\n                    <jats:italic>rsmF<\/jats:italic>\n                    ) modifications. The inhibition of rRNA modifications resulted in mRNA modification changes, including for genes\n                    <jats:italic>ompC<\/jats:italic>\n                    ,\n                    <jats:italic>cspC<\/jats:italic>\n                    ,\n                    <jats:italic>dbhA<\/jats:italic>\n                    ,\n                    <jats:italic>dbhB<\/jats:italic>\n                    and\n                    <jats:italic>secY<\/jats:italic>\n                    .\n                  <\/jats:p>\n                  <jats:p>\n                    Our work provides an approach for unravelling the epitranscriptome of\n                    <jats:italic>E. coli<\/jats:italic>\n                    to gain insight into its functional role.\n                  <\/jats:p>","DOI":"10.1002\/mbo3.70413","type":"journal-article","created":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T13:36:57Z","timestamp":1789997817000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Interrogating the\n                    <i>Escherichia coli<\/i>\n                    Epitranscriptome Via CRISPR Interference and Nanopore Native RNA Sequencing"],"prefix":"10.1002","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8255-4036","authenticated-orcid":false,"given":"Miranda E.","family":"Pitt","sequence":"first","affiliation":[{"name":"Australian Institute for Microbiology and Infection University of Technology Sydney Sydney New South Wales Australia"},{"name":"Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity University of Melbourne Melbourne Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-0871-5197","authenticated-orcid":false,"given":"Jianshu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity University of Melbourne Melbourne Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4893-6636","authenticated-orcid":false,"given":"An N. T.","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity University of Melbourne Melbourne Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3683-6208","authenticated-orcid":false,"given":"Michael B.","family":"Hall","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity University of Melbourne Melbourne Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4240-9528","authenticated-orcid":false,"given":"Leila","family":"Jebeli","sequence":"additional","affiliation":[{"name":"Enteric Diseases Group Murdoch Children's Research Institute Melbourne Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8878-1758","authenticated-orcid":false,"given":"Leo A.","family":"Featherstone","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity University of Melbourne Melbourne Victoria Australia"},{"name":"The Kirby Institute University of New South Wales Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Garry S. A.","family":"Myers","sequence":"additional","affiliation":[{"name":"Australian Institute for Microbiology and Infection University of Technology Sydney Sydney New South Wales Australia"},{"name":"School of Natural Sciences Macquarie University Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2556-8316","authenticated-orcid":false,"given":"Nichollas E.","family":"Scott","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity University of Melbourne Melbourne Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4300-455X","authenticated-orcid":false,"given":"Lachlan J. M.","family":"Coin","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity University of Melbourne Melbourne Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,21]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"crossref","first-page":"3113","DOI":"10.1093\/bioinformatics\/btac274","article-title":"Drummer\u2010Rapid Detection of RNA Modifications Through Comparative Nanopore Sequencing","volume":"38","author":"Abebe J. 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