{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,17]],"date-time":"2026-10-17T21:07:27Z","timestamp":1792271247602,"version":"4.4.0"},"reference-count":43,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T00:00:00Z","timestamp":1761177600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["MCB 2509382"],"award-info":[{"award-number":["MCB 2509382"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012394","name":"Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012394","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Gary and Eileen Morgenthaler fund"},{"DOI":"10.13039\/100000936","name":"Gordon and Betty Moore Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000936","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Chan Zuckerberg Biohub","award":["N\/A"],"award-info":[{"award-number":["N\/A"]}]},{"DOI":"10.13039\/100023581","name":"National Science Foundation Graduate Research Fellowship Program","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100023581","id-type":"DOI","asserted-by":"publisher"}]},{"name":"UCSF Discovery Fellowship"}],"content-domain":{"domain":["www.plosbiology.org"],"crossmark-restriction":false},"short-container-title":["PLoS Biol"],"abstract":"<jats:p>\n                    Retrons are bacterial immune systems that protect a bacterial population against phages by killing infected hosts. Retrons typically comprise a reverse transcriptase (RT), a template noncoding RNA that is partially reverse transcribed into RT-DNA, and a toxic effector. The reverse transcriptase (RT), noncoding RNA, and RT-DNA complex sequester the toxic effector until triggered by phage infection, at which point the toxin is released to induce cell death. Due to their ability to produce single-stranded DNA in vivo, retrons have also been engineered to produce donor templates for genome editing in both prokaryotes and eukaryotes. However, the current repertoire of experimentally characterized retrons is limited, with most retrons sourced from clinical and laboratory strains of bacteria. To better understand retron biology and natural diversity, and to expand the current toolbox of retron-based genome editors, we developed a pipeline to isolate retrons and their bacterial hosts from a variety of environmental samples. Here, we identify seven new retron systems, each isolated from a different host bacterium. We characterize DNA production by these retrons and test their ability to defend against a panel of\n                    <jats:italic>\n                      <jats:italic>Escherichia coli<\/jats:italic>\n                    <\/jats:italic>\n                    phages. We find that two of these retrons are disrupted by other elements, in one case a group II intron and in another a separate defense system, yet both retrons still produce RT-DNA. For two other retrons, we further unravel their mechanism of defense by identifying the phage genes responsible for triggering abortive infection. Finally, we engineer these retrons for genome editing in\n                    <jats:italic>\n                      <jats:italic>E. coli<\/jats:italic>\n                    <\/jats:italic>\n                    , demonstrating their potential use in a biotechnological application.\n                  <\/jats:p>","DOI":"10.1371\/journal.pbio.3003042","type":"journal-article","created":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T17:29:03Z","timestamp":1761240543000},"page":"e3003042","update-policy":"https:\/\/doi.org\/10.1371\/journal.pbio.corrections_policy","source":"Crossref","is-referenced-by-count":7,"title":["New retron systems from environmental bacteria identify triggers of anti-phage defense and expand tools for genome editing"],"prefix":"10.1371","volume":"23","author":[{"given":"Kazuo L.","family":"Nakamura","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mario R.","family":"Mestre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mat\u00edas","family":"Rojas-Montero","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3130-8043","authenticated-orcid":true,"given":"Seth L.","family":"Shipman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,10,23]]},"reference":[{"issue":"7925","key":"pbio.3003042.ref001","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1038\/s41586-022-05091-4","article-title":"Bacterial retrons encode phage-defending tripartite toxin-antitoxin systems","volume":"609","author":"J Bobonis","year":"2022","journal-title":"Nature"},{"issue":"6","key":"pbio.3003042.ref002","doi-asserted-by":"crossref","DOI":"10.1016\/j.cell.2020.09.065","article-title":"Bacterial retrons function in anti-phage defense","volume":"183","author":"A Millman","year":"2020","journal-title":"Cell"},{"issue":"6507","key":"pbio.3003042.ref003","doi-asserted-by":"crossref","first-page":"1077","DOI":"10.1126\/science.aba0372","article-title":"Diverse enzymatic activities mediate antiviral immunity in prokaryotes","volume":"369","author":"L Gao","year":"2020","journal-title":"Science"},{"issue":"7921","key":"pbio.3003042.ref004","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1038\/s41586-022-04994-6","article-title":"Recording gene expression order in DNA by CRISPR addition of retron barcodes","volume":"608","author":"S Bhattarai-Kline","year":"2022","journal-title":"Nature"},{"key":"pbio.3003042.ref005","volume-title":"Intracellular expression of a fluorogenic DNA aptamer using retron Eco2","author":"MA Vibhute","year":"2024"},{"issue":"1","key":"pbio.3003042.ref006","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1021\/acssynbio.3c00509","article-title":"Generation of DNAzyme in bacterial cells by a bacterial retron system","volume":"13","author":"J Liu","year":"2024","journal-title":"ACS Synth Biol"},{"issue":"2","key":"pbio.3003042.ref007","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/s41589-021-00927-y","article-title":"Precise genome editing across kingdoms of life using retron-derived DNA","volume":"18","author":"SC Lopez","year":"2022","journal-title":"Nat Chem Biol"},{"issue":"6211","key":"pbio.3003042.ref008","doi-asserted-by":"crossref","first-page":"1256272","DOI":"10.1126\/science.1256272","article-title":"Synthetic biology. 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