{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T13:56:43Z","timestamp":1790603803333,"version":"4.1.0"},"reference-count":69,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"content-version":"vor","delay-in-days":8,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"FRFS-WELBIO","award":["ADV X.1537.26F"],"award-info":[{"award-number":["ADV X.1537.26F"]}]},{"name":"International Brachet Stiftung, the Universit\u00e9 Libre de Bruxelles","id":[{"id":"https:\/\/ror.org\/01r9htc13","id-type":"ROR","asserted-by":"crossref"}]},{"name":"FNRS-FRS"},{"name":"\u201cLes Amis de l\u2019Institut Pasteur \u00e0 Bruxelles\u201d"},{"name":"European Union\u2019s Horizon 2020"},{"name":"Marie Sk\u0142odowska-Curie","award":["801505"],"award-info":[{"award-number":["801505"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Toxin\u2013antitoxin systems are widespread in bacterial genomes. Yet, their integration, persistence, and impact on chromosome dynamics remain unclear. Here, we identified 80 type II toxin\u2013antitoxin systems in the single chromosome of Photorhabdus laumondii TT01, 50 of which were experimentally validated. Comparative analysis across the Photorhabdus genus revealed a highly heterogeneous distribution, with toxin\u2013antitoxin systems frequently clustering within discrete genomic regions, either alone or associated with cointegrate-forming transposases and integrases. Toxin\u2013antitoxin systems rarely clustered with other putative defense systems and are preferentially associated with different types of recombinases, suggesting distinct pathways of acquisition for the two types of functions. Functional analyses showed that most validated toxin\u2013antitoxin systems display addictive properties and stabilize plasmids. These addictive toxin\u2013antitoxin systems are preferentially located in genomic regions characterized by high gene turnover, consistent with recent acquisition events. Despite their plasmid-stabilizing capacity, toxin\u2013antitoxin systems do not promote long-term conservation of their immediate chromosomal neighborhoods. Instead, we observed frequent toxin\u2013antitoxin loss, either through complete deletion or toxin pseudogenization, indicating relaxed selection for their persistence in bacterial lineages. We propose a stepwise model for toxin\u2013antitoxin evolution in bacterial chromosomes: initial acquisition mediated by mobile genetic elements, preferential integration into permissive genomic regions, subsequent genetic streamlining of linked loci, and progressive gene loss. The short-lasting linkage between toxin\u2013antitoxin systems and their genomic neighborhoods is consistent with the view that toxin\u2013antitoxin modules can behave as autonomous, selfish genetic elements.<\/jats:p>","DOI":"10.1093\/molbev\/msag230","type":"journal-article","created":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T11:36:45Z","timestamp":1788867405000},"source":"Crossref","is-referenced-by-count":0,"title":["Acquisition and erosion of toxin\u2013antitoxin systems in bacterial chromosomes"],"prefix":"10.1093","volume":"43","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-6323-994X","authenticated-orcid":false,"given":"Ludovic","family":"Belot","sequence":"first","affiliation":[{"name":"Bacterial Genetics and Physiology, Facult\u00e9 des Sciences, Universit\u00e9 Libre de Bruxelles (ULB) , Gosselies 6041 ,","place":["Belgium"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0584-9017","authenticated-orcid":false,"given":"Amaury","family":"Payelleville","sequence":"additional","affiliation":[{"name":"Bacterial Genetics and Physiology, Facult\u00e9 des Sciences, Universit\u00e9 Libre de Bruxelles (ULB) , Gosselies 6041 ,","place":["Belgium"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1660-1524","authenticated-orcid":false,"given":"Dukas","family":"Jur\u0117nas","sequence":"additional","affiliation":[{"name":"Bacterial Genetics and Physiology, Facult\u00e9 des Sciences, Universit\u00e9 Libre de Bruxelles (ULB) , Gosselies 6041 ,","place":["Belgium"]},{"name":"WEL Research Institute , Wavre 1300 ,","place":["Belgium"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7704-822X","authenticated-orcid":false,"given":"Eduardo P C","family":"Rocha","sequence":"additional","affiliation":[{"name":"Microbial Evolutionary Genomics, Institut Pasteur, Universit\u00e9 de Paris Cit\u00e9, CNRS UMR3525 , Paris 75015 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7778-1736","authenticated-orcid":false,"given":"Laurence","family":"Van Melderen","sequence":"additional","affiliation":[{"name":"Bacterial Genetics and Physiology, Facult\u00e9 des Sciences, Universit\u00e9 Libre de Bruxelles (ULB) , Gosselies 6041 ,","place":["Belgium"]},{"name":"WEL Research Institute , Wavre 1300 ,","place":["Belgium"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,9]]},"reference":[{"key":"2026092809120200400_msag230-B1","doi-asserted-by":"publisher","first-page":"R81","DOI":"10.1186\/gb-2003-4-12-r81","article-title":"New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system","volume":"4","author":"Anantharaman","year":"2003","journal-title":"Genome Biol"},{"key":"2026092809120200400_msag230-B2","doi-asserted-by":"publisher","DOI":"10.1128\/ecosalplus.esp-0014-2022","article-title":"Biology of host-dependent restriction-modification in prokaryotes","volume":"13","author":"Anton","year":"2025","journal-title":"EcoSal Plus"},{"key":"2026092809120200400_msag230-B3","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1111\/j.1466-8238.2009.00490.x","article-title":"Partitioning the turnover and nestedness components of beta diversity: partitioning beta diversity","volume":"19","author":"Baselga","year":"2010","journal-title":"Glob Ecol Biogeogr"},{"key":"2026092809120200400_msag230-B4","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.02938-21","article-title":"Cargo genes of Tn7-like transposons comprise an enormous diversity of defense systems, mobile genetic elements, and antibiotic resistance genes","volume":"12","author":"Benler","year":"2021","journal-title":"mBio"},{"key":"2026092809120200400_msag230-B5","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msae206","article-title":"Toxin-antitoxin systems reflect community interactions through horizontal gene transfer","volume":"41","author":"Bethke","year":"2024","journal-title":"Mol Biol Evol"},{"key":"2026092809120200400_msag230-B6","doi-asserted-by":"publisher","first-page":"18171","DOI":"10.1038\/s41598-020-72063-x","article-title":"Rapid growth inhibitory activity of a YafQ-family endonuclease toxin of the Helicobacter pylori tfs4 integrative and conjugative element","volume":"10","author":"Boampong","year":"2020","journal-title":"Sci Rep"},{"key":"2026092809120200400_msag230-B7","doi-asserted-by":"publisher","first-page":"2854","DOI":"10.1038\/ismej.2016.79","article-title":"Prophages mediate defense against phage infection through diverse mechanisms","volume":"10","author":"Bondy-Denomy","year":"2016","journal-title":"ISME J"},{"key":"2026092809120200400_msag230-B8","doi-asserted-by":"publisher","first-page":"1004","DOI":"10.1016\/j.chom.2025.04.021","article-title":"E. coli prophages encode an arsenal of defense systems to protect against temperate phages","volume":"33","author":"Brenes","year":"2025","journal-title":"Cell Host Microbe"},{"key":"2026092809120200400_msag230-B9","doi-asserted-by":"publisher","first-page":"6929","DOI":"10.1073\/pnas.81.22.6929","article-title":"Regulation of ribosomal RNA promoters with a synthetic lac operator","volume":"81","author":"Brosius","year":"1984","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026092809120200400_msag230-B10","doi-asserted-by":"publisher","first-page":"1303","DOI":"10.1038\/s41587-023-01953-y","article-title":"Identification of mobile genetic elements with geNomad","volume":"42","author":"Camargo","year":"2024","journal-title":"Nat Biotechnol"},{"key":"2026092809120200400_msag230-B11","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.220077897","article-title":"Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids","volume":"97","author":"Cooper","year":"2000","journal-title":"Proc Natl Acad Sci U S A."},{"key":"2026092809120200400_msag230-B12","doi-asserted-by":"publisher","first-page":"3149","DOI":"10.1098\/rspb.2010.0831","article-title":"Within-host competition selects for plasmid-encoded toxin\u2013antitoxin systems","volume":"277","author":"Cooper","year":"2010","journal-title":"Proc Biol Sci"},{"key":"2026092809120200400_msag230-B13","doi-asserted-by":"publisher","DOI":"10.1126\/science.ads0768","article-title":"Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems","volume":"388","author":"Darracq","year":"2025","journal-title":"Science"},{"key":"2026092809120200400_msag230-B14","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00763-19","article-title":"Type II toxin-antitoxin systems: evolution and revolutions","volume":"202","author":"Fraikin","year":"2020","journal-title":"J Bacteriol"},{"key":"2026092809120200400_msag230-B15","doi-asserted-by":"publisher","first-page":"1847","DOI":"10.1093\/nar\/gkae018","article-title":"Single-cell evidence for plasmid addiction mediated by toxin-antitoxin systems","volume":"52","author":"Fraikin","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026092809120200400_msag230-B16","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaf652","article-title":"The extended mobility of plasmids","volume":"53","author":"Garcill\u00e1n-Barcia","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026092809120200400_msag230-B17","doi-asserted-by":"publisher","first-page":"R117","DOI":"10.1186\/gb-2008-9-7-r117","article-title":"Plastic architecture of bacterial genome revealed by comparative genomics of Photorhabdus variants","volume":"9","author":"Gaudriault","year":"2008","journal-title":"Genome Biol"},{"key":"2026092809120200400_msag230-B18","doi-asserted-by":"publisher","first-page":"3116","DOI":"10.1073\/pnas.83.10.3116","article-title":"Unique type of plasmid maintenance function: postsegregational killing of plasmid-free cells","volume":"83","author":"Gerdes","year":"1986","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026092809120200400_msag230-B19","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1146\/annurev-virology-100422-125123","article-title":"Diverse antiphage defenses are widespread among prophages and mobile genetic elements","volume":"11","author":"Getz","year":"2024","journal-title":"Annu Rev Virol"},{"key":"2026092809120200400_msag230-B20","doi-asserted-by":"publisher","first-page":"2541","DOI":"10.1128\/JB.02266-12","article-title":"Relaxed cleavage specificity within the RelE toxin family","volume":"195","author":"Goeders","year":"2013","journal-title":"J Bacteriol"},{"key":"2026092809120200400_msag230-B21","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1012169","article-title":"Type II and IV toxin-antitoxin systems coordinately stabilize the integrative and conjugative element of the ICESa2603 family conferring multiple drug resistance in Streptococcus suis","volume":"20","author":"Gu","year":"2024","journal-title":"PLoS Pathog"},{"key":"2026092809120200400_msag230-B22","doi-asserted-by":"publisher","first-page":"4121","DOI":"10.1128\/jb.177.14.4121-4130.1995","article-title":"Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter","volume":"177","author":"Guzman","year":"1995","journal-title":"J Bacteriol"},{"key":"2026092809120200400_msag230-B23","doi-asserted-by":"publisher","first-page":"932","DOI":"10.1046\/j.1365-2958.2001.02436.x","article-title":"Experimental genome evolution: large-scale genome rearrangements associated with resistance to replacement of a chromosomal restriction-modification gene complex","volume":"40","author":"Handa","year":"2001","journal-title":"Mol Microbiol"},{"key":"2026092809120200400_msag230-B24","doi-asserted-by":"publisher","first-page":"386","DOI":"10.3109\/10409238.2011.600437","article-title":"Toxins-antitoxins: diversity, evolution and function","volume":"46","author":"Hayes","year":"2011","journal-title":"Crit Rev Biochem Mol Biol"},{"key":"2026092809120200400_msag230-B25","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1010694","article-title":"The defense island repertoire of the Escherichia coli pan-genome","volume":"19","author":"Hochhauser","year":"2023","journal-title":"PLoS Genet"},{"key":"2026092809120200400_msag230-B26","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.02616-24","article-title":"Shared mechanisms of enhanced plasmid maintenance and antibiotic tolerance mediated by the VapBC toxin:antitoxin system","volume":"16","author":"Hollingshead","year":"2025","journal-title":"mBio"},{"key":"2026092809120200400_msag230-B27","doi-asserted-by":"publisher","first-page":"4357","DOI":"10.1093\/nar\/gkaa198","article-title":"Type II and type IV toxin-antitoxin systems show different evolutionary patterns in the global Klebsiella pneumoniae population","volume":"48","author":"Horesh","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2026092809120200400_msag230-B28","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2026092809120200400_msag230-B29","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/s41579-021-00661-1","article-title":"Biology and evolution of bacterial toxin-antitoxin systems","volume":"20","author":"Jur\u0117nas","year":"2022","journal-title":"Nat Rev Microbiol"},{"key":"2026092809120200400_msag230-B30","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.815911","article-title":"Genome mining shows ubiquitous presence and extensive diversity of toxin-antitoxin systems in pseudomonas syringae","volume":"12","author":"Kandel","year":"2021","journal-title":"Front Microbiol"},{"key":"2026092809120200400_msag230-B31","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.03127-25","article-title":"Spatial-temporal genome analysis and its application for the prediction of functional systems in bacteria and archaea","volume":"17","author":"Karamycheva","year":"2026","journal-title":"mBio"},{"key":"2026092809120200400_msag230-B32","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2026092809120200400_msag230-B33","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2023.102293","article-title":"Toxin-antitoxin systems as mediators of phage defence and the implications for abortive infection","volume":"73","author":"Kelly","year":"2023","journal-title":"Curr Opin Microbiol"},{"key":"2026092809120200400_msag230-B34","doi-asserted-by":"publisher","DOI":"10.1126\/science.ads0915","article-title":"Mobile integrons encode phage defense systems","volume":"388","author":"Kieffer","year":"2025","journal-title":"Science"},{"key":"2026092809120200400_msag230-B35","doi-asserted-by":"publisher","first-page":"3742","DOI":"10.1093\/nar\/29.18.3742","article-title":"Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution","volume":"29","author":"Kobayashi","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"2026092809120200400_msag230-B36","doi-asserted-by":"publisher","DOI":"10.1126\/science.abg2166","article-title":"Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts","volume":"373","author":"LeGault","year":"2021","journal-title":"Science"},{"key":"2026092809120200400_msag230-B37","doi-asserted-by":"publisher","first-page":"5513","DOI":"10.1093\/nar\/gkr131","article-title":"Diversity of bacterial type II toxin\u2013antitoxin systems: a comprehensive search and functional analysis of novel families","volume":"39","author":"Leplae","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2026092809120200400_msag230-B38","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1146\/annurev-micro-020722-013730","article-title":"Toxin-antitoxin systems as phage defense elements","volume":"76","author":"LeRoux","year":"2022","journal-title":"Annu Rev Microbiol"},{"key":"2026092809120200400_msag230-B39","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00452-20","article-title":"Toxin-antitoxin gene pairs found in Tn3 family transposons appear to be an integral part of the transposition module","volume":"11","author":"Lima-Mendez","year":"2020","journal-title":"mBio"},{"key":"2026092809120200400_msag230-B40","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaf125","article-title":"A noncanonical intrinsic terminator in the HicAB toxin-antitoxin operon promotes the transmission of conjugative antibiotic resistance plasmids","volume":"53","author":"Lin","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026092809120200400_msag230-B41","doi-asserted-by":"publisher","first-page":"885","DOI":"10.1093\/molbev\/msv339","article-title":"Evolutionary paths that expand plasmid host-range: implications for spread of antibiotic resistance","volume":"33","author":"Loftie-Eaton","year":"2016","journal-title":"Mol Biol Evol"},{"key":"2026092809120200400_msag230-B42","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/1745-6150-4-19","article-title":"Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes","volume":"4","author":"Makarova","year":"2009","journal-title":"Biol Direct."},{"key":"2026092809120200400_msag230-B43","doi-asserted-by":"publisher","first-page":"6039","DOI":"10.1128\/JB.05535-11","article-title":"Defense islands in bacterial and archaeal genomes and prediction of novel defense systems","volume":"193","author":"Makarova","year":"2011","journal-title":"J Bacteriol"},{"key":"2026092809120200400_msag230-B44","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msaf192","article-title":"Impact of natural transformation on the acquisition of novel genes in bacteria","volume":"42","author":"Mazzamurro","year":"2025","journal-title":"Mol Biol Evol"},{"key":"2026092809120200400_msag230-B45","doi-asserted-by":"publisher","DOI":"10.1128\/jb.00232-25","article-title":"Beyond plasmid addiction: the role of toxin-antitoxin systems in the selfish behavior of mobile genetic elements","volume":"207","author":"Mendoza-Guido","year":"2025","journal-title":"J Bacteriol"},{"key":"2026092809120200400_msag230-B46","doi-asserted-by":"publisher","first-page":"1557","DOI":"10.1534\/genetics.108.095190","article-title":"The decay of the chromosomally encoded ccdO157 toxin-antitoxin system in the Escherichia coli species","volume":"181","author":"Mine","year":"2009","journal-title":"Genetics"},{"key":"2026092809120200400_msag230-B47","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1093\/nar\/gkt711","article-title":"To be or not to be: regulation of restriction-modification systems and other toxin-antitoxin systems","volume":"42","author":"Mruk","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2026092809120200400_msag230-B48","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"key":"2026092809120200400_msag230-B49","doi-asserted-by":"publisher","first-page":"568","DOI":"10.1186\/1471-2164-11-568","article-title":"Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus","volume":"11","author":"Ogier","year":"2010","journal-title":"BMC Genomics"},{"key":"2026092809120200400_msag230-B50","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1038\/s41467-017-00808-w","article-title":"The chromosomal organization of horizontal gene transfer in bacteria","volume":"8","author":"Oliveira","year":"2017","journal-title":"Nat Commun"},{"key":"2026092809120200400_msag230-B51","doi-asserted-by":"publisher","DOI":"10.1093\/nargab\/lqaa106","article-title":"PanACoTA: a modular tool for massive microbial comparative genomics","volume":"3","author":"Perrin","year":"2021","journal-title":"NAR Genom Bioinform"},{"key":"2026092809120200400_msag230-B52","doi-asserted-by":"publisher","first-page":"W200","DOI":"10.1093\/nar\/gky448","article-title":"HMMER web server: 2018 update","volume":"46","author":"Potter","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2026092809120200400_msag230-B53","doi-asserted-by":"publisher","DOI":"10.1093\/femsle\/fnv238","article-title":"Horizontal gene transfer of chromosomal type II toxin-antitoxin systems of Escherichia coli","volume":"363","author":"Ramisetty","year":"2016","journal-title":"FEMS Microbiol Lett"},{"key":"2026092809120200400_msag230-B54","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1011231","article-title":"Belt and braces: two escape ways to maintain the cassette reservoir of large chromosomal integrons","volume":"20","author":"Richard","year":"2024","journal-title":"PLoS Genet"},{"key":"2026092809120200400_msag230-B55","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.02060-21","article-title":"Tncentral: a prokaryotic transposable element database and web portal for transposon analysis","volume":"12","author":"Ross","year":"2021","journal-title":"mBio"},{"key":"2026092809120200400_msag230-B56","doi-asserted-by":"publisher","first-page":"4603","DOI":"10.1128\/JB.00357-08","article-title":"Chromosomal toxin-antitoxin systems may act as antiaddiction modules","volume":"190","author":"Saavedra De Bast","year":"2008","journal-title":"J Bacteriol."},{"key":"2026092809120200400_msag230-B57","doi-asserted-by":"publisher","first-page":"D32","DOI":"10.1093\/nar\/gkj014","article-title":"ISfinder: the reference centre for bacterial insertion sequences","volume":"34","author":"Siguier","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2026092809120200400_msag230-B58","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.03023-23","article-title":"Unraveling the evolutionary dynamics of toxin-antitoxin systems in diverse genetic lineages of Escherichia coli including the high-risk clonal complexes","volume":"15","author":"Singh","year":"2024","journal-title":"mBio"},{"key":"2026092809120200400_msag230-B59","doi-asserted-by":"publisher","first-page":"W244","DOI":"10.1093\/nar\/gki408","article-title":"The HHpred interactive server for protein homology detection and structure prediction","volume":"33","author":"S\u00f6ding","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2026092809120200400_msag230-B60","doi-asserted-by":"publisher","first-page":"4853","DOI":"10.1038\/s41598-017-04662-0","article-title":"Emerging patterns of plasmid-host coevolution that stabilize antibiotic resistance","volume":"7","author":"Stalder","year":"2017","journal-title":"Sci Rep"},{"key":"2026092809120200400_msag230-B61","doi-asserted-by":"publisher","first-page":"1026","DOI":"10.1038\/nbt.3988","article-title":"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets","volume":"35","author":"Steinegger","year":"2017","journal-title":"Nat Biotechnol"},{"key":"2026092809120200400_msag230-B62","doi-asserted-by":"publisher","first-page":"2561","DOI":"10.1038\/s41467-022-30269-9","article-title":"Systematic and quantitative view of the antiviral arsenal of prokaryotes","volume":"13","author":"Tesson","year":"2022","journal-title":"Nat Commun"},{"key":"2026092809120200400_msag230-B63","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae1171","article-title":"Exploring the diversity of anti-defense systems across prokaryotes, phages and mobile genetic elements","volume":"53","author":"Tesson","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026092809120200400_msag230-B64","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1016\/j.mib.2017.04.010","article-title":"Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer","volume":"38","author":"Touchon","year":"2017","journal-title":"Curr Opin Microbiol"},{"key":"2026092809120200400_msag230-B65","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1093\/nar\/gkj406","article-title":"Mage: a microbial genome annotation system supported by synteny results","volume":"34","author":"Vallenet","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2026092809120200400_msag230-B66","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1111\/j.1365-2958.1994.tb00391.x","article-title":"Lon-dependent proteolysis of CcdA is the key control for activation of CcdB in plasmid-free segregant bacteria","volume":"11","author":"Van Melderen","year":"1994","journal-title":"Mol Microbiol"},{"key":"2026092809120200400_msag230-B67","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000439","article-title":"A toxin\u2013antitoxin system promotes the maintenance of an integrative conjugative element","volume":"5","author":"Wozniak","year":"2009","journal-title":"PLoS Genet"},{"key":"2026092809120200400_msag230-B68","doi-asserted-by":"publisher","first-page":"3340","DOI":"10.1093\/bioinformatics\/btx433","article-title":"ISEScan: automated identification of insertion sequence elements in prokaryotic genomes","volume":"33","author":"Xie","year":"2017","journal-title":"Bioinformatics"},{"key":"2026092809120200400_msag230-B69","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1016\/j.compbiolchem.2018.07.010","article-title":"TAome analysis of type-II toxin-antitoxin system from Xenorhabdus nematophila","volume":"76","author":"Yadav","year":"2018","journal-title":"Comput Biol Chem"}],"container-title":["Molecular Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/mbe\/advance-article-pdf\/doi\/10.1093\/molbev\/msag230\/71009771\/msag230.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mbe\/article-pdf\/43\/9\/msag230\/71009771\/msag230.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mbe\/article-pdf\/43\/9\/msag230\/71009771\/msag230.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T13:12:49Z","timestamp":1790601169000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/mbe\/article\/doi\/10.1093\/molbev\/msag230\/8789390"}},"subtitle":[],"editor":[{"given":"Deepa","family":"Agashe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,9,1]]},"references-count":69,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2026,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/molbev\/msag230","relation":{},"ISSN":["0737-4038","1537-1719"],"issn-type":[{"value":"0737-4038","type":"print"},{"value":"1537-1719","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,9]]},"published":{"date-parts":[[2026,9,1]]},"article-number":"msag230"}}