{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T10:10:36Z","timestamp":1788862236942,"version":"build-2803163510"},"reference-count":74,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T00:00:00Z","timestamp":1788825600000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001654","name":"German Academic Exchange Service","doi-asserted-by":"publisher","award":["01IM19001"],"award-info":[{"award-number":["01IM19001"]}],"id":[{"id":"10.13039\/501100001654","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["468749960"],"award-info":[{"award-number":["468749960"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Health Sciences Career Development Postdoctoral Fellowship"},{"DOI":"10.13039\/100008247","name":"University of Otago","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008247","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014111","name":"Bioprotection Aotearoa","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014111","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Centre of Research Excellence"},{"DOI":"10.13039\/100007879","name":"Tertiary Education Commission, NZ","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100007879","id-type":"DOI","asserted-by":"crossref"}]},{"name":"James Cook Research Fellowship"},{"DOI":"10.13039\/501100001509","name":"Royal Society of New Zealand, Te Ap\u0101rangi","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100001509","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100008678","name":"Leipzig University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008678","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Many bacteriophages encode anti-CRISPR (Acr) proteins that inhibit bacterial CRISPR\u2013Cas immune systems. Rapid acr gene expression upon phage entry enables CRISPR\u2013Cas neutralization but can impact phage fitness if unregulated. Therefore, Acr production is often controlled by distinct families of co-encoded anti-CRISPR-associated (Aca) proteins, which are usually helix-turn-helix (HTH) regulators that bind DNA within acr\u2013aca operon promoters. Previously, we demonstrated that the Aca2 family additionally represses Acr production translationally by binding structured RNA motifs within the 5\u2032 untranslated region (UTR) of the\u00a0acr\u2013aca mRNA. Here, through systematic bioinformatic analyses, we provide evidence of structured RNA motifs in the 5\u2032 UTRs of operons encoding members of other Aca families and show that Aca1 also specifically binds its cognate RNA motif. Additionally, many Aca proteins are predicted to regulate not only their own but also adjacent operons with potential anti-defence genes. Indeed, we show that Aca14, newly identified in this study, represses two predicted anti-defence operons. Aca14 is a ribbon-helix-helix domain protein, revealing regulatory diversity beyond the canonical HTH Aca family members. Collectively, our findings expand our understanding of acr regulation in mobile genetic elements and reveal novel mechanisms by which phages fine-tune anti-defence gene expression.<\/jats:p>","DOI":"10.1093\/nar\/gkag862","type":"journal-article","created":{"date-parts":[[2026,8,22]],"date-time":"2026-08-22T11:42:25Z","timestamp":1787398945000},"source":"Crossref","is-referenced-by-count":0,"title":["An expanded realm of anti-CRISPR-associated proteins and regulatory mechanisms"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-2803-0496","authenticated-orcid":false,"given":"Maximilian","family":"Feussner","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University , 04107 Leipzig ,","place":["Germany"]},{"name":"Botnar Institute of Immune Engineering , 4056 Basel ,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5269-5228","authenticated-orcid":false,"given":"Nils","family":"Birkholz","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of Otago , PO Box 56, Dunedin 9054 ,","place":["New Zealand"]},{"name":"Bioprotection Aotearoa, University of Otago , PO Box 56, Dunedin 9054 ,","place":["New Zealand"]},{"name":"Genetics Otago, University of Otago , PO Box 56, Dunedin 9054 ,","place":["New Zealand"]},{"name":"Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago , PO Box 56, Dunedin 9054 ,","place":["New Zealand"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0444-2079","authenticated-orcid":false,"given":"So Yeon","family":"Lee","sequence":"additional","affiliation":[{"name":"College of Pharmacy, Chung-Ang University , Seoul 06974 ,","place":["Republic of Korea"]},{"name":"Department of Global Innovative Drugs, Graduate School of Chung-Ang University , Seoul 06974 ,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0650-9943","authenticated-orcid":false,"given":"Chase L","family":"Beisel","sequence":"additional","affiliation":[{"name":"Botnar Institute of Immune Engineering , 4056 Basel ,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9928-0847","authenticated-orcid":false,"given":"Hyun\u00a0Ho","family":"Park","sequence":"additional","affiliation":[{"name":"College of Pharmacy, Chung-Ang University , Seoul 06974 ,","place":["Republic of Korea"]},{"name":"Department of Global Innovative Drugs, Graduate School of Chung-Ang University , Seoul 06974 ,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0079-7067","authenticated-orcid":false,"given":"Chris M","family":"Brown","sequence":"additional","affiliation":[{"name":"Bioprotection Aotearoa, University of Otago , PO Box 56, Dunedin 9054 ,","place":["New Zealand"]},{"name":"Genetics Otago, University of Otago , PO Box 56, Dunedin 9054 ,","place":["New Zealand"]},{"name":"Department of Biochemistry, University of Otago , PO Box 56, Dunedin 9054 ,","place":["New Zealand"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4639-6704","authenticated-orcid":false,"given":"Peter C","family":"Fineran","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of Otago , PO Box 56, Dunedin 9054 ,","place":["New Zealand"]},{"name":"Bioprotection Aotearoa, University of Otago , PO Box 56, Dunedin 9054 ,","place":["New Zealand"]},{"name":"Genetics Otago, University of Otago , PO Box 56, Dunedin 9054 ,","place":["New Zealand"]},{"name":"Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago , PO Box 56, Dunedin 9054 ,","place":["New Zealand"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6681-3624","authenticated-orcid":false,"given":"Zasha","family":"Weinberg","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University , 04107 Leipzig ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,8]]},"reference":[{"key":"2026090805164958300_B1","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1038\/nrmicro1750","article-title":"Marine viruses\u2014major players in the global ecosystem","volume":"5","author":"Suttle","year":"2007","journal-title":"Nat Rev Microbiol"},{"key":"2026090805164958300_B2","doi-asserted-by":"crossref","first-page":"112672","DOI":"10.1016\/j.celrep.2023.112672","article-title":"A host of armor: prokaryotic immune strategies against mobile genetic elements","volume":"42","author":"Mayo-Mu\u00f1oz","year":"2023","journal-title":"Cell Rep"},{"key":"2026090805164958300_B3","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1038\/s41576-023-00676-9","article-title":"Inhibitors of bacterial immune systems: discovery, mechanisms and applications","volume":"25","author":"Mayo-Mu\u00f1oz","year":"2024","journal-title":"Nat Rev Genet"},{"key":"2026090805164958300_B4","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1038\/s41586-019-1894-8","article-title":"The arms race between bacteria and their phage foes","volume":"577","author":"Hampton","year":"2020","journal-title":"Nature"},{"key":"2026090805164958300_B5","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1038\/s41586-023-06612-5","article-title":"Bacteriophages suppress CRISPR\u2013Cas immunity using RNA-based anti-CRISPRs","volume":"623","author":"Camara-Wilpert","year":"2023","journal-title":"Nature"},{"key":"2026090805164958300_B6","doi-asserted-by":"publisher","article-title":"Phage-encoded single-guide RNAs subvert CRISPR\u2013Cas9 immunity","author":"Feussner","DOI":"10.64898\/2026.06.01.729453"},{"key":"2026090805164958300_B7","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1089\/crispr.2018.0043","article-title":"A unified resource for tracking anti-CRISPR Names","volume":"1","author":"Bondy-Denomy","year":"2018","journal-title":"CRISPR J"},{"key":"2026090805164958300_B8","doi-asserted-by":"publisher","first-page":"168120","DOI":"10.1016\/j.jmb.2023.168120","article-title":"Applications of anti-CRISPR proteins in genome editing and biotechnology","volume":"435","author":"Kraus","year":"2023","journal-title":"J Mol Biol"},{"key":"2026090805164958300_B9","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1038\/nrmicro.2017.120","article-title":"Anti-CRISPR: discovery, mechanism and function","volume":"16","author":"Pawluk","year":"2018","journal-title":"Nat Rev Microbiol"},{"key":"2026090805164958300_B10","doi-asserted-by":"publisher","first-page":"1452","DOI":"10.1016\/j.cell.2019.07.046","article-title":"Anti-CRISPR-associated proteins are crucial repressors of anti-CRISPR transcription","volume":"178","author":"Stanley","year":"2019","journal-title":"Cell"},{"key":"2026090805164958300_B11","doi-asserted-by":"publisher","first-page":"670","DOI":"10.1038\/s41586-024-07644-1","article-title":"Phage anti-CRISPR control by an RNA- and DNA-binding helix\u2013turn\u2013helix protein","volume":"631","author":"Birkholz","year":"2024","journal-title":"Nature"},{"key":"2026090805164958300_B12","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1016\/j.femsre.2004.12.008","article-title":"The many faces of the helix-turn-helix domain: transcription regulation and beyond","volume":"29","author":"Aravind","year":"2005","journal-title":"FEMS Microbiol Rev"},{"key":"2026090805164958300_B13","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1007\/BF02300748","article-title":"Many gene-regulatory proteins appear to have a similar \u03b1-helical fold that binds DNA and evolved from a common precursor","volume":"19","author":"Ohlendorf","year":"1983","journal-title":"J Mol Evol"},{"key":"2026090805164958300_B14","doi-asserted-by":"publisher","first-page":"744","DOI":"10.1038\/290744a0","article-title":"Structure of catabolite gene activator protein at 2.9 \u00c5 resolution suggests binding to left-handed B-DNA","volume":"290","author":"McKay","year":"1981","journal-title":"Nature"},{"key":"2026090805164958300_B15","doi-asserted-by":"publisher","first-page":"754","DOI":"10.1038\/290754a0","article-title":"Structure of the cro repressor from bacteriophage \u03bb and its interaction with DNA","volume":"290","author":"Anderson","year":"1981","journal-title":"Nature"},{"key":"2026090805164958300_B16","doi-asserted-by":"publisher","first-page":"9658","DOI":"10.1093\/nar\/gkz721","article-title":"The autoregulator Aca2 mediates anti-CRISPR repression","volume":"47","author":"Birkholz","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2026090805164958300_B17","doi-asserted-by":"publisher","first-page":"8615","DOI":"10.1093\/nar\/gkac674","article-title":"Widespread repression of anti-CRISPR production by anti-CRISPR-associated proteins","volume":"50","author":"Shehreen","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2026090805164958300_B18","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1093\/bioinformatics\/btk008","article-title":"CMfinder\u2014a covariance model based RNA motif finding algorithm","volume":"22","author":"Yao","year":"2006","journal-title":"Bioinformatics"},{"key":"2026090805164958300_B19","doi-asserted-by":"publisher","first-page":"gkaf694","DOI":"10.1093\/nar\/gkaf694","article-title":"Identification of regulatory sequences in Aca11 and Aca13 for detection of anti-CRISPR and protein\u2013protein interaction","volume":"53","author":"Song","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026090805164958300_B20","doi-asserted-by":"publisher","first-page":"W25","DOI":"10.1093\/nar\/gky329","article-title":"Freiburg RNA tools: a central online resource for RNA-focused research and teaching","volume":"46","author":"Raden","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2026090805164958300_B21","doi-asserted-by":"publisher","first-page":"2933","DOI":"10.1093\/bioinformatics\/btt509","article-title":"Infernal 1.1: 100-fold faster RNA homology searches","volume":"29","author":"Nawrocki","year":"2013","journal-title":"Bioinformatics"},{"key":"2026090805164958300_B22","doi-asserted-by":"publisher","first-page":"5159","DOI":"10.1038\/s41467-022-32829-5","article-title":"Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria","volume":"13","author":"LaFleur","year":"2022","journal-title":"Nat Commun"},{"key":"2026090805164958300_B23","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1038\/nmeth.4066","article-title":"A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs","volume":"14","author":"Rivas","year":"2017","journal-title":"Nat Methods"},{"key":"2026090805164958300_B24","doi-asserted-by":"publisher","first-page":"W39","DOI":"10.1093\/nar\/gkv416","article-title":"The MEME Suite","volume":"43","author":"Bailey","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2026090805164958300_B25","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"2026090805164958300_B26","doi-asserted-by":"publisher","first-page":"D723","DOI":"10.1093\/nar\/gkac976","article-title":"The IMG\/M data management and analysis system v.7: content updates and new features","volume":"51","author":"Chen","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"2026090805164958300_B27","doi-asserted-by":"publisher","first-page":"W521","DOI":"10.1093\/nar\/gkae241","article-title":"The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024","volume":"52","author":"Madeira","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026090805164958300_B28","doi-asserted-by":"publisher","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2\u2014approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PLoS One"},{"key":"2026090805164958300_B29","doi-asserted-by":"publisher","first-page":"W78","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool","volume":"52","author":"Letunic","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026090805164958300_B30","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"2026090805164958300_B31","doi-asserted-by":"publisher","first-page":"406","DOI":"10.2307\/2412116","article-title":"Toward defining the course of evolution: minimum change for a specific tree topology","volume":"20","author":"Fitch","year":"1971","journal-title":"Syst Zool"},{"key":"2026090805164958300_B32","doi-asserted-by":"publisher","first-page":"e1009885","DOI":"10.1371\/journal.pcbi.1009885","article-title":"Phylogenetic analysis of migration, differentiation, and class switching in B cells","volume":"18","author":"Hoehn","year":"2022","journal-title":"PLoS Comput Biol"},{"key":"2026090805164958300_B33","doi-asserted-by":"crossref","first-page":"D733","DOI":"10.1093\/nar\/gkv1189","article-title":"Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation","volume":"44","author":"O\u2019Leary","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2026090805164958300_B34","article-title":"The E-utilities in-depth: parameters, syntax and more","volume-title":"Entrez Programming Utilities Help [Internet]","author":"Sayers","year":"2022"},{"key":"2026090805164958300_B35","doi-asserted-by":"publisher","first-page":"D384","DOI":"10.1093\/nar\/gkac1096","article-title":"The conserved domain database in 2023","volume":"51","author":"Wang","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2026090805164958300_B36","doi-asserted-by":"publisher","first-page":"D419","DOI":"10.1093\/nar\/gkad932","article-title":"dbAPIS: a database of anti-prokaryotic immune system genes","volume":"52","author":"Yan","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026090805164958300_B37","doi-asserted-by":"publisher","first-page":"gkae1171","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":"2026090805164958300_B38","doi-asserted-by":"publisher","first-page":"e121","DOI":"10.1093\/nar\/gkt263","article-title":"Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions","volume":"41","author":"Mistry","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2026090805164958300_B39","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"2026090805164958300_B40","first-page":"82","article-title":"Pymol: an open-source molecular graphics tool","volume":"40","author":"DeLano","year":"2002","journal-title":"CCP4 Newsl Protein Crystallogr"},{"key":"2026090805164958300_B41","doi-asserted-by":"publisher","first-page":"W431","DOI":"10.1093\/nar\/gkab314","article-title":"Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures","volume":"49","author":"Sehnal","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026090805164958300_B42","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":"2026090805164958300_B43","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1038\/s41564-020-00822-7","article-title":"The Rcs stress response inversely controls surface and CRISPR\u2013Cas adaptive immunity to discriminate plasmids and phages","volume":"6","author":"Smith","year":"2021","journal-title":"Nat Microbiol"},{"key":"2026090805164958300_B44","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1177\/25731599251369720","article-title":"A phage variable region encodes anti-CRISPR proteins inhibiting all Streptococcus thermophilus CRISPR immune systems","volume":"8","author":"Johnson","year":"2025","journal-title":"CRISPR J"},{"key":"2026090805164958300_B45","doi-asserted-by":"publisher","first-page":"101357","DOI":"10.1016\/j.jbc.2021.101357","article-title":"Structural basis for anti-CRISPR repression mediated by bacterial operon proteins Aca1 and Aca2","volume":"297","author":"Liu","year":"2021","journal-title":"J Biol Chem"},{"key":"2026090805164958300_B46","doi-asserted-by":"publisher","first-page":"3699","DOI":"10.1038\/s41467-024-48074-x","article-title":"Regulatory sequence-based discovery of anti-defense genes in archaeal viruses","volume":"15","author":"Bhoobalan-Chitty","year":"2024","journal-title":"Nat Commun"},{"key":"2026090805164958300_B47","doi-asserted-by":"publisher","first-page":"e29","DOI":"10.1093\/nar\/gkab1207","article-title":"Identification and classification of reverse transcriptases in bacterial genomes and metagenomes","volume":"50","author":"Sharifi","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2026090805164958300_B48","doi-asserted-by":"publisher","first-page":"2604","DOI":"10.1038\/s41467-025-57851-1","article-title":"Bacterial Hachiman complex executes DNA cleavage for antiphage defense","volume":"16","author":"Cui","year":"2025","journal-title":"Nat Commun"},{"key":"2026090805164958300_B49","doi-asserted-by":"publisher","first-page":"1608","DOI":"10.3390\/cells11101608","article-title":"DEAD\/H-Box helicases in immunity, inflammation, cell differentiation, and cell death and disease","volume":"11","author":"Samir","year":"2022","journal-title":"Cells"},{"key":"2026090805164958300_B50","doi-asserted-by":"publisher","first-page":"4787","DOI":"10.1038\/s41467-026-70671-1","article-title":"A single viral enzyme drives tRNA-dependent hypermodification of DNA at adenine","volume":"17","author":"Silva","year":"2026","journal-title":"Nat Commun"},{"key":"2026090805164958300_B51","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1146\/annurev-micro-041222-014330","article-title":"DNA phosphorothioate modification systems and associated phage defense systems","volume":"78","author":"Wang","year":"2024","journal-title":"Annu Rev Microbiol"},{"key":"2026090805164958300_B52","doi-asserted-by":"publisher","first-page":"6382","DOI":"10.1038\/s41467-021-26636-7","article-title":"The origin and impeded dissemination of the DNA phosphorothioation system in prokaryotes","volume":"12","author":"Jian","year":"2021","journal-title":"Nat Commun"},{"key":"2026090805164958300_B53","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.1093\/nar\/gkad1213","article-title":"Reappraisal of the DNA phosphorothioate modification machinery: uncovering neglected functional modalities and identification of new counter-invader defense systems","volume":"52","author":"Rakesh","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026090805164958300_B54","doi-asserted-by":"publisher","first-page":"5294","DOI":"10.1093\/nar\/gkaa319","article-title":"Emergence of a novel immune-evasion strategy from an ancestral protein fold in bacteriophage Mu","volume":"48","author":"Karambelkar","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2026090805164958300_B55","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1038\/s41586-024-07923-x","article-title":"Diverse viral cas genes antagonize CRISPR immunity","volume":"634","author":"Katz","year":"2024","journal-title":"Nature"},{"key":"2026090805164958300_B56","doi-asserted-by":"publisher","first-page":"1075","DOI":"10.1038\/s41564-022-01157-1","article-title":"Phage\u2013host coevolution in natural populations","volume":"7","author":"Piel","year":"2022","journal-title":"Nat Microbiol"},{"key":"2026090805164958300_B57","doi-asserted-by":"publisher","first-page":"e00245","DOI":"10.1128\/JB.00245-17","article-title":"Polyvalent proteins, a pervasive theme in the intergenomic biological conflicts of bacteriophages and conjugative elements","volume":"199","author":"Iyer","year":"2017","journal-title":"J Bacteriol"},{"key":"2026090805164958300_B58","doi-asserted-by":"publisher","first-page":"710","DOI":"10.1038\/nrmicro1717","article-title":"Ribbon\u2013helix\u2013helix transcription factors: variations on a theme","volume":"5","author":"Schreiter","year":"2007","journal-title":"Nat Rev Microbiol"},{"key":"2026090805164958300_B59","doi-asserted-by":"publisher","first-page":"20240084","DOI":"10.1098\/rstb.2024.0084","article-title":"Diversity and abundance of ring nucleases in type III CRISPR\u2013Cas loci","volume":"380","author":"Hoikkala","year":"2025","journal-title":"Phil Trans R Soc B"},{"key":"2026090805164958300_B60","doi-asserted-by":"publisher","first-page":"572","DOI":"10.1038\/s41586-019-1909-5","article-title":"An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity","volume":"577","author":"Athukoralage","year":"2020","journal-title":"Nature"},{"key":"2026090805164958300_B61","doi-asserted-by":"publisher","first-page":"2883","DOI":"10.1038\/s41467-022-30553-8","article-title":"The RNA-bound proteome of MRSA reveals post-transcriptional roles for helix-turn-helix DNA-binding and Rossmann-fold proteins","volume":"13","author":"Chu","year":"2022","journal-title":"Nat Commun"},{"key":"2026090805164958300_B62","doi-asserted-by":"publisher","first-page":"26","DOI":"10.3389\/fcimb.2012.00026","article-title":"The staphylococcal accessory regulator, SarA, is an RNA-binding protein that modulates the mRNA turnover properties of late-exponential and stationary phase Staphylococcus aureus cells","volume":"2","author":"Morrison","year":"2012","journal-title":"Front Cell Inf Microbiol"},{"key":"2026090805164958300_B63","doi-asserted-by":"publisher","first-page":"2883","DOI":"10.1038\/s41467-022-30553-8","article-title":"The RNA-bound proteome of MRSA reveals post-transcriptional roles for helix-turn-helix DNA-binding and Rossmann-fold proteins","volume":"13","author":"Chu","year":"2022","journal-title":"Nat Commun"},{"key":"2026090805164958300_B64","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1038\/s41586-024-07994-w","article-title":"Diverse anti-defence systems are encoded in the leading region of plasmids","volume":"635","author":"Samuel","year":"2024","journal-title":"Nature"},{"key":"2026090805164958300_B65","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1038\/s41467-024-45068-7","article-title":"Structure-guided discovery of anti-CRISPR and anti-phage defense proteins","volume":"15","author":"Duan","year":"2024","journal-title":"Nat Commun"},{"key":"2026090805164958300_B66","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1038\/s41576-019-0172-9","article-title":"Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire","volume":"21","author":"Koonin","year":"2020","journal-title":"Nat Rev Genet"},{"key":"2026090805164958300_B67","doi-asserted-by":"publisher","first-page":"908","DOI":"10.1016\/j.cell.2018.05.058","article-title":"Anti-CRISPR phages cooperate to overcome CRISPR\u2013Cas immunity","volume":"174","author":"Landsberger","year":"2018","journal-title":"Cell"},{"key":"2026090805164958300_B68","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1038\/s41586-024-07642-3","article-title":"An anti-CRISPR that pulls apart a CRISPR\u2013Cas complex","volume":"632","author":"Trost","year":"2024","journal-title":"Nature"},{"key":"2026090805164958300_B69","doi-asserted-by":"publisher","first-page":"3172","DOI":"10.1016\/j.molcel.2024.08.008","article-title":"Anti-CRISPRs deconstruct bacterial defense","volume":"84","author":"Birkholz","year":"2024","journal-title":"Mol Cell"},{"key":"2026090805164958300_B70","doi-asserted-by":"publisher","first-page":"1806","DOI":"10.1038\/s41467-024-45987-5","article-title":"An anti-CRISPR that represses its own transcription while blocking Cas9-target DNA binding","volume":"15","author":"Deng","year":"2024","journal-title":"Nat Commun"},{"key":"2026090805164958300_B71","doi-asserted-by":"publisher","first-page":"11344","DOI":"10.1093\/nar\/gkac880","article-title":"Molecular basis of dual anti-CRISPR and auto-regulatory functions of AcrIF24","volume":"50","author":"Kim","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2026090805164958300_B72","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1016\/j.chom.2020.04.002","article-title":"Critical anti-CRISPR locus repression by a bi-functional Cas9 inhibitor","volume":"28","author":"Osuna","year":"2020","journal-title":"Cell Host Microbe"},{"key":"2026090805164958300_B73","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1096\/fasebj.9.8.7768350","article-title":"Zinc fingers","volume":"9","author":"Klug","year":"1995","journal-title":"FASEB J"},{"key":"2026090805164958300_B74","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1186\/gb-2004-5-6-226","article-title":"An overview of the basic helix-loop-helix proteins","volume":"5","author":"Jones","year":"2004","journal-title":"Genome Biol"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/54\/17\/gkag862\/70989742\/gkag862.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/54\/17\/gkag862\/70989742\/gkag862.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T09:17:01Z","timestamp":1788859021000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/doi\/10.1093\/nar\/gkag862\/8787810"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,7]]},"references-count":74,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2026,9,7]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkag862","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,9,23]]},"published":{"date-parts":[[2026,9,7]]},"article-number":"gkag862"}}