{"doi":"10.1093/nar/gkaf645","title":"Regulation of a phage defence island by RptR, a novel repressor that controls restriction–modification systems in diverse bacteria","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>Bacteria encode a panoply of defence systems to overcome phage infection. In recent years, over 100 defence systems have been identified, with the majority of these found co-localized in defence islands. Although there has been much progress in understanding the mechanisms of anti-phage defence employed by bacteria, far less is known about their regulation before and during phage infection. Here, we describe RptR (RMS-proximal transcriptional regulator), a small transcriptional regulator of a defence island in enteropathogenic Escherichia coli composed of a toxin–antitoxin system, DarTG2, embedded within a Type I restriction–modification system (RMS). We determined the molecular structure of a RptR homodimer and, using transcriptional reporter and in vitro DNA binding assays, show that RptR represses the promoter of the defence island by binding to a series of three direct repeats in the promoter. Furthermore, we demonstrate, using the structural models of RptR validated with electrophoretic mobility shift assays, that the minimal RptR binding site is a 6-bp palindrome, TAGCTA. Both RptR and its binding site are highly conserved across diverse bacterial genomes with a strong genetic association with Type I RMS, highlighting the role of RptR as a novel regulatory component of an important mechanism for anti-phage defence in bacteria.</jats:p>","journal":"Nucleic Acids Research","year":2025,"id":643685,"datarank":0.31191623125197543,"base_score":2.0794415416798357,"endowment":2.0794415416798357,"self_citation_contribution":0.31191623125197543,"citation_network_contribution":0.0,"self_endowment_contribution":0.31191623125197543,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1674910,"name":"Marion Schuller","orcid":null,"position":1,"is_corresponding":false},{"id":263641,"name":"Ivan Ahel","orcid":"0000-0002-9446-3756","position":2,"is_corresponding":false},{"id":1084863,"name":"Tim R. Blower","orcid":"0000-0002-7390-6458","position":3,"is_corresponding":false},{"id":1674911,"name":"Rachel M Exley","orcid":null,"position":4,"is_corresponding":false},{"id":294747,"name":"Christoph M. Tang","orcid":"0000-0001-8366-3245","position":5,"is_corresponding":false},{"id":1674909,"name":"YuGeng Zhang","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Regulation of a phage defence island by RptR, a novel repressor that controls restriction–modification systems in diverse bacteria","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>Bacteria encode a panoply of defence systems to overcome phage infection. In recent years, over 100 defence systems have been identified, with the majority of these found co-localized in defence islands. Although there has been much progress in understanding the mechanisms of anti-phage defence employed by bacteria, far less is known about their regulation before and during phage infection. Here, we describe RptR (RMS-proximal transcriptional regulator), a small transcriptional regulator of a defence island in enteropathogenic Escherichia coli composed of a toxin–antitoxin system, DarTG2, embedded within a Type I restriction–modification system (RMS). We determined the molecular structure of a RptR homodimer and, using transcriptional reporter and in vitro DNA binding assays, show that RptR represses the promoter of the defence island by binding to a series of three direct repeats in the promoter. Furthermore, we demonstrate, using the structural models of RptR validated with electrophoretic mobility shift assays, that the minimal RptR binding site is a 6-bp palindrome, TAGCTA. Both RptR and its binding site are highly conserved across diverse bacterial genomes with a strong genetic association with Type I RMS, highlighting the role of RptR as a novel regulatory component of an important mechanism for anti-phage defence in bacteria.</jats:p>","is_dataset_classified":null,"base_score":1.9459101490553132,"endowment":1.9459101490553132,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"40650974","pmcid":"PMC12255303","openalex_id":"https://openalex.org/W4412366184","authors":[],"funders":[{"funder_name":"Wellcome Trust","grant_id":"221924/Z/20/Z","title":null},{"funder_name":"Wellcome Trust","grant_id":"214374/Z/18/Z","title":null},{"funder_name":"BBSRC","grant_id":"BB/W016613/1","title":"ADP-ribosylation of DNA in Mycobacterium tuberculosis"},{"funder_name":"Wellcome Trust","grant_id":"223107","title":"Reversible ADP-ribosylation signaling in the control of coronavirus infection"},{"funder_name":"Wellcome Trust","grant_id":"302632","title":"ADP-ribosylation signalling in genome stability"},{"funder_name":"Wellcome Trust","grant_id":"221924","title":"Plasmid biology in human adapted pathogens"},{"funder_name":"Wellcome Trust","grant_id":"214374","title":"Gonococcal vaccine initiative"},{"funder_name":"Wellcome Trust","grant_id":"","title":null}],"total_grants":8,"fwci":5.4794,"citation_percentile":0.95701311,"influential_citations":0,"citation_trend":[{"year":2025,"count":3},{"year":2026,"count":3}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://academic.oup.com/nar/article-pdf/53/13/gkaf645/63735405/gkaf645.pdf","host_type":"journal"},{"url":"https://academic.oup.com/nar/article-pdf/53/13/gkaf645/63735405/gkaf645.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/nar/gkaf645","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/40650974","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12255303","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC12255303","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC12255303?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.1093/nar/gkaf645","host_type":""},{"url":"https://ora.ox.ac.uk/objects/uuid:b6f9b4cd-e9ef-44b2-806a-5fac5068d33f","host_type":""}],"fields_of_study":["Bacteriophages and microbial interactions","Bacterial Genetics and Biotechnology","Antibiotic Resistance in Bacteria","0301 basic medicine","03 medical and health sciences"],"mesh_terms":["Toxin-Antitoxin Systems","Bacteriophages","Binding Sites","Models, Molecular","Promoter Regions, Genetic","Repressor Proteins","DNA Restriction-Modification Enzymes","Gene Expression Regulation, Bacterial","Escherichia coli Proteins","Genomic Islands","Enteropathogenic Escherichia coli"],"keywords":["Biology","Repressor","Bacteriophage","Genetics","Binding site","DNA","Escherichia coli","Transcriptional regulation","Bacterial genome size","Electrophoretic mobility shift assay","Promoter","Bacteria","Antitoxin","Genome","Gene","Transcription factor","Toxin","Gene expression","Models, Molecular","Binding Sites","Genomic Islands","Escherichia coli Proteins","Gene regulation, Chromatin and Epigenetics","Toxin-Antitoxin Systems","Gene Expression Regulation, Bacterial","Repressor Proteins","Enteropathogenic Escherichia coli","DNA Restriction-Modification Enzymes","Bacteriophages","Promoter Regions, Genetic"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life below water"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-08T18:22:45.320159Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}