{"doi":"10.1101/2024.02.16.579611","title":"Molecular switching of a DNA-sliding clamp to a repressor mediates long-range gene silencing","abstract":"Long-range gene regulation is rare in bacteria and is confined to the classical DNA looping model. Here, we use a combination of biophysical approaches, including X-ray crystallography and single-molecule analysis, to show that long-range gene silencing on the plasmid RK2, a source of multidrug resistance across diverse Gram-negative bacteria, is achieved cooperatively by a DNA-sliding clamp, KorB, and a clamp-locking protein, KorA. We find that KorB is a CTPase clamp that can entrap and slide along DNA to reach distal target promoters. We resolved the tripartite crystal structure of a KorB-KorA-DNA co-complex, revealing that KorA latches KorB into a closed-clamp state. KorA thus stimulates repression by stalling KorB sliding at target promoters to occlude RNA polymerase holoenzymes. Altogether, our findings explain the mechanistic basis for KorB role-switching from a DNA-sliding clamp to a co-repressor, and provide a new paradigm for the long-range regulation of gene expression.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":485049,"datarank":0.34407306516323666,"base_score":1.9459101490553132,"endowment":1.9459101490553132,"self_citation_contribution":0.29188652235829704,"citation_network_contribution":0.05218654280493964,"self_endowment_contribution":0.29188652235829704,"citer_contribution":0.05218654280493964,"corpus_percentile":null,"corpus_rank":null,"citation_count":6,"citer_count":4,"citers_with_citation_signal":2,"citers_with_endowment":2,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9493,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1135680,"name":"Francisco de Asís Balaguer","orcid":"0000-0002-6393-2863","position":1,"is_corresponding":false},{"id":893169,"name":"Joshua Chandanani","orcid":"0000-0003-2671-2412","position":2,"is_corresponding":false},{"id":924041,"name":"Christopher M. Thomas","orcid":"0000-0002-2810-0455","position":3,"is_corresponding":false},{"id":678695,"name":"Clara Aicart-Ramos","orcid":"0000-0002-1114-4259","position":4,"is_corresponding":false},{"id":1327674,"name":"Sophia Burick","orcid":"0009-0009-1160-2414","position":5,"is_corresponding":false},{"id":471220,"name":"Paul Dominic B. Olinares","orcid":"0000-0002-3429-6618","position":6,"is_corresponding":false},{"id":1328119,"name":"Giulia Gobbato","orcid":null,"position":7,"is_corresponding":false},{"id":1327675,"name":"Julia E. A. Mundy","orcid":"0009-0006-6232-7254","position":8,"is_corresponding":false},{"id":51698,"name":"Brian T. Chait","orcid":"0000-0003-3524-557X","position":9,"is_corresponding":false},{"id":1327676,"name":"David M. Lawson","orcid":"0000-0002-7637-4303","position":10,"is_corresponding":false},{"id":258065,"name":"Seth A. Darst","orcid":"0000-0002-8241-3153","position":11,"is_corresponding":false},{"id":461537,"name":"Elizabeth A. Campbell","orcid":"0000-0002-1332-128X","position":12,"is_corresponding":false},{"id":678699,"name":"Fernando Moreno‐Herrero","orcid":"0000-0003-4083-1709","position":13,"is_corresponding":false},{"id":887088,"name":"Tung B. K. Le","orcid":"0000-0003-4764-8851","position":14,"is_corresponding":false},{"id":1327673,"name":"Thomas C. McLean","orcid":"0000-0002-6467-4974","position":0,"is_corresponding":true}],"reference_count":123,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:07:47.633574Z","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":[]}