{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Henriksen FOG"],"funding":["Danmarks Frie Forskningsfond","Novo Nordisk Fonden"],"pagination":["e1011749"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12204516"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["21(6)"],"pubmed_abstract":["Transcriptional regulation by binding of transcription factors to palindromic sequences in promoter regions is a fundamental process in bacteria. Some transcription factors have multiple dimeric DNA-binding domains, in principle enabling interaction with higher-order DNA structures; however, mechanistic and structural insights into this phenomenon remain limited. The Pseudomonas putida toxin-antitoxin (TA) system Xre-RES has an unusual 4:2 stoichiometry including two potential DNA-binding sites, compatible with a complex mechanism of transcriptional autoregulation. Here, we show that the Xre-RES complex interacts specifically with a palindromic DNA repeat in the promoter in a 1:1 molar ratio, leading to transcriptional repression. We determine the 2.7 Å crystal structure of the protein-DNA complex, revealing an unexpected asymmetry in the interaction and suggesting the presence of a secondary binding site, which is supported by structural prediction of the binding to the intact promoter region. Additionally, we show that the antitoxin can be partially dislodged from the Xre-RES complex, resulting in Xre monomers and a 2:2 Xre-RES complex, neither of which repress transcription. These findings highlight a dynamic, concentration-dependent model of transcriptional autoregulation, in which the Xre-RES complex transitions between a non-binding (2:2) and a DNA-binding (4:2) form."],"journal":["PLoS genetics"],"pubmed_title":["Structural basis for higher-order DNA binding by a bacterial transcriptional regulator."],"pmcid":["PMC12204516"],"funding_grant_id":["NNF22OC0079855","NNF18OC0030646","0135-00072B"],"pubmed_authors":["Brodersen DE","Skjerning RB","Van LB","Henriksen FOG"],"additional_accession":[]},"is_claimable":false,"name":"Structural basis for higher-order DNA binding by a bacterial transcriptional regulator.","description":"Transcriptional regulation by binding of transcription factors to palindromic sequences in promoter regions is a fundamental process in bacteria. Some transcription factors have multiple dimeric DNA-binding domains, in principle enabling interaction with higher-order DNA structures; however, mechanistic and structural insights into this phenomenon remain limited. The Pseudomonas putida toxin-antitoxin (TA) system Xre-RES has an unusual 4:2 stoichiometry including two potential DNA-binding sites, compatible with a complex mechanism of transcriptional autoregulation. Here, we show that the Xre-RES complex interacts specifically with a palindromic DNA repeat in the promoter in a 1:1 molar ratio, leading to transcriptional repression. We determine the 2.7 Å crystal structure of the protein-DNA complex, revealing an unexpected asymmetry in the interaction and suggesting the presence of a secondary binding site, which is supported by structural prediction of the binding to the intact promoter region. Additionally, we show that the antitoxin can be partially dislodged from the Xre-RES complex, resulting in Xre monomers and a 2:2 Xre-RES complex, neither of which repress transcription. These findings highlight a dynamic, concentration-dependent model of transcriptional autoregulation, in which the Xre-RES complex transitions between a non-binding (2:2) and a DNA-binding (4:2) form.","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Jun","modification":"2026-06-01T15:38:00.748Z","creation":"2026-04-08T13:42:14.387Z"},"accession":"S-EPMC12204516","cross_references":{"pubmed":["40577318"],"doi":["10.1371/journal.pgen.1011749"]}}