{"doi":"10.1073/pnas.2220874120","title":"A general mechanism for transcription bubble nucleation in bacteria","abstract":"Bacterial transcription initiation requires σ factors for nucleation of the transcription bubble. The canonical housekeeping σ factor, σ 70 , nucleates DNA melting via recognition of conserved bases of the promoter −10 motif, which are unstacked and captured in pockets of σ 70 . By contrast, the mechanism of transcription bubble nucleation and formation during the unrelated σ N -mediated transcription initiation is poorly understood. Herein, we combine structural and biochemical approaches to establish that σ N , like σ 70 , captures a flipped, unstacked base in a pocket formed between its N-terminal region I (RI) and extra-long helix features. Strikingly, RI inserts into the nascent bubble to stabilize the nucleated bubble prior to engagement of the obligate ATPase activator. Our data suggest a general paradigm of transcription initiation that requires σ factors to nucleate an early melted intermediate prior to productive RNA synthesis.","journal":"Proceedings of the National Academy of Sciences","year":2023,"id":349289,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":10,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9464,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":258067,"name":"James Chen","orcid":"0000-0002-2311-003X","position":1,"is_corresponding":false},{"id":287918,"name":"Mengyu Wu","orcid":"0000-0002-2248-9383","position":2,"is_corresponding":false},{"id":482258,"name":"Courtney Chiu","orcid":null,"position":3,"is_corresponding":false},{"id":871190,"name":"B. Tracy Nixon","orcid":"0000-0002-3568-5703","position":4,"is_corresponding":false},{"id":461537,"name":"Elizabeth A. Campbell","orcid":"0000-0002-1332-128X","position":5,"is_corresponding":false},{"id":258065,"name":"Seth A. Darst","orcid":"0000-0002-8241-3153","position":6,"is_corresponding":false},{"id":1092470,"name":"Mueller AU","orcid":"0000-0003-3002-3695","position":0,"is_corresponding":true}],"reference_count":48,"raw_metadata":null,"created_at":"2026-07-19T01:12:14.919810Z","pmid":"36972428","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":[]}