{"doi":"10.1101/2020.02.05.936344","title":"<i>Escherichia coli σ</i> <sup>38</sup> promoters use two UP elements instead of a −35 element: resolution of a paradox and discovery that <i>σ</i> <sup>38</sup> transcribes ribosomal promoters","abstract":"1 Abstract In E. coli , one RNA polymerase (RNAP) transcribes all RNA species, and different regulons are transcribed by employing different sigma ( σ ) factors. RNAP containing σ 38 ( σ S ) activates genes responding to stress conditions such as stationary phase. The structure of σ 38 promoters has been controversial for more than two decades. To construct a model of σ 38 promoters using information theory, we aligned proven transcriptional start sites to maximize the sequence information, in bits, and identified a −10 element similar to σ 70 promoters. We could not align any −35 sequence logo; instead we found two patterns upstream of the −35 region. These patterns have dyad symmetry sequences and correspond to the location of UP elements in ribosomal RNA (rRNA) promoters. Additionally the UP element dyad symmetry suggests that the two polymerase α subunits, which bind to the UPs, should have two-fold dyad axis of symmetry on the polymerase and this is indeed observed in an X-ray crystal structure. Curiously the α CTDs should compete for overlapping UP elements. In vitro experiments confirm that σ 38 recognizes the rrnB P1 promoter, requires a −10, UP elements and no −35. This clarifies the long-standing paradox of how σ 38 promoters differ from those of σ 70 .","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":128890,"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":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9527,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":579628,"name":"Zhe Sun","orcid":"0000-0002-0634-7983","position":1,"is_corresponding":false},{"id":579629,"name":"Yixiong Chen","orcid":"0000-0002-4425-3216","position":2,"is_corresponding":false},{"id":579630,"name":"Cédric Cagliero","orcid":"0000-0001-7404-5453","position":3,"is_corresponding":false},{"id":435438,"name":"Y. Zuo","orcid":"0000-0003-1810-4580","position":4,"is_corresponding":false},{"id":579631,"name":"Yan Zhou","orcid":"0000-0002-5444-9271","position":5,"is_corresponding":false},{"id":392644,"name":"Mikhail Kashlev","orcid":"0000-0002-1260-6486","position":6,"is_corresponding":false},{"id":580145,"name":"Ding Jun Jin","orcid":null,"position":7,"is_corresponding":false},{"id":579632,"name":"Thomas D. Schneider","orcid":"0000-0002-9841-1531","position":8,"is_corresponding":false},{"id":579627,"name":"Kevin S. Franco","orcid":"0000-0002-1670-7874","position":0,"is_corresponding":true}],"reference_count":78,"raw_metadata":null,"created_at":"2026-07-18T23:15:42.522809Z","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":[]}