{"doi":"10.1093/nar/gkv391","title":"New insights into the regulatory mechanisms of ppGpp and DksA on Escherichia coli RNA polymerase–promoter complex","abstract":null,"journal":"Nucleic Acids Research","year":2015,"id":593585,"datarank":0.5101796072493234,"base_score":3.4011973816621555,"endowment":3.4011973816621555,"self_citation_contribution":0.5101796072493234,"citation_network_contribution":0.0,"self_endowment_contribution":0.5101796072493234,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":29,"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":1087886,"name":"Piere Rodriguez-Aliaga","orcid":"0000-0002-3828-4235","position":1,"is_corresponding":false},{"id":1519227,"name":"Davide Amidani","orcid":null,"position":2,"is_corresponding":false},{"id":118474,"name":"Jorge A. Bardales","orcid":null,"position":3,"is_corresponding":false},{"id":57658,"name":"Carlos Bustamante","orcid":"0000-0002-0816-6406","position":4,"is_corresponding":false},{"id":567023,"name":"Daniel G. Guerra","orcid":"0000-0002-2410-722X","position":5,"is_corresponding":false},{"id":594803,"name":"Claudio Rivetti","orcid":"0000-0003-3775-6779","position":6,"is_corresponding":false},{"id":1519225,"name":"Nicola Doniselli","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"New insights into the regulatory mechanisms of ppGpp and DksA on Escherichia coli RNA polymerase–promoter complex","abstract":"The stringent response modulators, guanosine tetraphosphate (ppGpp) and protein DksA, bind RNA polymerase (RNAP) and regulate gene expression to adapt bacteria to different environmental conditions. Here, we use Atomic Force Microscopy and in vitro transcription assays to study the effects of these modulators on the conformation and stability of the open promoter complex (RPo) formed at the rrnA P1, rrnB P1, its discriminator (dis) variant and λ pR promoters. In the absence of modulators, RPo formed at these promoters show different extents of DNA wrapping which correlate with the position of UP elements. Addition of the modulators affects both DNA wrapping and RPo stability in a promoter-dependent manner. Overall, the results obtained under different conditions of ppGpp, DksA and initiating nucleotides (iNTPs) indicate that ppGpp allosterically prevents the conformational changes associated with an extended DNA wrapping that leads to RPo stabilization, while DksA interferes directly with nucleotide positioning into the RNAP active site. At the iNTPs-sensitive rRNA promoters ppGpp and DksA display an independent inhibitory effect, while at the iNTPs-insensitive pR promoter DksA reduces the effect of ppGpp in accordance with their antagonistic role.","is_dataset_classified":null,"base_score":3.4011973816621555,"endowment":3.4011973816621555,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"25916853","pmcid":"PMC4446441","openalex_id":"https://openalex.org/W2076006427","authors":[],"funders":[{"funder_name":"NIGMS NIH HHS","grant_id":"R01 GM32543","title":null},{"funder_name":"FIC NIH HHS","grant_id":"R03 TW008610","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"R37 GM032543","title":null},{"funder_name":"National Institutes of Health","grant_id":"1R03TW008610-01","title":"Characterization of wild-type and mutant initiation/elongation complexes in Esche"},{"funder_name":"National Institutes of Health","grant_id":"5R01GM032543-11","title":"PHYSICAL CHEMISTRY OF NUCLEIC ACIDS"},{"funder_name":"Howard Hughes Medical Institute","grant_id":"","title":null},{"funder_name":"Howard Hughes Medical Institute","grant_id":"","title":null}],"total_grants":7,"fwci":2.2509,"citation_percentile":0.88572671,"influential_citations":0,"citation_trend":[{"year":2016,"count":3},{"year":2017,"count":5},{"year":2018,"count":2},{"year":2019,"count":2},{"year":2020,"count":4},{"year":2021,"count":4},{"year":2022,"count":2},{"year":2023,"count":1},{"year":2025,"count":4},{"year":2026,"count":2}],"oa_status":"gold","license":"CC BY NC","oa_locations":[{"url":"https://academic.oup.com/nar/article-pdf/43/10/5249/17435279/gkv391.pdf","host_type":"journal"},{"url":"https://academic.oup.com/nar/article-pdf/43/10/5249/17435279/gkv391.pdf","host_type":"publisher"},{"url":"http://academic.oup.com/nar/article-pdf/43/10/5249/17435279/gkv391.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/nar/gkv391","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/25916853","host_type":"repository"},{"url":"https://escholarship.org/uc/item/31c7m6d9","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4446441","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC4446441","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC4446441?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.1093/nar/gkv391","host_type":""},{"url":"https://dx.doi.org/10.1093/nar/gkv391","host_type":""},{"url":"https://hdl.handle.net/20.500.12866/5374","host_type":""},{"url":"https://hdl.handle.net/11381/2816682","host_type":""},{"url":"https://escholarship.org/content/qt31c7m6d9/qt31c7m6d9.pdf","host_type":""},{"url":"https://doi.org/https://doi.org/10.1093/nar/gkv391","host_type":""}],"fields_of_study":["Bacterial Genetics and Biotechnology","Bacteriophages and microbial interactions","RNA and protein synthesis mechanisms","0301 basic medicine","0303 health sciences","03 medical and health sciences","Bacteriophage lambda","DNA, Bacterial","DNA-Directed RNA Polymerases","Escherichia coli","Escherichia coli Proteins","Gene Expression Regulation, Bacterial","Genes, rRNA","Guanosine Tetraphosphate","Promoter Regions, Genetic","Ribonucleotides","Transcription Initiation, Genetic","Transcription, Genetic"],"mesh_terms":["DNA, Bacterial","Escherichia coli","Guanosine Tetraphosphate","Bacteriophage lambda","Promoter Regions, Genetic","Ribonucleotides","DNA-Directed RNA Polymerases","Transcription, Genetic","Gene Expression Regulation, Bacterial","Genes, rRNA","Escherichia coli Proteins","Transcription Initiation, Genetic"],"keywords":["Stringent response","Biology","RNA polymerase","Promoter","DNA","Transcription (linguistics)","Guanosine","Polymerase","Cell biology","RNA","Biochemistry","Sigma factor","Genetics","Escherichia coli","Gene","Molecular biology","Gene expression","Bacteriophage lambda; DNA, Bacterial; DNA-Directed RNA Polymerases; Escherichia coli; Escherichia coli Proteins; Genes, rRNA; Guanosine Tetraphosphate; Ribonucleotides; Transcription, Genetic; Gene Expression Regulation, Bacterial; Promoter Regions, Genetic; Transcription Initiation, Genetic; Genetics; Medicine (all)","Transcription, Genetic","Structural Biology","Escherichia coli Protein","DNA-Directed RNA Polymerase","rRNA","Promoter Regions, Genetic","Transcription Initiation, Genetic","Ribonucleotides/metabolism","DNA, Bacterial/chemistry/ultrastructure","https://purl.org/pe-repo/ocde/ford#1.06.07","Medicine (all)","Escherichia coli Proteins","Bacterial","Escherichia coli Proteins/metabolism","DNA-Directed RNA Polymerases","Biological Sciences","Bacteriophage lambda","Escherichia coli/enzymology/genetics","Transcription","Transcription Initiation","DNA, Bacterial","570","Ribonucleotide","Guanosine Tetraphosphate","Promoter Regions","Genetic","Information and Computing Sciences","616","Genes, rRNA","Gene Expression Regulation, Bacterial","Ribonucleotides","Environmental sciences","Bacteriophage lambda/genetics","Gene Expression Regulation","Genes","Chemical sciences","Biochemistry and Cell Biology","DNA-Directed RNA Polymerases/metabolism","Guanosine Tetraphosphate/metabolism","Developmental Biology"],"sdg_mappings":[{"sdg_number":3,"sdg_label":"3. Good health"},{"sdg_number":0,"sdg_label":"Reduced inequalities"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-27T11:32:59.763781Z","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":[]}