{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Gao F"],"funding":["UKRI | Biotechnology and Biological Sciences Research Council","Wellcome Trust","Biotechnology and Biological Sciences Research Council"],"pagination":["e2425868122"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12054792"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["122(17)"],"pubmed_abstract":["Bacterial RNA polymerase (RNAP) is a multisubunit enzyme that copies DNA into RNA in a process known as transcription. Bacteria use σ factors to recruit RNAP to promoter regions of genes that need to be transcribed, with 60% bacteria containing at least one specialized σ factor, σ<sup>54</sup>. σ<sup>54</sup> recruits RNAP to promoters of genes associated with stress responses and forms a stable closed complex that does not spontaneously isomerize to the open state where promoter DNA is melted out and competent for transcription. The σ<sup>54</sup>-mediated open complex formation requires specific AAA+ proteins (<u>A</u>TPases <u>A</u>ssociated with diverse cellular <u>A</u>ctivities) known as bacterial enhancer-binding proteins (bEBPs). We have now obtained structures of new intermediate states of bEBP-bound complexes during transcription initiation, which elucidate the mechanism of DNA melting driven by ATPase activity of bEBPs and suggest a mechanistic model that couples the Adenosine triphosphate (ATP) hydrolysis cycle within the bEBP hexamer with σ<sup>54</sup> unfolding. Our data reveal that bEBP forms a nonplanar hexamer with the hydrolysis-ready subunit located at the furthest/highest point of the spiral hexamer relative to the RNAP. ATP hydrolysis induces conformational changes in bEBP that drives a vectoral transiting of the regulatory N terminus of σ<sup>54</sup> into the bEBP hexamer central pore causing the partial unfolding of σ<sup>54</sup>, while forming specific bEBP contacts with promoter DNA. Furthermore, our data suggest a mechanism of the bEBP AAA+ protein that is distinct from the hand-over-hand mechanism proposed for many other AAA+ proteins, highlighting the versatile mechanisms utilized by the large protein family."],"journal":["Proceedings of the National Academy of Sciences of the United States of America"],"pubmed_title":["Subunit specialization in AAA+ proteins and substrate unfolding during transcription complex remodeling."],"pmcid":["PMC12054792"],"funding_grant_id":["BB/M011178/1"],"pubmed_authors":["Buck M","Zhang X","Ye F","Gao F"],"additional_accession":[]},"is_claimable":false,"name":"Subunit specialization in AAA+ proteins and substrate unfolding during transcription complex remodeling.","description":"Bacterial RNA polymerase (RNAP) is a multisubunit enzyme that copies DNA into RNA in a process known as transcription. Bacteria use σ factors to recruit RNAP to promoter regions of genes that need to be transcribed, with 60% bacteria containing at least one specialized σ factor, σ<sup>54</sup>. σ<sup>54</sup> recruits RNAP to promoters of genes associated with stress responses and forms a stable closed complex that does not spontaneously isomerize to the open state where promoter DNA is melted out and competent for transcription. The σ<sup>54</sup>-mediated open complex formation requires specific AAA+ proteins (<u>A</u>TPases <u>A</u>ssociated with diverse cellular <u>A</u>ctivities) known as bacterial enhancer-binding proteins (bEBPs). We have now obtained structures of new intermediate states of bEBP-bound complexes during transcription initiation, which elucidate the mechanism of DNA melting driven by ATPase activity of bEBPs and suggest a mechanistic model that couples the Adenosine triphosphate (ATP) hydrolysis cycle within the bEBP hexamer with σ<sup>54</sup> unfolding. Our data reveal that bEBP forms a nonplanar hexamer with the hydrolysis-ready subunit located at the furthest/highest point of the spiral hexamer relative to the RNAP. ATP hydrolysis induces conformational changes in bEBP that drives a vectoral transiting of the regulatory N terminus of σ<sup>54</sup> into the bEBP hexamer central pore causing the partial unfolding of σ<sup>54</sup>, while forming specific bEBP contacts with promoter DNA. Furthermore, our data suggest a mechanism of the bEBP AAA+ protein that is distinct from the hand-over-hand mechanism proposed for many other AAA+ proteins, highlighting the versatile mechanisms utilized by the large protein family.","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Apr","modification":"2025-08-13T03:06:37.417Z","creation":"2025-08-13T03:06:37.417Z"},"accession":"S-EPMC12054792","cross_references":{"pubmed":["40273105"],"doi":["10.1073/pnas.2425868122"]}}