title: Mechanism of T7 RNAP pausing and termination at the T7 concatemer junction: a local change in transcription bubble structure drives a large change in transcription complex architecture.
abstract: The T7RNA polymerase (RNAP) elongation complex (EC) pauses and is destabilized at a unique 8 nucleotide (nt) sequence found at the junction of the head-to-tail concatemers of T7 genomic DNA generated during T7 DNA replication. The paused EC may recruit the T7 DNA processing machinery, which cleaves the concatemerized DNA within this 8 nt concatemer junction (CJ). Pausing of the EC at the CJ involves structural changes in both the RNAP and transcription bubble. However, these structural changes have not been fully defined, nor is it understood how the CJ sequence itself causes the EC to change its structure, to pause, and to become less stable. Here we use solution and RNAP-tethered chemical nucleases to probe the CJ transcript and changes in the EC structure as the polymerase pauses and terminates at the CJ. Together with extensive mutational scanning of regions of the polymerase that are likely to be involved in recognition of the CJ, we are able to develop a description of the events that occur as the EC transcribes through the CJ and subsequently pauses. In this process, a local change in the structure of the transcription bubble drives a large change in the architecture of the EC. This altered EC structure may then serve as the signal that recruits the processing machinery to the CJ.
authors.affiliation: Department of Biochemistry, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA.
authors.forename: Dhananjaya
authors.initials: D
authors.lastname: Nayak
authors.forename: Sylvester
authors.initials: S
authors.lastname: Siller
authors.forename: Qing
authors.initials: Q
authors.lastname: Guo
authors.forename: Rui
authors.initials: R
authors.lastname: Sousa
mesh_terms: D001483:Base Sequence; D002413:Cations, Divalent / Q000494:pharmacology; D018360:Crystallography, X-Ray; D004279:DNA, Viral / Q000235:genetics / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000235:genetics* / Q000378:metabolism*; D004305:Dose-Response Relationship, Drug; D004926:Escherichia coli / Q000235:genetics; D007854:Lead / Q000494:pharmacology; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009113:Muramidase / Q000378:metabolism / Q000494:pharmacology; D009154:Mutation; D011401:Promoter Regions, Genetic; D011487:Protein Conformation; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016914:Ribonuclease H / Q000494:pharmacology; D006163:Ribonuclease T1 / Q000494:pharmacology; D013698:Templates, Genetic; D013728:Terminator Regions, Genetic; D013997:Time Factors; D014158:Transcription, Genetic; D014764:Viral Proteins / Q000235:genetics* / Q000378:metabolism*
chemical_list: D002413:Cations, Divalent; D004279:DNA, Viral; D012367:RNA, Viral; D014764:Viral Proteins; D007854:Lead; C062210:bacteriophage T7 RNA polymerase; D012321:DNA-Directed RNA Polymerases; D016914:Ribonuclease H; D006163:Ribonuclease T1; D009113:Muramidase