title: The orientation of DNA in an archaeal transcription initiation complex.
abstract: RNA polymerase from the hyperthermophile archaeon Pyrococcus furiosus (Pfu) forms specific and transcriptionally active complexes with its conjugate transcription factors TBP (the archaeal TATA binding protein homolog) and TFB (the archaeal homolog of eukaryotic RNA polymerase II and III transcription factors TFIIB and Brf) at the Pfu glutamate dehydrogenase promoter. A photochemical crosslinking method was used to map the vicinity of the catalytic subunits of Pfu RNA polymerase to DNA locations distributed along the polymerase-promoter interface. The largest component of this archaeal polymerase is split into two subunits, A' and A", whose relatively sharp boundary of DNA crosslinking (probed on the transcribed strand) is centered five to six base pairs downstream of the transcriptional start site. A strong argument based on this information, on the well-defined homology between the core bacterial, archaeal and eukaryotic RNA polymerase subunits, and on the recently determined structure of a bacterial RNA polymerase specifies the directionality of DNA in the archaeal transcription complex and its trajectory downstream of the transcriptional start site.
authors.affiliation: Department of Biology and Center for Molecular Genetics, University of California, San Diego, La Jolla, California 92093-0634, USA. bartlett@biomail.ucsd.edu
authors.forename: M S
authors.initials: MS
authors.lastname: Bartlett
authors.forename: M
authors.initials: M
authors.lastname: Thomm
authors.forename: E P
authors.initials: EP
authors.lastname: Geiduschek
mesh_terms: D019843:Archaeal Proteins / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D020134:Catalytic Domain; D003432:Cross-Linking Reagents; D019641:DNA, Archaeal / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000378:metabolism; D019766:Genes, Archaeal / Q000235:genetics; D005969:Glutamate Dehydrogenase / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009687:Nuclear Proteins / Q000378:metabolism; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic / Q000235:genetics; D020027:Pyrococcus furiosus / Q000201:enzymology* / Q000235:genetics*; D035181:TATA-Box Binding Protein; D013698:Templates, Genetic; D035581:Transcription Factor TFIIB; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic; D014466:Ultraviolet Rays
chemical_list: D019843:Archaeal Proteins; D003432:Cross-Linking Reagents; D019641:DNA, Archaeal; D004268:DNA-Binding Proteins; D009687:Nuclear Proteins; D035181:TATA-Box Binding Protein; D035581:Transcription Factor TFIIB; D014157:Transcription Factors; C106466:transcription factor B, Archaea; D005969:Glutamate Dehydrogenase; D012321:DNA-Directed RNA Polymerases