title: Template misalignment in multisubunit RNA polymerases and transcription fidelity.
abstract: Recent work showed that the single-subunit T7 RNA polymerase (RNAP) can generate misincorporation errors by a mechanism that involves misalignment of the DNA template strand. Here, we show that the same mechanism can produce errors during transcription by the multisubunit yeast RNAP II and bacterial RNAPs. Fluorescence spectroscopy reveals a reorganization of the template strand during this process, and molecular modeling suggests an open space above the polymerase active site that could accommodate a misaligned base. Substrate competition assays indicate that template misalignment, not misincorporation, is the preferred mechanism for substitution errors by cellular RNAPs. Misalignment could account for data previously taken as evidence for additional NTP binding sites downstream of the active site. Analysis of the effects of different template topologies on misincorporation indicates that the duplex DNA immediately downstream of the active site plays an important role in transcription fidelity.
authors.affiliation: Department of Cell Biology, School of Osteopathic Medicine, University of Medicine and Dentistry of New Jersey, 42 East Laurel Road, Stratford, New Jersey 08084, USA.
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Kashkina
authors.forename: Michael
authors.initials: M
authors.lastname: Anikin
authors.forename: Florian
authors.initials: F
authors.lastname: Brueckner
authors.forename: Richard T
authors.initials: RT
authors.lastname: Pomerantz
authors.forename: William T
authors.initials: WT
authors.lastname: McAllister
authors.forename: Patrick
authors.initials: P
authors.lastname: Cramer
authors.forename: Dmitry
authors.initials: D
authors.lastname: Temiakov
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D001667:Binding, Competitive; D004247:DNA / Q000737:chemistry; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000235:genetics*; D004926:Escherichia coli / Q000201:enzymology; D008957:Models, Genetic; D008969:Molecular Sequence Data; D012441:Saccharomyces cerevisiae / Q000201:enzymology; D013050:Spectrometry, Fluorescence; D013824:Thermus / Q000201:enzymology; D013997:Time Factors; D014158:Transcription, Genetic; D014764:Viral Proteins / Q000737:chemistry*
chemical_list: D014764:Viral Proteins; D004247:DNA; C062210:bacteriophage T7 RNA polymerase; D012321:DNA-Directed RNA Polymerases