title: Upstream promoter sequences and alphaCTD mediate stable DNA wrapping within the RNA polymerase-promoter open complex.
abstract: We show that the extent of stable DNA wrapping by Escherichia coli RNA polymerase (RNAP) in the RNAP-promoter open complex depends on the sequence of the promoter and, in particular, on the sequence of the upstream region of the promoter. We further show that the extent of stable DNA wrapping depends on the presence of the RNAP alpha-subunit carboxy-terminal domain and on the presence and length of the RNAP alpha-subunit interdomain linker. Our results indicate that the extensive stable DNA wrapping observed previously in the RNAP-promoter open complex at the lambda P(R) promoter is not a general feature of RNAP-promoter open complexes.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Parma, Viale G.P. Usberti 23/A, 43100 Parma, Italy.
authors.forename: Sara
authors.initials: S
authors.lastname: Cellai
authors.forename: Laura
authors.initials: L
authors.lastname: Mangiarotti
authors.forename: Nicola
authors.initials: N
authors.lastname: Vannini
authors.forename: Nikolai
authors.initials: N
authors.lastname: Naryshkin
authors.forename: Ekaterine
authors.initials: E
authors.lastname: Kortkhonjia
authors.forename: Richard H
authors.initials: RH
authors.lastname: Ebright
authors.forename: Claudio
authors.initials: C
authors.lastname: Rivetti
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D018625:Microscopy, Atomic Force; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic / Q000235:genetics*; D017434:Protein Structure, Tertiary
chemical_list: D004247:DNA; D012321:DNA-Directed RNA Polymerases; C113275:RNA polymerase alpha subunit