title: Key roles of the downstream mobile jaw of Escherichia coli RNA polymerase in transcription initiation.
abstract: Differences in kinetics of transcription initiation by RNA polymerase (RNAP) at different promoters tailor the pattern of gene expression to cellular needs. After initial binding, large conformational changes occur in promoter DNA and RNAP to form initiation-capable complexes. To understand the mechanism and regulation of transcription initiation, the nature and sequence of these conformational changes must be determined. Escherichia coli RNAP uses binding free energy to unwind and separate 13 base pairs of λP(R) promoter DNA to form the unstable open intermediate I(2), which rapidly converts to much more stable open complexes (I(3), RP(o)). Conversion of I(2) to RP(o) involves folding/assembly of several mobile RNAP domains on downstream duplex DNA. Here, we investigate effects of a 42-residue deletion in the mobile β' jaw (ΔJAW) and truncation of promoter DNA beyond +12 (DT+12) on the steps of initiation. We find that in stable ΔJAW open complexes the downstream boundary of hydroxyl radical protection shortens by 5-10 base pairs, as compared to wild-type (WT) complexes. Dissociation kinetics of open complexes formed with ΔJAW RNAP and/or DT+12 DNA resemble those deduced for the structurally uncharacterized intermediate I(3). Overall rate constants (k(a)) for promoter binding and DNA opening by ΔJAW RNAP are much smaller than for WT RNAP. Values of k(a) for WT RNAP with DT+12 and full-length λP(R) are similar, though contributions of binding and isomerization steps differ. Hence, the jaw plays major roles both early and late in RP(o) formation, while downstream DNA functions primarily as the assembly platform after DNA opening.
authors.affiliation: Department of Biochemistry, The University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Amanda
authors.initials: A
authors.lastname: Drennan
authors.forename: Mark
authors.initials: M
authors.lastname: Kraemer
authors.forename: Michael
authors.initials: M
authors.lastname: Capp
authors.forename: Theodore
authors.initials: T
authors.lastname: Gries
authors.forename: Emily
authors.initials: E
authors.lastname: Ruff
authors.forename: Carol
authors.initials: C
authors.lastname: Sheppard
authors.forename: Sivaramesh
authors.initials: S
authors.lastname: Wigneshweraraj
authors.forename: Irina
authors.initials: I
authors.lastname: Artsimovitch
authors.forename: M Thomas
authors.initials: MT
authors.lastname: Record
mesh_terms: D020134:Catalytic Domain; D004269:DNA, Bacterial / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology; D007700:Kinetics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D011487:Protein Conformation; D061785:Transcription Initiation, Genetic / Q000502:physiology*
chemical_list: D004269:DNA, Bacterial; D012321:DNA-Directed RNA Polymerases