title: RNA polymerase pausing and nascent-RNA structure formation are linked through clamp-domain movement.
abstract: The rates of RNA synthesis and the folding of nascent RNA into biologically active structures are linked via pausing by RNA polymerase (RNAP). Structures that form within the RNA-exit channel can either increase pausing by interacting with RNAP or decrease pausing by preventing backtracking. Conversely, pausing is required for proper folding of some RNAs. Opening of the RNAP clamp domain has been proposed to mediate some effects of nascent-RNA structures. However, the connections among RNA structure formation and RNAP clamp movement and catalytic activity remain uncertain. Here, we assayed exit-channel structure formation in Escherichia coli RNAP with disulfide cross-links that favor closed- or open-clamp conformations and found that clamp position directly influences RNA structure formation and RNAP catalytic activity. We report that exit-channel RNA structures slow pause escape by favoring clamp opening through interactions with the flap that slow translocation.
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.
authors.forename: Pyae P
authors.initials: PP
authors.lastname: Hein
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.
authors.forename: Kellie E
authors.initials: KE
authors.lastname: Kolb
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.
authors.forename: Tricia
authors.initials: T
authors.lastname: Windgassen
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Bellecourt
authors.affiliation: Laboratory of Molecular Biophysics, Rockefeller University, New York, New York, USA.
authors.forename: Seth A
authors.initials: SA
authors.lastname: Darst
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.
authors.forename: Rachel A
authors.initials: RA
authors.lastname: Mooney
authors.affiliation: 1] Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA. [2] Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Landick
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D020134:Catalytic Domain; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000378:metabolism*; D004926:Escherichia coli / Q000737:chemistry / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D059370:RNA Folding
chemical_list: D029968:Escherichia coli Proteins; D012313:RNA; D012321:DNA-Directed RNA Polymerases
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