A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing.
Transcriptional pausing by RNA polymerase is an underlying event in the regulation of transcript elongation, yet the physical changes in the transcribing complex that create the initially paused conformation remain poorly understood. We report that this nonbacktracked elemental pause results from an active-site rearrangement whose signature includes a trigger-loop conformation positioned near the RNA 3' nucleotide and a conformation of betaDloopII that allows fraying of the RNA 3' nucleotide away from the DNA template. During nucleotide addition, trigger-loop movements or folding appears to assist NTP-stimulated translocation and to be crucial for catalysis. At a pause, the trigger loop directly contributes to the paused conformation, apparently by restriction of its movement or folding, whereas a previously postulated unfolding of the bridge helix does not. This trigger-loop-centric model can explain many properties of transcriptional pausing.
Toulokhonov
Innokenti
I
Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.
Zhang
Jinwei
J
Palangat
Murali
M
Landick
Robert
R
D000595:Amino Acid Sequence; D001665:Binding Sites; D003432:Cross-Linking Reagents; D018983:DNA Footprinting; D012321:DNA-Directed RNA Polymerases / Q000502:physiology*; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D017386:Sequence Homology, Amino Acid; D014158:Transcription, Genetic
D003432:Cross-Linking Reagents; D012321:DNA-Directed RNA Polymerases