title: A Mechanistic Model for Cooperative Behavior of Co-transcribing RNA Polymerases.
abstract: In fast-transcribing prokaryotic genes, such as an rrn gene in Escherichia coli, many RNA polymerases (RNAPs) transcribe the DNA simultaneously. Active elongation of RNAPs is often interrupted by pauses, which has been observed to cause RNAP traffic jams; yet some studies indicate that elongation seems to be faster in the presence of multiple RNAPs than elongation by a single RNAP. We propose that an interaction between RNAPs via the torque produced by RNAP motion on helically twisted DNA can explain this apparent paradox. We have incorporated the torque mechanism into a stochastic model and simulated transcription both with and without torque. Simulation results illustrate that the torque causes shorter pause durations and fewer collisions between polymerases. Our results suggest that the torsional interaction of RNAPs is an important mechanism in maintaining fast transcription times, and that transcription should be viewed as a cooperative group effort by multiple polymerases.
authors: Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America.
authors: Tamra
authors: T
authors: Heberling
authors: Department of Mathematical Sciences, Montana State University, Bozeman, Montana, United States of America.
authors: Lisa
authors: L
authors: Davis
authors: Computer Science Department, Montana State University, Bozeman, Montana, United States of America.
authors: Jakub
authors: J
authors: Gedeon
authors: Department of Mathematical Sciences, Montana State University, Bozeman, Montana, United States of America.
authors: Charles
authors: C
authors: Morgan
authors: Department of Mathematical Sciences, Montana State University, Bozeman, Montana, United States of America.
authors: Tomáš
authors: T
authors: Gedeon
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D003198:Computer Simulation; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D012321:DNA-Directed RNA Polymerases / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D008962:Models, Theoretical; D013269:Stochastic Processes; D019415:Torque; D014158:Transcription, Genetic / Q000235:genetics* / Q000502:physiology
chemical_list: D004269:DNA, Bacterial; D012321:DNA-Directed RNA Polymerases