Balanced branching in transcription termination.
The theory of stochastic transcription termination based on free-energy competition [von Hippel, P. H. & Yager, T. D. (1992) Science 255, 809-812 and von Hippel, P. H. & Yager, T. D. (1991) Proc. Natl. Acad. Sci. USA 88, 2307-2311] requires two or more reaction rates to be delicately balanced over a wide range of physical conditions. A large body of work on glasses and large molecules suggests that this balancing should be impossible in such a large system in the absence of a new organizing principle of matter. We review the experimental literature of termination and find no evidence for such a principle, but do find many troubling inconsistencies, most notably, anomalous memory effects. These effects suggest that termination has a deterministic component and may conceivably not be stochastic at all. We find that a key experiment by Wilson and von Hippel [Wilson, K. S. & von Hippel, P. H. (1994) J. Mol. Biol. 244, 36-51] thought to demonstrate stochastic termination was an incorrectly analyzed regulatory effect of Mg(2+) binding.
Harrington
K J
KJ
Department of Physics, Stanford University, Stanford, CA 94305, USA.
Laughlin
R B
RB
Liang
S
S
D001435:Bacteriophages / Q000235:genetics; D001483:Base Sequence; D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000378:metabolism; D004789:Enzyme Activation; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics; D005798:Genes, Bacterial / Q000235:genetics; D005814:Genes, Viral / Q000235:genetics; D005898:Glass; D006207:Half-Life; D007700:Kinetics; D008274:Magnesium / Q000378:metabolism / Q000494:pharmacology; D008957:Models, Genetic; D009154:Mutation / Q000235:genetics; D011336:Probability; D011401:Promoter Regions, Genetic / Q000235:genetics; D013269:Stochastic Processes; D013696:Temperature; D013698:Templates, Genetic; D013728:Terminator Regions, Genetic / Q000235:genetics; D013816:Thermodynamics; D014158:Transcription, Genetic / Q000187:drug effects / Q000235:genetics
D012321:DNA-Directed RNA Polymerases; D008274:Magnesium