Balanced branching in transcription termination.

K J Harrington, R B Laughlin, S Liang

Journal: Proceedings of the National Academy of Sciences of the United States of America 2001;98(9):5019-24

PMID: 11309513

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Abstract

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.

Address: Department of Physics, Stanford University, Stanford, CA 94305, USA.

DOI: 10.1073/pnas.240431598

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MeSH Terms: Bacteriophages, Base Sequence, DNA-Directed RNA Polymerases, Enzyme Activation, Escherichia coli, Genes, Bacterial, Genes, Viral, Glass, Half-Life, Kinetics, Magnesium, Models, Genetic, Mutation, Probability, Promoter Regions, Genetic, Stochastic Processes, Temperature, Templates, Genetic, Terminator Regions, Genetic, Thermodynamics, Transcription, Genetic