A design principle for posttranslational chaotic oscillators

Hiroto Q. Yamaguchi; Koji L. Ode; Hiroki R. Ueda

iScience (Jan 2021)

A design principle for posttranslational chaotic oscillators

Hiroto Q. Yamaguchi,
Koji L. Ode,
Hiroki R. Ueda

Affiliations

Hiroto Q. Yamaguchi: Department of Systems Pharmacology, Graduate School of Medicine, the University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan; Center for Information and Neural Networks, National Institute of Information and Communications Technology, 1-4 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
Koji L. Ode: Department of Systems Pharmacology, Graduate School of Medicine, the University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan; Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
Hiroki R. Ueda: Department of Systems Pharmacology, Graduate School of Medicine, the University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan; Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Corresponding author

Journal volume & issue: Vol. 24, no. 1
p. 101946

Abstract

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Summary: Chaos behavior has been observed in various cellular and molecular processes. Here, we modeled reversible phosphorylation dynamics to elucidate a design principle for autonomous chaos generation that may arise from generic enzymatic reactions. A comprehensive parameter search demonstrated that the reaction system composed of a set of kinases and phosphatases and two substrates with two modification sites exhibits chaos behavior. All reactions are described according to the Michaelis-Menten reaction scheme without exotic functions being applied to enzymes and substrates. Clustering analysis of parameter sets that can generate chaos behavior revealed the existence of motif structures. These chaos motifs allow the two-substrate species to interact via enzyme availability and constrain the two substrates' dynamic changes in phosphorylation status so that they occur at different timescales. This chaos motif structure is found in several enzymatic reactions, suggesting that chaos behavior may underlie cellular autonomy in a variety of biochemical systems.

Published in iScience

ISSN: 2589-0042 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science
Website: http://www.cell.com/iscience/home

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