Kernel Architecture of the Genetic Circuitry of the Arabidopsis Circadian System

Mathias Foo, David E. Somers, Pan Jun Kim

Research output: Contribution to journalArticle

9 Citations (Scopus)
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Abstract

A wide range of organisms features molecular machines, circadian clocks, which generate endogenous oscillations with ~24 h periodicity and thereby synchronize biological processes to diurnal environmental fluctuations. Recently, it has become clear that plants harbor more complex gene regulatory circuits within the core circadian clocks than other organisms, inspiring a fundamental question: are all these regulatory interactions between clock genes equally crucial for the establishment and maintenance of circadian rhythms? Our mechanistic simulation for Arabidopsis thaliana demonstrates that at least half of the total regulatory interactions must be present to express the circadian molecular profiles observed in wild-type plants. A set of those essential interactions is called herein a kernel of the circadian system. The kernel structure unbiasedly reveals four interlocked negative feedback loops contributing to circadian rhythms, and three feedback loops among them drive the autonomous oscillation itself. Strikingly, the kernel structure, as well as the whole clock circuitry, is overwhelmingly composed of inhibitory, rather than activating, interactions between genes. We found that this tendency underlies plant circadian molecular profiles which often exhibit sharply-shaped, cuspidate waveforms. Through the generation of these cuspidate profiles, inhibitory interactions may facilitate the global coordination of temporally-distant clock events that are markedly peaked at very specific times of day. Our systematic approach resulting in experimentally-testable predictions provides insights into a design principle of biological clockwork, with implications for synthetic biology.
Original languageEnglish
Article numbere1004748
Number of pages21
JournalPLoS Computational Biology
Volume12
Issue number2
DOIs
Publication statusPublished - 1 Feb 2016

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Arabidopsis
circadian rhythm
Clocks
Circadian Clocks
kernel
Circadian Rhythm
gene
seeds
oscillation
Interaction
Synthetic Biology
Genes
Biological Phenomena
Feedback Loop
Gene
Gene Regulatory Networks
Periodicity
synthetic biology
biological processes
periodicity

Bibliographical note

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Kernel Architecture of the Genetic Circuitry of the Arabidopsis Circadian System. / Foo, Mathias; Somers, David E.; Kim, Pan Jun.

In: PLoS Computational Biology, Vol. 12, No. 2, e1004748, 01.02.2016.

Research output: Contribution to journalArticle

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