Biological clocks in theory and experiments
Eukaryotes and some prokaryotes have adapted to the 24h day/night cycle by
evolving circadian clocks. The circadian clock now controls 24-hour rhythms in
very many aspects of metabolism, physiology and behaviour. Day-length
(photoperiod) measurement depends on the circadian clock, so the 24h clock
mechanism also governs seasonal rhythms, such as reproduction. In the model
plant species,
Arabidopsis thaliana, the clock controls the expression of
about 10% of genes, and this proportion is similar in other eukaryotes.
Fundamental properties of the clock are shared across taxonomic groups, such
as phase resetting by light signals and temperature compensation of the
circadian period.
All the known clock mechanisms include a gene circuit with negative feedback,
involving 24h rhythms in the levels of positive- and negatively-acting
transcriptional regulators. Molecular genetics has identified ~10 genes that
are involved in constructing these regulatory loops in cyanobacteria,
Drosophila, Neurospora, Arabidopsis and mouse, though other components almost
certainly remain to be discovered. Strikingly, the protein sequences of the
clock components are distinct to each taxonomic group, suggesting that clocks
may have evolved several times. Some features of the regulatory circuits are
shared among groups, suggesting that the circuit architecture may be important
for clock function. Circadian regulation is ubiquitous, pervasive and has
complex properties, yet the number of components in the clock is relatively
small, making this an excellent prototype for reverse engineering of a genetic
sub-network.
My experimental group has identified new components of the plant circadian
clock, using the bioluminescent reporter gene luciferase (LUC) to reveal gene
expression rhythms with high spatial and temporal resolution. As the details
revealed by molecular genetics do not necessarily lead to greater
understanding of a regulatory circuit, we have also developed differential
equation models for the plant clock and photoperiod sensor, together with our
collaborators in IPCR. The models incorporate molecular components in a
realistic manner, so numerical simulations using the models are now directing
the design and evaluation of molecular experiments. We have developed an
experimentalist-friendly interface for the models, to allow other groups to
use these methods (online at http://www.amillar.org/Downloads.html). David
Rand and colleagues have established a novel analytical method to assess the
contribution of each component of the model (RNA or protein) at each phase of
the cycle. This work indicates a general explanation for the evolution of
multi-loop structures, to allow flexible regulation, providing one of the
design principles that may underlie the architecture of the circadian clock
gene circuits. Funded by BBSRC, EPSRC and DTI.
References
Young, M.W., and Kay, S.A. (2001). Time zones: A comparative genetics of
circadian clocks. Nat. Rev. Genet. 2, 702-715.
Goldbeter, A. (2002). Computational approaches to cellular rhythms. Nature
420, 238-245.
Rand, D.A., Shulgin, B.V., Salazar, D., and Millar, A.J. (2004). Design
principles underlying circadian clocks. J.Roy.Soc. Interface 1, 119-130.
Locke, J.C., Millar, A.J., and Turner, M.S. (2005). Modelling genetic networks
with noisy and varied experimental data: the circadian clock in Arabidopsis
thaliana. J. Theor. Biol. 234, 383-393.
Vincent Moulton
© 2005, CBL
Computational Biology Laboratory,
School of Computing Sciences,
University of East Anglia,
Norwich, NR4 7TJ, UK.