Operational Mechanism Of The Neurospora Crassa Circadian Clock

The circadian clock refers to intrinsic oscillations with period of?24 h and is widely found in nature.From simple single-celled organisms to complex mammals,their physiological and metabolic processes are regulated by the circadian clock.The circadian clock helps the creature to better adapt to the external environment and maintain the internal homeostasis.Many diseases,such as depression,sleep disorders,metabolic syndrome and even cancer,are directly related to the disorder of the circadian clock.The study of metabolic pathways downstream of the circadian clock provides a theoretical idea for the treatment of such diseases.In recent years,the research on gene regulatory networks has been an important topic in molecular biology.Those studies on the core circadian oscillators have remarkably advanced the understanding of the structure,dynamics and functions of gene regulatory networks.As a premier model organism,the filamentous fungus Neurospora has been extensively investigated.Its circadian clock comprises WCC(white collar complex)and FRQ(Frequency)proteins.In this thesis,we build the models of Neurospora circadian oscillator,and explore the effect of post-translational modifications on circadian rhythm and the crosstalk between the circadian clock and reactive oxygen species(ROS).These studies markedly advance our understanding of the operational mechanism of the Neurospora clock.The thesis is divided into four chapters.Chapter 1 first briefly introduces systems biology,gene regulation network,and methods exploited to investigate gene regulation networks.The concept of circadian rhythm and its underlying mechanism are then described.Finally,the motivation and main results of this thesis are presented.Feedback loops and posttranslational modifications play key roles in circadian rhythmicity.In Chapter 2,we build a minimal model of the Neurospora circadian clock composed of WCC and FRQ,and examine the function of phosphorylation-based interlinked positive and negative feedback loops(IPNFLs).Both deterministic and stochastic simulations are performed,and simulation results quantitatively reproduce the basic features of circadian rhythm,such as period length and phase relationships.The circadian rhythm still exists even when the numbers of molecules are at the order of hundreds.We can interpret the relationship between conidiation periods and quinic acid concentrations in the qa-WC-1 strain and the circadian cycle of WCC stability.The stabilization of hyperphosphorylated WCC has functional importance,maintaining the antiphase relationship between FRQ and WCC.Our results suggest that the system of IPNFLs is optimal for circadian rhythm by constraining the oscillation period in the physiological range over a relatively wide parameter domain.Chapter 3 explores the crosstalk between the Neurospora clock and ROS.It was experimentally shown that ROS are controlled by clock-controlled genes and in turn regulate the circadian rhythm itself.We build an integrative network model.characterizing the circadian oscillator,ROS system and their interactions.Notably,the(de)phosphorylation and nuclear-cytoplasmic shuttling of clock proteins are modeled in detail.Simulation results quantitatively reproduce the essential features of circadian rhythm(both in constant darkness and under light/dark cycles).Increasing the average concentrations of O2-and H2O2 lead to the phase advancement of frq mRNA,consistent with experimental data.Among the three interactions between ROS and the clock,i.e.,O2--enhanced PP2A activity.H2O2-enhanced binding of WCC to gene promoters,and inhibition of dimerization of WC-I and WC-2 by H2O2,the regulation of WCC activity by PP2A in an O2--dependent manner plays a predominant role.The functional significance of such modulations is also discussed.Chapter 4 is a summary of main results of this thesis and outlook for future work.