Uncovering Molecular Mechanisms Regulating Circadian Amplitude Across the Tree of Life

Abstract

Circadian rhythms are 24 hour rhythms in behavior or physiology that occur in almost all organisms on Earth. These rhythms are generated at the cellular level through transcription-translation feedback loops formed by genes termed core clock genes. Some of these clock genes function as transcription factors to control the timely expression of each other as well as thousands of downstream clock-controlled genes. The amplitude of circadian rhythms, or the daily variation of a rhythm's peak to the nadir, has been broadly implicated in growth and survival, as a higher amplitude is often associated with improved health in humans. Despite this, it is not well understood how the amplitude of circadian rhythms is regulated at the molecular level. The purpose of this study is uncover the mechanism(s) that modulate circadian amplitude in both plants and mammals. In the following chapters, I describe my research for two core projects: 1) how the production of flavonoids, an abundant metabolite in plants, modulates the amplitude of the plant circadian clock, and 2) how Rors (Retinoic Acid-Related Orphan Receptors) function as amplitude regulators within the mammalian clock circuitry. For project 1, I found that in Arabidopsis thaliana, a loss of dihydroxy B-ring flavonoids leads to elevated circadian amplitude, most likely due to the antioxidant function of these flavonoids. For project 2, I found that the expression of RORs positively regulates circadian amplitude in mouse hepatocytes, and the ROR paralog Rora has a stronger impact on amplitude than Rorc. This is due to the disordered hinge region and the ligand binding domains of RORɑ, and in silico models predict that these regions are critical for formation of a homodimer that does not occur in ROR. These findings advance our understanding of how circadian amplitude is regulated in various species and may help future studies identify strategies to manipulate amplitude to improve human health or agricultural growth and yield.