Document Type


Date of Award


Degree Name

Doctor of Philosophy in Chemistry - (Ph.D.)


Chemistry and Environmental Science

First Advisor

Yong Ick Kim

Second Advisor

Kevin D. Belfield

Third Advisor

Tamara M. Gund

Fourth Advisor

Yuanwei Zhang

Fifth Advisor

Casey Diekman


The circadian rhythms arise as an adaptation to the environmental 24-hour day and night cycle due to Earth's rotation. These rhythms prepare organisms to align their internal biological activities and day to day behavior or events with the environmental change of the 24-hour day and night cycle. Circadian rhythms are found widely in all living kingdoms of life on Earth. Cyanobacteria are photosynthetic prokaryotes which first used to study these circadian rhythms. Among cyanobacterial species, Synechococcus elongatus PCC 7942 (henceforth, S. Elongatus) is the simplest organism with a durable and sturdy circadian clock and is study as a model organism. The S.Elongatus central pacemaker is a posttranslational oscillator(PTO) consisting of three proteins KaiA, KaiB, and KaiC, and these proteins can replicate in a test tube with ATP and Magnesium. The circadian oscillator mechanism revolves around KaiC phosphorylation at residues S431 and T432 in the CII domain throughout ~24-hours. KaiA initiates KaiC phosphorylation by binding to the KaiC region known as A-loop. KaiB then commences the process of dephosphorylation by sequestering KaiA from A-loop. This ordered phosphorylation with A loop confirmation change does not provide a detailed explanation about the molecular mechanism acting downstream of A loop. This oscillator mechanism is not well studied, yet the shift in protein concentrations, the addition of cofactors in an oscillator, and protein mutations in the circadian period are still unknown.

This dissertation addresses how important it is to investigate each clock component, their protein mutations, and interactions to solve the oscillator mechanism and the whole developmental biological chronometer's hidden complexity. Here I discuss the Aloop downstream mechanism for KaiC phosphorylation and how cofactors and mutations influence its oscillation in this report. And also propose the current self-sustained circadian oscillator possibly evolved from the KaiC-alone hourglass controlled by magnesium



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