Circadian Clocks

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What is a circadian clock?

A circadian clock is an internal biological clock that is found in almost all organisms, which regulates many metabolic processes. This biological clock allows organisms to adjust physiologically to changes in the environment. It is also influential in an organism’s behavior based on environmental differences.

What do circadian clocks regulate?

In plants, circadian clocks control flowering, response to seasons, and photosynthesis such as the opening and closing of the stomata.

In mammals, circadian clocks manage sleeping, waking, feeding, and controlling whether an animal is nocturnal (most active at night) or diurnal (most active during the day).

In cyanobacteria, circadian clocks regulate nitrogen fixation.

In general, circadian clocks direct cell replication, amino acid uptake, and carbohydrate synthesis.

Why are circadian clocks important?

Circadian clocks are an integral part of everyday life for most all organisms on Earth. They regulate the most important functions in each organism. Without these biological clocks, processes such as metabolism would be completely disorganized and all of our bodies would go entirely awry. Life as we know it today would not exist in the regular predictable pattern.

It’s as easy as Kai A, B, C!

General Info about Cyanobacteria: (the organisms studied in this experiment)

* Cyanobacteria are among the oldest organisms on Earth
* They are very diverse: different species of cyanobacteria can survive in a broad range of environmental conditions
* Even though cyanobacteria are unicellular, they perform many metabolic activities: photosynthesis, carbon fixation, and nitrogen fixation
* Their circadian rhythms (which were also studied in this experiment) are among the oldest and simplest on Earth
* Because they are easily amenable to genetic studies, they are ideal organisms to study


There are three genes that are responsible for the circadian rhythms in cyanobacteria: kaiA, kaiB, and kaiC, which code for the three proteins KaiA, KaiB, and KaiC, respectively

About the proteins:

* KaiA has two subunits separated by a groove, and is a complex structure
* KaiB is still being studied, especially the exact role it plays in circadian rhythm expression
* KaiC is an autokinase. Its phosphorylated and unphosphorylated forms correspond to the clock; however, this only occurs in equilibrium

It is believed that the interaction between KaiA and KaiC is the key to understanding how circadian rhythms work

LiWang and colleagues (authors of the report) looked at the structures of KaiA-KaiC complexes in vivo and in vitro to study the regions at which they interact.

Materials and Methods

The protein samples were prepared, and then their structures were analyzed by NMR


KaiC was expected to be composed of Rec-A like domains. RecA is a type of recombination protein that modifies DNA structure and function

KaiC peptides were also expected to pass through a groove in KaiA

The structure of KaiA: it is a 4 helix bundle with 2 subunits, which makes it a dimer. It has a groove in the middle that is stabilized by electrostatic and hydrophobic hydrogen bonds.

KaiC peptides were found in the experiment to follow this middle groove (lie along it), which was different than the original hypothesis

It is necessary for KaiA to have a dimer structure because KaiC peptides interact with both of the KaiA subunits

The angle of dimerization (which in English means the angle formed between the two KaiA subunits) changes upon KaiC binding. Taken one step further, this means that KaiC changes the quarternary structure of the C-terminal of KaiA

So...what does all of this mean in terms of the circadian clock? Basically, the goal of this experiment was to study the interactions between KaiA and KaiC proteins and determine how these interactions play a role in the regulation of circadian clocks (if at all). After performing the experiment, the researchers discovered that the location of KaiA and KaiC interaction is important because it is the same location at which some substituted amino acids cause changes in the clock period. In plainer terms, the amino acid substitutions weaken the interactions between KaiA and KaiC, which lengthens the clock.


Protein interactions (possibly due to the CikA, which is a sensory protein that starts a protein cascade) result in changes in KaiA, which affect its affinity for KaiC

Since KaiA enhances the ability of KaiC to phosphorylate itself (autokinase activity), this regulates the clock period

There is more KaiC in vivo than KaiA; therefore it is proposed that each KaiA binds to 2 KaiC molecules. This in turn may indicate that KaiA is a linker module that allows 2 KaiCs to transphosphorylate

Why study Cyanobacterium?

It is a model organism, for the following reasons: it is easily amenable to genetic studies, and it also performs many eukaryotic-type functions such as photosynthesis, carbon fixation, and nitrogen fixation even though it is a unicellular organism. Furthermore, its circadian clock is believed to work in ways similar to those of eukaryotic organisms and possibly even humans. Therefore, we can learn about our own circadian clocks through the studies of cyanobacterium. There is still much to learn about circadian clocks, because they are very complex and complicated, and the type of research addressed in this paper is very new and revolutionary. There is not a lot of previous research to build upon, so studying simple organisms such as cyanobacteria is a good place to start. Studying a simple organism is the best place to start when scientists are faced with a new and complicated question. This is because they are much easier to characterize and their systems are easier to study. It is also much easier to figure out how systems in simpler organisms work. Once the entire circadian clock system of cyanobacterium is known, it will be easier to study the circadian clocks of more highly evolved organisms and eventually to even figure out exactly how our own circadian clocks work.

Why is it important for us to know about our circadian clocks?

Circadian clocks are very important; they control our basic primitive needs and many systems in our bodies that allow us to be functional organisms. It would be very useful and beneficial for us to eventually be able to understand how our own circadian clocks work. Once we figure out the mechanisms used by our circadian clocks, we may be able to find ways to help people who have circadian clocks that may have been thrown off-balance, such as those who work at night and people who have difficulty functioning in the earlier hours of the morning. If the metabolic pathways incorporated by circadian clocks are fully studied and then carefully analyzed, we can find ways to help these sorts of people adjust to their situations. We could also find a way to prevent jet lag, so people can enjoy their first few days in exciting and exotic new places. New studies have even shown that circadian clocks may control the growth of tumors. Studies like this may eventually even lead to a cure for cancer!


Ditty, J.L, S.B. Williams and S.S. Golden. 2003. "A Cyanobacterial Circadian Timing Mechanism." The Annual Review of Genetics 37:513-517. Available at .

Golden, Susan S. 2003. "Timekeeping in bacteria: the cyanobacterial circadian clock." Current Opinion in Microbiology 6:535-540. Available at .

Johnson, Carl H. and Martin Egli. 2004."Visualizing a biological clockwork's cogs." Nature Structural & Molecular Biology 11(7):584-585. Available at .

Vakonakis, Ionannis and Andy C. LiWang. 2004. "Structure of the C-terminal domain of the clock protein KaiA in complex with a KaiC-derived peptide: Implications for KaiC regulation." PNAS 101(30):10925-10930. Available at .

How to Cite this Page

MLA Citation:
"Circadian Clocks." 09 Feb 2016

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