Chronobiologists identify key circadian clock mechanism in cyanobacteria

Researchers have identified a key mechanism involved with the setting of the circadian clock of cyanobacteria—a model organism for study by chronobiologists due to the organism having one of the earliest circadian systems to evolve, and thus shining a light on how our own such systems work.

A paper describing the findings appeared in the Proceedings of the National Academy of Sciences on 4^th May, 2022.

Chronobiologists—researchers who study the timing processes, including circadian clocks, of organisms—have long been interested in cyanobacteria (aka blue-green algae) as a model organism for investigation, and its KaiC protein in particular.

The KaiC protein forms a key part of the cyanobacteria’s master clock, and regulation of the genes that produce this protein and others it interacts with is crucial for maintaining the bacterium’s circadian rhythm, and thus when to engage in its core life processes such as photosynthesis and cell division. Further elucidation of how the system works thus shines a light on how circadian clocks work throughout the living world.

KaiC is an ATPase, an enzyme that initiates (catalyzes) the chemical reaction that splits off a phosphoryl group (an ion containing phosphorus and oxygen) from adenosine triphosphate (ATP) by using a water molecule, a process that releases energy that can then be harnessed to power actions throughout living things.

But KaiC is a special type of ATPase in that it has a double-domain structure, with one active site (location on an enzyme where the chemical reaction takes place) in one domain and another active site in the other. The cyanobacteria’s circadian clock system is governed through a slow and orderly—but also very complex—coordination of the two sites (Figure 1).

To do this, the KaiC protein uses two types of ATP molecules to produce diverse chemical reactions and thereby govern the circadian rhythm. The ATP molecules attach themselves to a Walker motif—a loop structure in proteins that is associated with phosphate binding—present in the two domains, called N-terminal C1 and C-terminal C2. The ATP molecule bound to the C1 domain is the main source of the ATP hydrolysis reaction whose rate determines the speed of the clock system. In the presence of KaiC’s sister proteins KaiA and KaiB, the ATP molecules bound not only in the C1 domain but also in the C2 domain are activated and then inactivated periodically (left upper panel of Figure 2).

“In recent years, this C1/C2-ATPase interaction of KaiC has become an important research target to achieve a better understanding of the circadian clock system in cyanobacteria,” said Shuji Akiyama, a biophysicist with the Institute for Molecular Science at Japan’s National Institutes of Natural Sciences, and co-author of the study, “as it closely relates to the clock’s properties of oscillation, period-tuning, and adjustment of the system to compensate for the effects of changes in temperature.”

A great deal of research has explored KaiC ATPase’s biochemistry and structure, but the precise mechanisms of its activation and inactivation until now have remained unknown.

The researchers used biochemical and structural biology techniques, including substitutions of amino acids in KaiC itself, to characterize the properties and interplay of the dual ATPase active sites. They also performed an analysis of the crystal structure of KaiC to visualize the activated and inactivated forms of the ATP and catalytic water molecules in the C1 domain (Right upper panels of Figure 2).

They found that the N-terminal and C-terminal ATPases communicate with each other through an interface between the N-terminal and C-terminal domains in KaiC. The dual ATPase sites are regulated rhythmically in a concerted or opposing manner depending on the phase of the circadian clock system, to control the assembly and disassembly cycle of the other clock proteins, KaiA and KaiB. The results suggest that the activation of dual KaiC ATPases through an auto-catalytic mechanism (a product of a reaction then becomes a catalyst for the same reaction, lower panel of Figure 2,) contributes to a sudden disassembly at dawn of the protein complexes built over night.

This is crucial for resetting “subjective night”, or what the organism’s clock predicts the length of night to be, and then pushing the whole system forward in its cycle.

Many structural details of the C2-ATPase remain unclear even after the researchers’ analysis, partly because they were unable to identify some catalytic water molecules involved, suggesting further areas of research to fine-tune their understanding of the clock system. The researchers were also amazed at the enormous range of activity of the C2-ATPase, which can be suppressed down to zero. The physiological significance of this is also the next important research target for the scientists.