How a cyanobacterium tells time

Abstract

The cyanobacterium Synechococcus elongatus builds a circadian clock on an oscillator composed of three proteins, KaiA, KaiB, and KaiC, which can recapitulate a circadian rhythm of KaiC phosphorylation in vitro. The molecular structures of all three proteins are known, and the phosphorylation steps of KaiC, the interaction dynamics among the three Kai proteins, and a weak ATPase activity of KaiC have all been characterized. An input pathway of redox-sensitive proteins uses photosynthetic function to relay light/dark information to the oscillator, and signal transduction proteins of well-known families broadcast temporal information to the genome, where global changes in transcription and a compaction of the chromosome are clock regulated.

Figure 1. A model of the KaiC phosphorylation rhythm

During a circadian cycle (represented by a circle), the phosphorylation states of KaiC proceed in an orderly manner. The relative timing of the peak for each phosphoform, based on published data [5,6], is shown by its position on the circle. KaiA stimulates KaiC phosphorylation by repeated association with KaiC. Starting from unphosphorylated KaiC (U); KaiC is first phosphorylated at T432 (T), which is further phosphorylated to the fully phosphorylated form (ST); T432 residue dephosphorylates from ST-KaiC first, resulting in KaiC phosphorylated only at S431 (S). KaiB preferentially binds S-KaiC, which forms a ternary complex with KaiA and, presumably, inactivates it and allows KaiC to return to the unphosphorylated state. The phosphorylation phase is represented in green and the dephosphorylation phase in red.

Figure 2. An Overview of the Molecular Mechanism of the Circadian Clock in S. elongatus

The central oscillator is composed of KaiA, KaiB and KaiC. KaiA stimulates KaiC phosphorylation, and KaiB inactivates KaiA when KaiC reaches a certain phosphorylation state (see Figure 1 for details). In the input pathway, both LdpA and CikA sense the cellular redox state, which is regulated by light and cell metabolism. LdpA affects the stability of CikA and KaiA through an unknown mechanism. Through its PsR domain, CikA binds quinone molecules directly, which destabilizes CikA. CikA affects phosphorylaton states of KaiC, but where and how it works in the signal transduction pathway is unknown. Pex is a transcriptional repressor of KaiA, and its abundance is sensitive to light, but it is not clear whether the pathway that regulates pex senses light directly or does it through cellular redox. In the output pathway, SasA interacts physically with KaiC and autophosphorylates, and then transfers the phosphoryl group to RpaA, a response regulator with a DNA binding domain. The target of RpaA has not been identified. LabA works upstream of RpaA and downstream of KaiC, but its exact function is not clear. A SasA- and RpaA- independent output pathway might exist. The output pathway controls DNA topology, which is proposed to regulate global gene expression. A transcription/translation rhythm could interact with and reinforce the post-translational rhythm of KaiC activities. Figure legends: a solid line indicates a direct effect whereas a dotted line indicates an indirect effect or an effect whose mechanism is unknown. Arrows indicate the direction of the information flow or a stimulation of activity or both. Blunt-ends represent an inhibition of protein activity or abundance, whereas an end with a filled circle suggests a regulation of unspecified direction.