The Circadian Clock-A Molecular Tool for Survival in Cyanobacteria

Abstract

Cyanobacteria are photosynthetic organisms that are known to be responsible for oxygenating Earth's early atmosphere. Having evolved to ensure optimal survival in the periodic light/dark cycle on this planet, their genetic codes are packed with various tools, including a sophisticated biological timekeeping system. Among the cyanobacteria is Synechococcus elongatus PCC 7942, the simplest clock-harboring organism with a powerful genetic tool that enabled the identification of its intricate timekeeping mechanism. The three central oscillator proteins-KaiA, KaiB, and KaiC-drive the 24 h cyclic gene expression rhythm of cyanobacteria, and the "ticking" of the oscillator can be reconstituted inside a test tube just by mixing the three recombinant proteins with ATP and Mg²⁺. Along with its biochemical resilience, the post-translational rhythm of the oscillation can be reset through sensing oxidized quinone, a metabolite that becomes abundant at the onset of darkness. In addition, the output components pick up the information from the central oscillator, tuning the physiological and behavioral patterns and enabling the organism to better cope with the cyclic environmental conditions. In this review, we highlight our understanding of the cyanobacterial circadian clock and discuss how it functions as a molecular chronometer that readies the host for predictable changes in its surroundings.

Keywords: CikA; KaiABC; RpaA; SasA; circadian clock; circadian rhythm; cyanobacteria.

Figure 1

Simplified schematic diagram of photosynthesis and cellular respiration in the thylakoid membrane of cyanobacteria: (a) photosynthesis during the day and (b) cellular respiration at night. Black arrows represent the transfer of electrons. The transition from day to night causes the plastoquinone (PQ) pool to become acutely oxidized, and conversely, the transition to the day leads to its transient reduction. COX: cytochrome-c oxidase, Cyt b₆f: cytochrome b₆f, PQH₂: plastoquinol, PSI/PSII: Photosystem I/II.

Figure 2

Ordered phosphorylation and dephosphorylation of KaiC. The initial unphosphorylated KaiC hexamer has the A-loops in their buried conformation by default. KaiA’s binding tethers the A-loops in their exposed conformation, initiating autokinase activity and phosphorylating T432 first. Then, KaiC reaches its fully phosphorylated state by phosphorylating its remaining S431. At this point, KaiC’s affinity for KaiB greatly increases due to their conformational changes [19,20]. KaiC–KaiB complexation ensues, sequestering KaiA away from the A-loop; the A-loops’ burial leads to the dephosphorylation of T432. Through further dephosphorylation, the KaiC hexamer returns to its unphosphorylated state.

Figure 3

The entrainment of a circadian rhythm with a dark pulse. The white part on the x-axis represents light or daytime; the dark area represents either the application of a dark pulse in vivo or the application of ADP or oxidized quinone in vitro. The y-axis represents the circadian gene expression pattern or KaiC phosphorylation rhythm in cyanobacteria. (a) A free-running rhythm that still runs even under a continuous light condition. (b) A phase advance that is caused by a dark-related cue during the rising phase of the clock. (c) A phase delay that is caused by a dark-related cue during the falling phase.

Figure 4

Schematic diagram of quinone entrainment. Oxidized quinone (“Q” in a black rhombus) becomes acutely abundant at night as a proxy for darkness. As KaiC autophosphorylation takes place, quinone application at this point inactivates KaiA, leading to premature dephosphorylation and a phase advance (lime arrows). On the other hand, in the in vitro mixture containing CikA and KaiABC, as fully phosphorylated KaiC enters the autodephosphorylating phase, quinone application at this point inactivates CikA, adding an extra time frame for the KaiA sequestration to take place, delaying the phase (yellow arrows).