Cyanobacterial Circadian Clock: Molecular Mechanisms and Physiological Outputs

Earth’s rotation produces day and night cycles that are a primary selective pressure driving the evolution of endogenous circadian clocks. Cyanobacteria are the most studied prokaryotic model, and their timekeeping core is a protein oscillator composed of KaiA, KaiB, and KaiC. This oscillator sustains a near-24 h rhythm independently of transcription–translation feedback, challenging the long-standing assumption that prokaryotes merely respond passively to environmental cues. Moreover, it offers unique insights into the evolution and operational logic of circadian clocks. This review summarizes advances in cyanobacterial circadian research. We first analyze the KaiABC oscillator’s molecular basis, including synergistic conformational changes, phosphorylation and dephosphorylation cascades, and temperature compensation, which confer robustness and tunability. We compare oscillator compositions across cyanobacterial lineages, showing evolutionary plasticity. We then outline input and output networks, clarifying how environmental signals reset the oscillator phase and how temporal information is relayed to downstream processes. We further explain how the clock coordinates photosynthesis, nitrogen fixation, respiration, and cell division through predictive regulation, temporal decoupling, and resource prioritization, thereby resolving metabolic conflicts and enhancing fitness under light and dark cycles. This framework provides a theoretical basis for microbial survival strategies in fluctuating environments and offers insights for synthetic biology circuit design. Finally, we discuss open questions, including coupling between the oscillator and the cell cycle, functional divergence among ecotypes, and roles at the community level. Further research on the cyanobacterial clock will help clarify general principles of biological timing and its evolutionary origins.