Protocols for in vitro reconstitution of the cyanobacterial circadian clock

Circadian clocks are intracellular systems that orchestrate metabolic processes in anticipation of sunrise and sunset by providing an internal representation of local time. Because the ~24-h metabolic rhythms they produce are important to health across diverse life forms there is growing interest in their mechanisms. However, mechanistic studies are challenging in vivo due to the complex, that is, poorly defined, milieu of live cells. Recently, we reconstituted the intact circadian clock of cyanobacteria in vitro. It oscillates autonomously and remains phase coherent for many days with a fluorescence-based readout that enables real-time observation of individual clock proteins and promoter DNA simultaneously under defined conditions without user intervention. We found that reproducibility of the reactions required strict adherence to the quality of each recombinant clock protein purified from Escherichia coli. Here, we provide protocols for preparing in vitro clock samples so that other labs can ask questions about how changing environments, like temperature, metabolites, and protein levels are reflected in the core oscillator and propagated to regulation of transcription, providing deeper mechanistic insights into clock biology.

The inner workings of an ancient biological clock

Circadian clocks evolved in diverse organisms as an adaptation to the daily swings in ambient light and temperature that derive from Earth's rotation. These timing systems, based on intracellular molecular oscillations, synchronize organisms' behavior and physiology with the 24-h environmental rhythm. The cyanobacterial clock serves as a special model for understanding circadian rhythms because it can be fully reconstituted in vitro. This review summarizes recent advances that leverage new biochemical, biophysical, and mathematical approaches to shed light on the molecular mechanisms of cyanobacterial Kai proteins that support the clock, and their homologues in other bacteria. Many questions remain in circadian biology, and the tools developed for the Kai system will bring us closer to the answers.

Biphasic amplitude oscillator characterized by distinct dynamics of trough and crest

Biphasic amplitude dynamics (BAD) of oscillation have been observed in many biological systems. However, the specific topology structure and regulatory mechanisms underlying these biphasic amplitude dynamics remain elusive. Here, we searched all possible two-node circuit topologies and identified the core oscillator that enables robust oscillation. This core oscillator consists of a negative feedback loop between two nodes and a self-positive feedback loop of the input node, which result in the fast and slow dynamics of the two nodes, thereby achieving relaxation oscillation. Landscape theory was employed to study the stochastic dynamics and global stability of the system, allowing us to quantitatively describe the diverse positions and sizes of the Mexican hat. With increasing input strength, the size of the Mexican hat exhibits a gradual increase followed by a subsequent decrease. The self-activation of input node and the negative feedback on input node, which dominate the fast dynamics of the input node, were observed to regulate BAD in a bell-shaped manner. Both deterministic and statistical analysis results reveal that BAD is characterized by the linear and nonlinear dependence of the oscillation trough and crest on the input strength. In addition, combining with computational and theoretical analysis, we addressed that the linear response of trough to input is predominantly governed by the negative feedback, while the nonlinear response of crest is jointly regulated by the negative feedback loop and the self-positive feedback loop within the oscillator. Overall, this study provides a natural and physical basis for comprehending the occurrence of BAD in oscillatory systems, yielding guidance for the design of BAD in synthetic biology applications.

Occurrence of Harmful Algal Blooms in Freshwater Sources of Mindu and Nyumba ya Mungu Dams, Tanzania

Harmful algal blooms (HABs) pose a significant threat to aquatic ecosystems and human health due to the production of toxins. The identification and quantification of these toxins are crucial for water quality management decisions. This study used DNA analysis (PCR techniques) to identify toxin-producing strains and liquid-chromatography-tandem mass spectrometry (LC-MS/MS) to quantify microcystins in samples from Mindu and Nyumba ya Mungu Dams in Tanzania. The results showed that HABs were detected in both dams. The BLAST results revealed that the 16S gene sequences of uncultured samples were very similar to an Antarctic cyanobacterium, Leptolyngbya sp, Anabaena sp, and Microcystis aeruginosa. Sequences of the cultured samples were most similar to Nodularia spumigena, Amazoninema brasiliense, Anabaena sp, and Microcystis aeruginosa. Further analyses showed that the nucleotide sequence similarity of uncultured isolates from this study and those from the GenBank ranged from 85 to 100%. For cultured isolates from this study and others from the GenBank, nucleotide identity ranged from 81 to 100%. The molecular identification of Microcystis aeruginosa confirmed the presence of HABs in both Mindu and Nyumba ya Mungu Dams in Tanzania. At Mindu Dam, the mean concentrations (± standard deviation) of microcystin-LR, -RR, and -YR were 1.08 ± 0.749 ppm, 0.120 ± 0.0211 ppm, and 1.37 ± 0.862 ppm, respectively. Similarly, at Nyumba ya Mungu Dam, the concentrations of microcystin-LR, -RR, and -YR were 1.07 ± 0.499 ppm, 0.124 ± 0.0224 ppm, and 0.961 ± 0.408 ppm, respectively. This paper represents the first application of PCR and LC-MS/MS to study microcystins in small freshwater reservoirs in Tanzania. This study confirms the presence of toxin-producing strains of Microcystis aeruginosa in both dams and also provides evidence of the occurrence of microcystins from these strains. These findings contribute in improving the monitoring of HABs contamination and their potential impact on water quality in Tanzanian reservoirs.

Damped Oscillating Phosphoryl Transfer Reaction in the Cyanobacterial Circadian Clock

Most organisms have circadian clocks to ensure the metabolic cycle to resonate with the rhythmic environmental changes without "damping," or losing robustness. Cyanobacteria is the oldest and simplest form of life that is known to harbor this biological intricacy. Its KaiABC-based central oscillator proteins can be reconstituted inside a test tube, and the post-translational modification cycle occurs with 24 h periodicity. KaiC's two major phosphorylation sites, Ser-431 and Thr-432, become phosphorylated and dephosphorylated by interacting with KaiA and KaiB, respectively. Here, we mutate Thr-432 into Ser to find the oscillatory phosphoryl transfer reaction damps. Previously, this mutant KaiC was reported to be arrhythmic in vivo. However, we found that the mutant KaiC gradually loses the ability to run in an autonomous manner and stays constitutively phosphorylated after 3 cycles in vitro.

A Night-Time Edge Site Intermediate in the Cyanobacterial Circadian Clock Identified by EPR Spectroscopy

As the only circadian oscillator that can be reconstituted in vitro with its constituent proteins KaiA, KaiB, and KaiC using ATP as an energy source, the cyanobacterial circadian oscillator serves as a model system for detailed mechanistic studies of day-night transitions of circadian clocks in general. The day-to-night transition occurs when KaiB forms a night-time complex with KaiC to sequester KaiA, the latter of which interacts with KaiC during the day to promote KaiC autophosphorylation. However, how KaiB forms the complex with KaiC remains poorly understood, despite the available structures of KaiB bound to hexameric KaiC. It has been postulated that KaiB-KaiC binding is regulated by inter-KaiB cooperativity. Here, using spin labeling continuous-wave electron paramagnetic resonance spectroscopy, we identified and quantified two subpopulations of KaiC-bound KaiB, corresponding to the "bulk" and "edge" KaiBC sites in stoichiometric and substoichiometric KaiB_iC₆ complexes (i = 1-5). We provide kinetic evidence to support the intermediacy of the "edge" KaiBC sites as bridges and nucleation sites between free KaiB and the "bulk" KaiBC sites. Furthermore, we show that the relative abundance of "edge" and "bulk" sites is dependent on both KaiC phosphostate and KaiA, supporting the notion of phosphorylation-state controlled inter-KaiB cooperativity. Finally, we demonstrate that the interconversion between the two subpopulations of KaiC-bound KaiB is intimately linked to the KaiC phosphorylation cycle. These findings enrich our mechanistic understanding of the cyanobacterial clock and demonstrate the utility of EPR in elucidating circadian clock mechanisms.

Shift in Conformational Equilibrium Underlies the Oscillatory Phosphoryl Transfer Reaction in the Circadian Clock

Oscillatory phosphorylation/dephosphorylation can be commonly found in a biological system as a means of signal transduction though its pivotal presence in the workings of circadian clocks has drawn significant interest: for example in a significant portion of the physiology of Synechococcus elongatus PCC 7942. The biological oscillatory reaction in the cyanobacterial circadian clock can be visualized through its reconstitution in a test tube by mixing three proteins—KaiA, KaiB and KaiC—with adenosine triphosphate and magnesium ions. Surprisingly, the oscillatory phosphorylation/dephosphorylation of the hexameric KaiC takes place spontaneously and almost indefinitely in a test tube as long as ATP is present. This autonomous post-translational modification is tightly regulated by the conformational change of the C-terminal peptide of KaiC called the “A-loop” between the exposed and the buried states, a process induced by the time-course binding events of KaiA and KaiB to KaiC. There are three putative hydrogen-bond forming residues of the A-loop that are important for stabilizing its buried conformation. Substituting the residues with alanine enabled us to observe KaiB’s role in dephosphorylating hyperphosphorylated KaiC, independent of KaiA’s effect. We found a novel role of KaiB that its binding to KaiC induces the A-loop toward its buried conformation, which in turn activates the autodephosphorylation of KaiC. In addition to its traditional role of sequestering KaiA, KaiB’s binding contributes to the robustness of cyclic KaiC phosphorylation by inhibiting it during the dephosphorylation phase, effectively shifting the equilibrium toward the correct phase of the clock.

Reconstitution of an intact clock reveals mechanisms of circadian timekeeping

[Figure: see text].

Evolution of kaiA, a key circadian gene of cyanobacteria

The circadian system of cyanobacteria is built upon a central oscillator consisting of three genes, kaiA, kaiB, and kaiC. The KaiA protein plays a key role in phosphorylation/dephosphorylation cycles of KaiC, which occur over the 24-h period. We conducted a comprehensive evolutionary analysis of the kaiA genes across cyanobacteria. The results show that, in contrast to the previous reports, kaiA has an ancient origin and is as old as cyanobacteria. The kaiA homologs are present in nearly all analyzed cyanobacteria, except Gloeobacter, and have varying domain architecture. Some Prochlorococcales, which were previously reported to lack the kaiA gene, possess a drastically truncated homolog. The existence of the diverse kaiA homologs suggests significant variation of the circadian mechanism, which was described for the model cyanobacterium, Synechococcus elongatus PCC7942. The major structural modifications in the kaiA genes (duplications, acquisition and loss of domains) have apparently been induced by global environmental changes in the different geological periods.

The Circadian Clock-A Molecular Tool for Survival in Cyanobacteria

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.

CikA, an Input Pathway Component, Senses the Oxidized Quinone Signal to Generate Phase Delays in the Cyanobacterial Circadian Clock

The circadian clock is a timekeeping system in most organisms that keeps track of the time of day. The rhythm generated by the circadian oscillator must be constantly synchronized with the environmental day/night cycle to make the timekeeping system truly advantageous. In the cyanobacterial circadian clock, quinone is a biological signaling molecule used for entraining and fine-tuning the oscillator, a process in which the external signals are transduced into biological metabolites that adjust the phase of the circadian oscillation. Among the clock proteins, the pseudo-receiver domain of KaiA and CikA can sense external cues by detecting the oxidation state of quinone, a metabolite that reflects the light/dark cycle, although the molecular mechanism is not fully understood. Here, we show the antagonistic phase shifts produced by the quinone sensing of KaiA and CikA. We introduced a new cyanobacterial circadian clock mixture that includes an input component in vitro. KaiA and CikA cause phase advances and delays, respectively, in this circadian clock mixture in response to the quinone signal. In the entrainment process, oxidized quinone modulates the functions of KaiA and CikA, which dominate alternatively at day and night in the cell. This in turn changes the phosphorylation state of KaiC-the central oscillator in cyanobacteria-ensuring full synchronization of the circadian clock. Moreover, we reemphasize the mechanistic input functionality of CikA, contrary to other reports that focus only on its output action.

Magnesium Regulates the Circadian Oscillator in Cyanobacteria

The circadian clock controls 24-h biological rhythms in our body, influencing many time-related activities such as sleep and wake. The simplest circadian clock is found in cyanobacteria, with the proteins KaiA, KaiB, and KaiC generating a self-sustained circadian oscillation of KaiC phosphorylation and dephosphorylation. KaiA activates KaiC phosphorylation by binding the A-loop of KaiC, while KaiB attenuates the phosphorylation by sequestering KaiA from the A-loop. Structural analysis revealed that magnesium regulates the phosphorylation and dephosphorylation of KaiC by dissociating from and associating with catalytic Glu residues that activate phosphorylation and dephosphorylation, respectively. High magnesium causes KaiC to dephosphorylate, whereas low magnesium causes KaiC to phosphorylate. KaiC alone behaves as an hourglass timekeeper when the magnesium concentration is alternated between low and high levels in vitro. We suggest that a magnesium-based hourglass timekeeping system may have been used by ancient cyanobacteria before magnesium homeostasis was established.