Structure, function, and mechanism of the core circadian clock in cyanobacteria

Swan, Jeffrey A.; Golden, Susan S.; LiWang, Andy; Partch, Carrie L.

doi:10.1074/jbc.tm117.001433

Cited by 70 publications

(60 citation statements)

References 87 publications

(43 reference statements)

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“…The proteins that these genes encode had not been described previously and held few clues as to how they contribute to a circadian clock. The combined efforts of geneticists, biochemists and structural biologists over a decade led to a clear picture of an elegant nanomachine whose basic timing loop can be reconstituted in vitro (Nakajima et al., ; Swan, Golden, LiWang, & Partch, ). The in vitro oscillator stands out as a fascinating achievement in biochemistry, with implications well beyond the realm of circadian biology.…”

Section: The Kai‐complex Nanomachinementioning

confidence: 99%

“…Many unforeseen steps contribute to the timekeeping mechanism, in which KaiC plays a central role as the foundation structure on which other components dock. The simplest description of the oscillator is that KaiC autophosphorylates when stimulated to do so by the binding of KaiA, and autodephosphorylates when KaiB associates and, thereby, blocks the stimulatory action of KaiA (Swan et al., ). More detailed structural investigation has revealed intra‐ and inter‐protein interactions that contribute to timing, as each interaction makes the forward tick of the clock hand more favourable and a backwards tick less so.…”

Section: The Kai‐complex Nanomachinementioning

confidence: 99%

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Principles of rhythmicity emerging from cyanobacteria

Golden

2019

Eur J of Neuroscience

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Section: The Kai‐complex Nanomachinementioning

confidence: 99%

Section: The Kai‐complex Nanomachinementioning

confidence: 99%

Principles of rhythmicity emerging from cyanobacteria

Golden

2019

Eur J of Neuroscience

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“…Thus, despite recent renewed interest in the interaction between the circadian clock and ROS stress tolerance, our current understanding on the interaction is very limited. Cyanobacterium Synechococcus elongatus PCC7942 (hereafter, S. elongatus), a photosynthetic autotrophic bacterium, is an appropriate model species for investigating these interactions because the molecular mechanism underlying its circadian clock is well understood, as summarized in recent reviews (10,11). Here, we developed an assay to examine the effect of ROS stress on cell viability in an attempt to characterize the circadian rhythm of ROS stress tolerance.…”

Section: Textmentioning

confidence: 99%

Time-of-day-dependent responses of cyanobacterial cellular viability against oxidative stress

Tanaka

Shimakawa

Nakanishi

2019

Preprint

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As an adaptation to periodic fluctuations of environmental light, photosynthetic organisms have evolved a circadian clock. The gene expression of ROS scavenging enzymes is regulated by circadian clock genes, which has been considered to help deal with the diurnal photogeneration of reactive oxygen species (ROS). Although a series of recent discoveries have suggested the correlation between circadian clock control and ROS scavenging mechanisms, circadian rhythms of ROS stress tolerance have not been experimentally demonstrated to date. In the present work, we constructed a novel assay using methyl viologen (MV) which generates ROS under light irradiation and experimentally verified the circadian rhythms of ROS stress tolerance in photosynthetic cells of cyanobacterium Synechococcus elongatus PCC7942, a standard model species for the investigation of circadian clock. Here, we report that ROS generated by MV treatment causes damage to stroma components and not to the photosynthetic electron transportation chain, leading to reduced cell viability. The degree of decrease in cell viability was dependent on the subjective time at which ROS stress was applied. Thus, ROS stress tolerance was shown to exhibit circadian rhythms. Notably, rhythms of ROS stress tolerance disappeared in mutant cells lacking the essential clock genes.Further, ROS stress tolerance showed irregular behaviors under irregular light/dark cycles that mismatched the subjective time. These results clearly show that the antioxidant ability in the stroma varies periodically under the control of clock genes. This is the first demonstration of ROS stress tolerance in cyanobacterial cells at a phenotypic level showing circadian oscillation. Significance statementReactive oxygen species (ROS) in photosynthetic organisms are the molecular basis of oxidative stress and are photogenerated in synchrony with the daily light cycles. Recent studies have revealed crosstalk between ROS scavenging systems and circadian clocks in organisms, but their mutual influence on physiological activities in a cell has not been fully elucidated. Here, we demonstrate for the first time that cellular viability against the ROS stress (i.e., ROS stress tolerance) exhibits circadian rhythms that are under the control of a clock system for cyanobacterium Synechococcus elongatus PCC7942, a standard model species for the investigation of the circadian clock.

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“…The phosphorylation cycle can be reconstituted in vitro while still retaining the hallmarks of circadian rhythms in living organisms (Nakajima et al, 2005; Yoshida et al, 2009; Rust et al, 2011; Leypunskiy et al, 2017). Previous work has clearly articulated the basic biochemical events in the phosphorylation cycle (Johnson et al, 2011; Swan et al, 2018), allowing specification of a model topology with few ambiguities.…”

Section: Introductionmentioning

confidence: 99%

Bayesian Modeling Reveals Ultrasensitivity Underlying Metabolic Compensation in the Cyanobacterial Circadian Clock

Lavrentovich

Chavan³

et al. 2019

Preprint

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24Mathematical models can enable a predictive understanding of mechanism in cell biology by quantitatively 25 describing complex networks of interactions, but such models are often poorly constrained by available 26 data. Owing to its relative biochemical simplicity, the core circadian oscillator in Synechococcus elongatus 27 has become a prototypical system for studying how collective dynamics emerge from molecular interac-28 tions. The oscillator consists of only three proteins, KaiA, KaiB, and KaiC, and near-24-h cycles of KaiC phos-29 phorylation can be reconstituted in vitro. Here, we formulate a molecularly-detailed but mechanistically 30 agnostic model of the KaiA-KaiC subsystem and fit it directly to experimental data within a Bayesian pa-31 rameter estimation framework. Analysis of the fits consistently reveals an ultrasensitive response for KaiC 32 phosphorylation as a function of KaiA concentration, which we confirm experimentally. This ultrasensitivity 33 primarily results from the differential affinity of KaiA for competing nucleotide-bound states of KaiC. We ar-34 gue that the ultrasensitive stimulus-response relation is critical to metabolic compensation by suppressing 35 premature phosphorylation at nighttime. 36 Synopsis 37This study takes a data-driven kinetic modeling approach to characterizing the interaction between KaiA and 38 KaiC in the cyanobacterial circadian oscillator and understanding how the oscillator responds to changes in 39 cellular metabolic conditions. 40 • An extensive dataset of KaiC autophosphorylation measurements was gathered and fit to a detailed 41 yet mechanistically agnostic kinetic model within a Bayesian parameter estimation framework. 42 • KaiA concentration tunes the sensitivity of KaiC autophosphorylation and the period of the full oscil-43 lator to %ATP. 44 • The model reveals an ultrasensitive dependence of KaiC phosphorylation on KaiA concentration as a 45 result of differential KaiA binding affinity to ADP-vs. ATP-bound KaiC. 46 • Ultrasensitivity in KaiC phosphorylation contributes to metabolic compensation by suppressing pre-47 Achieving a predictive understanding of biological systems and chemical reaction networks is challenging 50 because complex behavior can emerge from even a small number of interacting components. Classic ex-51 amples include the propagation of action potentials in neurobiology and chemical oscillators such as the 52 Belousov-Zhabotinsky reaction. The collective dynamics in such systems cannot be easily intuited through 53 qualitative reasoning alone, and thus mathematical modeling has long played an important role in summa-54 rizing and interpreting existing observations and formulating testable, quantitative hypotheses. 55 In general, mathematical modeling can be classified as either "forward" or "reverse." In forward mod-56 eling, known interactions are expressed mathematically, which allows a researcher to draw out the logical 57 implications of the model and its underlying assumptions (Gunawardena,...

show abstract

Structure, function, and mechanism of the core circadian clock in cyanobacteria

Abstract: Circadian rhythms enable cells and organisms to coordinate their physiology

Cited by 70 publications

References 87 publications

Principles of rhythmicity emerging from cyanobacteria

Principles of rhythmicity emerging from cyanobacteria

Time-of-day-dependent responses of cyanobacterial cellular viability against oxidative stress

Bayesian Modeling Reveals Ultrasensitivity Underlying Metabolic Compensation in the Cyanobacterial Circadian Clock

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