Molecular models for the circadian clock. I. The chronon concept

Ion dynamics and the regulation of circadian cellular physiology

Circadian rhythms in physiology and behavior allow organisms to anticipate the daily environmental changes imposed by the rotation of our planet around its axis. Although these rhythms eventually manifest at the organismal level, a cellular basis for circadian rhythms has been demonstrated. Significant contributors to these cell-autonomous rhythms are daily cycles in gene expression and protein translation. However, recent data revealed cellular rhythms in other biological processes, including ionic currents, ion transport, and cytosolic ion abundance. Circadian rhythms in ion currents sustain circadian variation in action potential firing rate, which coordinates neuronal behavior and activity. Circadian regulation of metal ions abundance and dynamics is implicated in distinct cellular processes, from protein translation to membrane activity and osmotic homeostasis. In turn, studies showed that manipulating ion abundance affects the expression of core clock genes and proteins, suggestive of a close interplay. However, the relationship between gene expression cycles, ion dynamics, and cellular function is still poorly characterized. In this review, I will discuss the mechanisms that generate ion rhythms, the cellular functions they govern, and how they feed back to regulate the core clock machinery.

Earthquake prediction, biological clocks, and the cold war psy-ops: Using animals as seismic sensors in the 1970s California

A familiar story of seismology is that of a small field originally focused on local studies of earthquakes through diverse disciplinary perspectives being transformed, in the second half of the twentieth century, into a highly specialized field focused on global studies of the earth's deep interior via sophisticated instruments and transnational networks of seismological stations. Against this backdrop, this essay offers a complementing account, highlighting the significance of local circumstances and disciplinary agendas that were contingent not only on transformations in the geophysical sciences but also on the concurrently changing biological sciences during the Cold War. Using examples of the studies of unusual animal behavior prior to earthquakes conducted under the auspices of the US Geological Survey on the West Coast of the United States in the 1970s, this essay examines a variety of motivations behind the attempts to bridge geophysics and biology. These examples illustrate the ways in which earthquake prediction became entangled with concerns over the use of seismological data, pioneering research on biological rhythms, and the troubled field of Cold War-driven military brain studies.

Cellular Timekeeping: It's Redox o'Clock

Mounting evidence in recent years supports the extensive interaction between the circadian and redox systems. The existence of such a relationship is not surprising because most organisms, be they diurnal or nocturnal, display daily oscillations in energy intake, locomotor activity, and exposure to exogenous and internally generated oxidants. The transcriptional clock controls the levels of many antioxidant proteins and redox-active cofactors, and, conversely, the cellular redox poise has been shown to feed back to the transcriptional oscillator via redox-sensitive transcription factors and enzymes. However, the circadian cycles in the S-sulfinylation of the peroxiredoxin (PRDX) proteins constituted the first example of an autonomous circadian redox oscillation, which occurred independently of the transcriptional clock. Importantly, the high phylogenetic conservation of these rhythms suggests that they might predate the evolution of the transcriptional oscillator, and therefore could be a part of a primordial circadian redox/metabolic oscillator. This discovery forced the reappraisal of the dogmatic transcription-centered view of the clockwork and opened a new avenue of research. Indeed, the investigation into the links between the circadian and redox systems is still in its infancy, and many important questions remain to be addressed.

Modeling circadian clocks: Roles, advantages, and limitations

Circadian rhythms are endogenous oscillations characterized by a period of about 24h. They constitute the biological rhythms with the longest period known to be generated at the molecular level. The abundance of genetic information and the complexity of the molecular circuitry make circadian clocks a system of choice for theoretical studies. Many mathematical models have been proposed to understand the molecular regulatory mechanisms that underly these circadian oscillations and to account for their dynamic properties (temperature compensation, entrainment by light dark cycles, phase shifts by light pulses, rhythm splitting, robustness to molecular noise, intercellular synchronization). The roles and advantages of modeling are discussed and illustrated using a variety of selected examples. This survey will lead to the proposal of an integrated view of the circadian system in which various aspects (interlocked feedback loops, inter-cellular coupling, and stochasticity) should be considered together to understand the design and the dynamics of circadian clocks. Some limitations of these models are commented and challenges for the future identified.

Identification of a high molecular weight polypeptide that may be part of the circadian clockwork in Acetabularia

In the chloroplast fraction of the unicellular and uninucleate green alga Acetabularia, we have detected a M(r) approximately 230,000 protein (p230) whose synthesis exhibits a pronounced endogenous diurnal rhythm. As judged by scanning densitometry of fluorographs of NaDodSO(4)/polyacrylamide gels, the synthesis of other proteins in the same fraction was independent of the time in the cycle. The incorporation of [(35)S]methionine into p230 was completely inhibited by cycloheximide, whereas chloramphenicol had no effect. This strongly suggests that p230 is translated on 80S ribosomes. Eighthour periods of exposure to cycloheximide produced a shift in the phase of the oscillation of p230 synthesis. The results are consistent with the hypothesis that p230 is essential for expression of circadian rhythms in Acetabularia.

Bacterial circadian programs

Twenty years ago, it was widely believed that prokaryotes were too "simple" to have evolved circadian programs. Since that time, however, the cyanobacterial circadian system has progressed from a curiosity to a major model system for analyzing clock phenomena. In addition to globally regulating gene expression, cyanobacteria are one of the only systems in which the adaptive fitness of a circadian system has been rigorously evaluated. Moreover, cyanobacteria are the only clock system in which all essential proteins of the core oscillator have been crystallized and structurally determined, namely, the KaiA, KaiB, and KaiC proteins. A biochemical oscillator can be reconstituted in vitro with these three purified Kai proteins and displays the key properties of temperature-compensated rhythmicity. This result spectacularly demonstrates that a strictly posttranslational clock is sufficient to elaborate circadian phenomena and that a transcription-translation feedback loop is not obligatory. The conjunction of structural information on essential clock proteins with a defined system that reconstitutes circadian oscillations in vitro leads to a turning point whereby biophysical and biochemical approaches bring analyses of circadian clock-work to an unprecedented level of molecular detail.

Stochastic simulation of the mammalian circadian clock

Circadian (nearly 24-h) clocks are remarkably accurate at timing biological events despite the randomness of their biochemical reactions. Here we examine the causes of their immunity to molecular noise in the context of a detailed stochastic mathematical model of the mammalian circadian clock. This stochastic model is a direct generalization of the deterministic mammalian circadian clock model previously developed. A feature of that model is that it completely specifies all molecular reactions, leaving no ambiguity in the formulation of a stochastic version of the model. With parameters based on experimental data concerning clock protein concentrations within a cell, we find accurate circadian rhythms in our model only when promoter interaction occurs on the time scale of seconds. As the model is scaled up by proportionally increasing the numbers of molecules of all species and the reaction rates with the promoter, the observed variability scales as 1/n(0.5), where n is the number of molecules of any species. Our results show that gene duplication increases robustness by providing more promoters with which the transcription factors of the model can interact. Although PER2 mutants were not rhythmic in the deterministic version of this model, they are rhythmic in the stochastic version.

Membranes, Ions, and Clocks: Testing the Njus–Sulzman–Hastings Model of the Circadian Oscillator

Current circadian clock models based on interlocking autoregulatory transcriptional?translational negative feedback loops have arisen out of an explosion of molecular genetic data obtained over the last decade (for review, see Stanewsky, 2003; Young and Kay, 2001). An earlier model of circadian oscillation was based on feedback interactions between membrane ion transport systems and ion concentration gradients (Njus et al., 1974, 1976). This membrane model was posited as a more plausible alternative at the time to the even earlier "chronon" model, which was based on autoregulatory genetic feedback loops (Ehret and Trucco, 1967). The membrane model has been tested in a number of experimental systems by pharmacologically manipulating either ionic gradients across the plasma membrane or ion transport systems, but with inconsistent results. In the meantime, the scope and explanatory power of the genetic models overshadowed inquiries into the role of membrane ion fluxes in clock function. However, several recently developed techniques described in this article have provided a new glimpse into the essential role that membrane ion fluxes play in the mechanism of the core circadian oscillator and indicate that a complete understanding of the clock must include both genetic and membrane-based feedback loops.

Circadian rhythm of tumor promotion in the two-stage model of mouse tumorigenesis

The question of whether cancer risk is influenced by time-of-day exposure to potentially carcinogenic agents was approached in this study by exposing mouse skin to a single initiating dose of 7,12-dimethylbenz [A-]anthracene, followed by a 12 week regime of bi-weekly skin treatments with the tumor promoter, 12-0-tetradecanoyl-phorbol acetate (TPA), given at four different circadian clock times (CCTs). Tumor incidence, average number of tumors per mouse and tumor size showed a dominant circadian component with an acrophase occurring at 23:00 h CCT. Pre-treatment with all trans-retinoic acid, prior to bi-weekly TPA promotion, reduced tumor incidence, average number and size of tumors per animal by greater than 80%, but did not suppress the underlying circadian rhythm of sensitivity to TPA-induced tumor formation.

Significance of circadian gene expression in higher plants

The significance of the circadian clock for living organisms is not fully understood. Recent findings demonstrate circadian control of transcription of quite a number of genes with individual maxima throughout the entire day. Evidence in favor of circadian-clock-controlled translation has also been documented. In this article, we want to promote the idea that in plants the clock functions as a regulator which coordinates critical cellular processes, such as cell division, nitrate reduction, or synthesis of chlorophyll-protein complexes, in such a way that the generation of dangerous, oxidative radicals or exposure to harmful light is minimized. This has been achieved by plant organisms either by confining gene expression to the dark phase or by a tight coordination of different tiers of gene expression during the light phase. This leads to the consequence for the researcher that the time of experimentation needs to be carefully considered and documented. It also follows that one might lose important findings if only a particular portion of the day is investigated.

A constant of temporal structure in the human hierarchy and other systems

The levels that compose biological hierarchies each have their own energetic, spatial and temporal structure. Indeed, it is the discontinuity in energy relationships between levels, as well as the similarity of sub-systems that support them, that permits levels to be defined. In this paper, the temporal structure of living hierarchies, in particular that pertaining to Human society, is examined. Consideration is given to the period defining the lifespan of entities at each level and to a periodic event considered fundamental to the maintenance of that level. The ratio between the duration of these two periods is found to be approximately 2.5 x 10(4). A similar relationship is found when lower, non-living levels of molecules and atoms are considered. This suggests that there is a constant factor of amplification between analogous periodic events at successive levels of the Human hierarchy.

Stopping the circadian pacemaker with inhibitors of protein synthesis

The requirement for protein synthesis in the mechanism of a circadian pacemaker was investigated by using inhibitors of protein synthesis. Continuous treatment of the ocular circadian pacemaker of the mollusc Bulla gouldiana with anisomycin or cycloheximide substantially lengthened (up to 39 and 52 hr, respectively) the free-running period of the rhythm. To determine whether high concentrations of inhibitor could stop the pacemaker, long pulse treatments of various durations (up to 44 hr) were applied and the subsequent phase of the rhythm was assayed. The observed phases of the rhythm after the treatments were a function of the time of the end of the treatment pulse, but only for treatments which spanned subjective dawn. The results provide evidence that protein synthesis is required in a phase-dependent manner for motion of the circadian pacemaker to continue.

Identification of two clock proteins in Acetabularia cliftonii and construction of cDNA libraries from Acetabularia cliftonii and Acetabularia mediterranea

1. Two clock proteins were identified in A. cliftonii. The first has a molecular weight (mol. wt) of 200 kDa (P200) and its synthesis shows a 24 hr periodicity. The second has mol. wt of 130 kDa (P130) and shows a semicircadian rhythm with a periodicity of about 12 hr. 2. cDNA libraries from A. cliftonii and A. mediterranea were prepared by cloning cDNA in lambda gt10 and lambda gt11, respectively. 3. One clone each of the two libraries hybridized with the human beta-actin pseudogene. One clone of the A. mediterranea and 4 clones of the A. cliftonii libraries hybridized to Chlamydomonas heat-shock gene.

Multiple levels in the control of rhythms in enzyme synthesis and activity by circadian clocks: recent trends

It is now well established that circadian clocks can control rhythmicity at different stages of the sequence of events leading from gene activity to a functional enzyme molecule. Conceptual and experimental distinction of the effective control targets is emphasized, with particular attention to recent results obtained on circadian clock control of transcription and to data indicating that proteins can behave as conformational oscillators. Thus circadian rhythmicity both in gene expression and in the dynamics of the enzyme molecule would contribute to the temporal compartmentation of processes such as metabolic co-ordination and channeling necessary for the adaptive efficiency of physiological programmes.

The cellular mechanism of circadian rhythms--a view on evidence, hypotheses and problems

A stable period length is a characteristic property of circadian oscillations. The question about whether higher frequency oscillators (0.5-8 hr) contribute to or establish the stable circadian periodicity cannot be answered at present. A sequential coupling of quantal subcycles appears possible on the basis of known "ultradian" oscillations. There is, however, no supporting evidence for such a concept. Phase response curves of the circadian clock derived from various perturbing pulses allow qualitative conclusions concerning the perturbed clock process. Deductions from computer simulations also allow conclusions about the phase of this oscillatory process. The distinction between processes (a) essential to the clock mechanism, (b) maintaining and controlling the clock (inputs) and (c) depending on the clock (outputs) on the basis of "oscillatory" and "change of psi or tau after perturbation" seems to be useful but not stringent. Protein synthesis may be an essential or input process. Oscillatory changes of this process may be due to periodic translational control or RNA-supply. Circadian changes in protein concentration and/or activity may depend on periodic synthesis, proteolysis, covalent modifications or aggregations. Specific essential proteins have not been identified conclusively. The large overlap between the group of agents and treatments that phase shift the clock and the group that induces stress proteins suggest that the latter may play a role in the controlling (input) or essential domain. The role of membranes in the clock mechanism is not clear: concepts assuming an essential function are based on circumstantial evidence. The membrane potential as well as Ca2+ may be involved in either input or essential function. Ca(2+)-calmodulin may also be important as concluded from inhibitor experiments. It is tempting to assume that a calmodulin-dependent kinase is part of a periodic protein phosphorylation process, yet it is not clear whether the periodic protein phosphorylation that has been observed is essential or is just another output process.

Plastid and nuclear mRNA fluctuations in tomato leaves - diurnal and circadian rhythms during extended dark and light periods

Steady-state mRNA levels of nuclear (rbcS, cab, tubA) and plastid (rbcL, psbA) encoded genes were determined in tomato leaves of different developmental stages. Transcripts were analyzed at four-hour intervals throughout a diurnal cycle in 4 cm-long terminal leaflets, while mRNA levels of the chlorophyll a/b-binding protein (cab), and the small and large subunit of RuBPC/Oase (rbcS, rbcL) are high. At different time points during the day the mRNAs accumulate to characteristic levels. Minor fluctuations of such mRNA levels were determined in the case of rbcS, rbcL, psbA and tubA, while significant alterations are observed for the chlorophyll a/b-binding protein transcript levels. LHCP II transcripts accumulate during the day, reach highest levels at noon and decline to non-detectable levels at 5 a.m. The cab mRNA fluctuates with a periodic length of approximately 24 hours suggesting the existence of a circadian rhythm ("biological clock"), which is involved in gene activation and inactivation. The mRNA oscillation with the same periodic length, but altered amplitude, continues to be present in plants which are kept under extended dark or light conditions. Different mRNA fluctuation patterns are observed for rbcS, rbcL, and psbA under such experimental conditions.

On the role of protein synthesis in the circadian clock of Neurospora crassa

Inhibitors of protein synthesis reset the biological clocks of many organisms. This has been interpreted to mean either that the synthesis per se of proteins is a step in the oscillatory feedback loop or merely that certain unstable protein(s) are required at certain times of the cycle to complete the feedback loop. We report here that Neurospora strains bearing the clock mutation frq-7 are relatively insensitive to the resetting action of the protein-synthesis-inhibitor cycloheximide. Protein synthesis itself in this mutant is inhibited by the drug to the same extent as in wild type. Since the clock of frq-7 continues to run relatively unimpeded even in the virtual absence of protein synthesis, it is unlikely that synthesis per se can be a part of the feedback cycle. Rather, we suggest that for normal operation of the Neurospora clock, certain protein(s) with a high turnover rate are required daily and, thus, must be resynthesized each day (at least) during discrete times in the cycle. The frq-7 mutation simultaneously alters several distinct clock characteristics--period length, temperature compensation, and resetting by cycloheximide. A model is presented to unify these observations.

Circadian rhythms in Neurospora crassa: membrane composition of a mutant defective in temperature compensation

The cel mutant of Neurospora, partially blocked in fatty acid synthesis and lacking temperature compensation of its circadian rhythm below 22 degrees C, had a phospholipid fatty acid composition in liquid shaker culture distinctly different from that of a cel+ control strain. During growth, cel+ exhibited a reproducible increase in its linoleic acid level from about 32 to a plateau at 63 mol%, and a corresponding decrease in its linolenic acid level from about 40 to a plateau at 10 mol%. The level of palmitic acid was constant at 19 mol%. In the cel strain, the linoleic acid level was constant at 54 mol% while the palmitic acid level increased from about 12 to about 23 mol%. Supplementation with palmitic or linoleic acids altered the patterns of fatty acid composition of cel, but did not affect the pattern of cel+. Altered fatty acid composition cosegregated with the cel marker. The mitochondrial phospholipids of cel in liquid culture also had abnormal fatty acid composition, as did the whole mycelial phospholipids on solid medium. These results are consistent with the involvement of membrane homeostasis in the temperature compensation of circadian rhythms.

Ultradian photosynchronization in Tetrahymena pyriformis GLC is related to modal cell generation time: further evidence for a common timer model

This study contains the first report of the photosynchronization of Tetrahymena in the ultradian mode of cell division. Ultradian mode cultures of T. pyriformis GLC were grown at low cell titers in a nephelostat under five different ultradian photocycles and also under constant conditions of illumination. Entrainment was achieved only when the period of the synchronizer did not exceed the nearest modal generation time observed in free-running single cells. Thus, the discrete ranges for photentrainment of ultradian rhythms in Tetrahymena were restricted to modal windows for the generation times in free-run. Cell division was found to be a function of the phase of the ultradian zeitgeber cycle. The cells did not behave as if they had been forced into synchrony by physiological shock; the synchronous populations obtained by this technique behaved like the populations commonly used in circadian studies which had been phased by a cyclic variation within the tolerance range of the organism.

Diurnal and circadian rhythmicity in the expression of light-induced plant nuclear messenger RNAs

The levels of nuclear mRNAs for three light-inducible proteins (light-harvesting chlorophyll a/b protein, small subunit of ribulose-1,5-bisphosphate carboxylase and early light-induced protein) have been analyzed under light-dark and constant light conditions. The levels of all three mRNAs have been found to vary considerably during the day, both under ligh-dark and under constant light conditions, demonstrating the existence of diurnal and circadian rhythmicity in the expressionoof these nuclear-coded plant proteins. The levels of two of these mRNAs have been found to be enhanced 2 h before the beginning of illumination when active phytochrome levels are still low.

Biochemical modeling of an autonomously oscillatory circadian clock in Euglena

Eukaryotic microorganisms, as well as higher animals and plants, display many autonomous physiological and biochemical rhythmicities having periods approximating 24 hours. In an attempt to determine the nature of the timing mechanisms that are responsible for these circadian periodicities, two primary operational assumptions were postulated. Both the perturbation of a putative element of a circadian clock within its normal oscillatory range and the direct activation as well as the inhibition of such an element should yield a phase shift of an overt rhythm generated by the underlying oscillator. Results of experiments conducted in the flagellate Euglena suggest that nicotinamide adenine dinucleotide (NAD+), the mitochondrial Ca2+-transport system, Ca2+, calmodulin, NAD+ kinase, and NADP+ phosphatase represent clock "gears" that, in ensemble, might constitute a self-sustained circadian oscillating loop in this and other organisms.

Chronobiology: anatomy in time

Chronobiology is that branch of science that objectively explores and quantifies mechanisms of biological time structure, including the important rhythmic manifestations of life. It is the study of biological rhythms. This paper introduces chronobiology and some of its vocabulary, principles, and techniques. A circadian rhythm is a regularly repetitive, quantitative physiological change with a period of about 24 hr (20-28), but the spectrum of rhythms includes those with periods less than 20 hr (ultradian) and longer than 28 hr (infradian). These rhythms are ubiquitous among the eukaryotes, innate and endogenous; their periods are precisely controlled by synchronizers in the environment. Rhythms can be manipulated by altering their synchronizers or by introducing more dominant ones. When organisms are removed from their environment and placed in constant conditions, rhythms revert to their natural frequencies and free-run. All of an organism's rhythms operate simultaneously, but their peaks and troughs do not necessarily occur at the same time. There are rhythms in susceptibility to drugs; a fixed dose may have a therapeutic effect at one point along the 24 hr time scale and a harmful one at another. Knowledge of these rhythms can be important when designing experimental or treatment protocols and interpreting results. Examples are provided to show that single-time-point sampling can lead to erroneous results, unless biological periodicity is taken into consideration.

Chronobiology at the cellular and molecular levels: models and mechanisms for circadian timekeeping

This review considers cellular chronobiology and examines, at least in a superficial way, several classes of models and mechanisms that have been proposed for circadian rhythmicity and some of the experimental approaches that have appeared to be most productive. After a brief discussion of temporal organization and the metabolic, epigenetic, and circadian time domains, the general properties of circadian rhythms are enumerated. A survey of independent oscillations in isolated organs, tissues, and cells is followed by a review of selected circadian rhythms in eukaryotic microorganisms, with particular emphasis placed on the rhythm of cell division in the algal flagellate Euglena as a model system illustrating temporal differentiation. In the ensuing section, experimental approaches to circadian clock mechanisms are considered. The dissection of the clock by the use of chemical inhibitors is illustrated for the rhythm of bioluminescence in the marine dinoflagellate Gonyaulax and for the rhythm of photosynthetic capacity in the unicellular green alga Acetabularia. Alternatively, genetic analysis of circadian oscillators is considered in the green alga Chlamydomonas and in the bread mold Neurospora, both of which have yielded clock mutants and mutants having biochemical lesions that exhibit altered clock properties. On the basis of the evidence generated by these experimental approaches, several classes of biochemical and molecular models for circadian clocks have been proposed. These include strictly molecular models, feedback loop (network) models, transcriptional (tape-reading) models, and membrane models; some of their key elements and predictions are discussed. Finally, a number of general unsolved problems at the cellular level are briefly mentioned: cell cycle interfaces, the evolution of circadian rhythmicity, the possibility of multiple cellular oscillators, chronopharmacology and chronotherapy, and cell-cycle clocks in development and aging.

Eukaryotic genome: model considerations

The paper presents a new model of chromosome structure based on the assumption that multiple circular subunits of DNA exist. The essential difference with previously described models is the circular DNA unit forms a central chromosome axis. Chromosome configurations during various phases of the cell cycle depend on the various conformations of this central integrating unit. The described model can be generalized for all haploid set of eukaryotic nucleus. Some aspects of the chromosome structure and their functions have been discussed.

Clocked cell cycle clocks

The cell division cycle of both mammalian cells and microorganisms, which apparently has both deterministic and probabilistic features, is a clock of sorts in that the sequence of events that comprise it measures time under a given set of environmental conditions. The cell division cycle may itself be regulated by a programmable clock that, under certain conditions, can generate circadian periodicities by interaction with a circadian pacemaker. These clocks must insert time segments into the cell division cycle in order to generate the observed variability in cellular generation times.