The circadian machinery links metabolic disorders and depression: A review of pathways, proteins and potential pharmacological interventions

Circadian rhythms are responsible for regulating a number of physiological processes. The central oscillator is located within the suprachiasmatic nucleus (SCN) of the hypothalamus and the SCN synchronises the circadian clocks that are found in our peripheral organs through neural and humoral signalling. At the molecular level, biological clocks consist of transcription-translation feedback loops (TTFLs) and these pathways are influenced by transcription factors, post-translational modifications, signalling pathways and epigenetic modifiers. When disruptions occur in the circadian machinery, the activities of the proteins implicated in this network and the expression of core clock or clock-controlled genes (CCGs) can be altered. Circadian misalignment can also arise when there is desychronisation between our internal clocks and environmental stimuli. There is evidence in the literature demonstrating that disturbances in the circadian rhythm contribute to the pathophysiology of several diseases and disorders. This includes the metabolic syndrome and recently, it has been suggested that the 'circadian syndrome' may be a more appropriate term to use to not only describe the cardio-metabolic risk factors but also the associated comorbidities. Here we overview the molecular architecture of circadian clocks in mammals and provide insight into the effects of shift work, exposure to artificial light, food intake and stress on the circadian rhythm. The relationship between circadian rhythms, metabolic disorders and depression is reviewed and this is a topic that requires further investigation. We also describe how particular proteins involved in the TTFLs can be potentially modulated by small molecules, including pharmacological interventions and dietary compounds.

In silico Determination of Some Conditions Leading to Glycolytic Oscillations and Their Interference With Some Other Processes in E. coli Cells

Autonomous oscillations of species levels in the glycolysis express the self-control of this essential cellular pathway belonging to the central carbon metabolism (CCM), and this phenomenon takes place in a large number of bacteria. Oscillations of glycolytic intermediates in living cells occur according to the environmental conditions and to the cell characteristics, especially the adenosine triphosphate (ATP) recovery system. Determining the conditions that lead to the occurrence and maintenance of the glycolytic oscillations can present immediate practical applications. Such a model-based analysis allows in silico (model-based) design of genetically modified microorganisms (GMO) with certain characteristics of interest for the biosynthesis industry, medicine, etc. Based on our kinetic model validated in previous works, this paper aims to in silico identify operating parameters and cell factors leading to the occurrence of stable glycolytic oscillations in the Escherichia coli cells. As long as most of the glycolytic intermediates are involved in various cellular metabolic pathways belonging to the CCM, evaluation of the dynamics and average level of its intermediates is of high importance for further applicative analyses. As an example, by using a lumped kinetic model for tryptophan (TRP) synthesis from literature, and its own kinetic model for the oscillatory glycolysis, this paper highlights the influence of glycolytic oscillations on the oscillatory TRP synthesis through the PEP (phosphoenolpyruvate) glycolytic node shared by the two oscillatory processes. The numerical analysis allows further TRP production maximization in a fed-batch bioreactor (FBR).

Surface-Structure Libraries: Multifrequential Oscillations in Catalytic Hydrogen Oxidation on Rhodium

Multifrequential oscillating spatiotemporal patterns in the catalytic hydrogen oxidation on rhodium have been observed in situ in the 10-6 mbar pressure range using photoemission electron microscopy. The effect is manifested by periodic chemical waves, which travel over the polycrystalline Rh surface and change their oscillation frequency while crossing boundaries between different Rh(hkl) domains. Each crystallographically specific μm-sized Rh(hkl) domain exhibits an individual wave pattern and oscillation frequency, despite the global diffusional coupling of the surface reaction, altogether creating a structure library. This unique reaction behavior is attributed to the ability of stepped surfaces of high-Miller-index domains to facilitate the formation of subsurface oxygen, serving as a feedback mechanism of kinetic oscillations. Formation of a network of subsurface oxygen as a result of colliding reaction fronts was observed in situ. Microkinetic model analysis was used to rationalize the observed effects and to reveal the relation between the barriers for surface oxidation and oscillation frequency. Structural limits of the oscillations, the existence range of oscillations, as well as the effect of varying hydrogen pressure are demonstrated.

Robust concentration and frequency control in oscillatory homeostats

Homeostatic and adaptive control mechanisms are essential for keeping organisms structurally and functionally stable. Integral feedback is a control theoretic concept which has long been known to keep a controlled variable A robustly (i.e. perturbation-independent) at a given set-point A(set) by feeding the integrated error back into the process that generates A. The classical concept of homeostasis as robust regulation within narrow limits is often considered as unsatisfactory and even incompatible with many biological systems which show sustained oscillations, such as circadian rhythms and oscillatory calcium signaling. Nevertheless, there are many similarities between the biological processes which participate in oscillatory mechanisms and classical homeostatic (non-oscillatory) mechanisms. We have investigated whether biological oscillators can show robust homeostatic and adaptive behaviors, and this paper is an attempt to extend the homeostatic concept to include oscillatory conditions. Based on our previously published kinetic conditions on how to generate biochemical models with robust homeostasis we found two properties, which appear to be of general interest concerning oscillatory and homeostatic controlled biological systems. The first one is the ability of these oscillators ("oscillatory homeostats") to keep the average level of a controlled variable at a defined set-point by involving compensatory changes in frequency and/or amplitude. The second property is the ability to keep the period/frequency of the oscillator tuned within a certain well-defined range. In this paper we highlight mechanisms that lead to these two properties. The biological applications of these findings are discussed using three examples, the homeostatic aspects during oscillatory calcium and p53 signaling, and the involvement of circadian rhythms in homeostatic regulation.

Circadian oscillators in eukaryotes

The biological clock, present in nearly all eukaryotes, has evolved such that organisms can adapt to our planet's rotation in order to anticipate the coming day or night as well as unfavorable seasons. As all modern high-precision chronometers, the biological clock uses oscillation as a timekeeping element. In this review, we describe briefly the discovery, historical development, and general properties of circadian oscillators. The issue of temperature compensation (TC) is discussed, and our present understanding of the underlying genetic and biochemical mechanisms in circadian oscillators are described with special emphasis on Neurospora crassa, mammals, and plants.

Oscillatory kinetics and spatio-temporal self-organization in reactions at solid surfaces

Chemical reactions far from equilibrium on solid surfaces may exhibit typical phenomena of nonlinear dynamics, as exemplified by the catalytic oxidation of carbon monoxide on a platinum(110) single-crystal surface. Depending on the external parameters (temperature and partial pressures of the reactants), the temporal variation of the reaction rate may become oscillatory or even chaotic. In a parallel way, the concentration distributions of the adsorbed species on the surface form spatio-temporal patterns including propagating and standing waves, rotating spirals, as well as irregular and rapidly changing structures denoted "chemical turbulence."

The relationship between FRQ-protein stability and temperature compensation in the Neurospora circadian clock

Temperature compensation is an important property of all biological clocks. In Neurospora crassa, negative-feedback regulation on the frequency (frq) gene's transcription by the FRQ protein plays a central role in the organism's circadian pacemaker. Earlier model calculations predicted that the stability of FRQ should determine the period length of Neurospora's circadian rhythm as well as the rhythm's temperature compensation. Here, we report experimental FRQ protein stabilities in frq mutants at 20 degrees C and 25 degrees C, and estimates of overall activation energies for mutant FRQ protein degradation. The results are consistent with earlier model predictions, i.e., temperature compensation of Neurospora's circadian rhythm is a highly regulated process where the stability of FRQ is an important factor in determining Neurospora's circadian period as well as the clock's temperature compensation. The partial loss of temperature compensation in frq7 and frq(S513I) mutants can be described by a simple negative-feedback model (the Goodwin oscillator) when the experimentally obtained activation energies of FRQ degradation for theses mutants are incorporated into the model.

PER/TIM-mediated amplification, gene dosage effects and temperature compensation in an interlocking-feedback loop model of the Drosophila circadian clock

We have analysed a first-order kinetic representation of a interlocking-feedback loop model for the Drosophila circadian clock. In this model, the transcription factor Drosophila CLOCK (dCLK) which activates the clock genes period (per) and timeless (tim) is subjected to positive and negative regulations by the proteins 'PAR Domain Protein 1' (PDP1) and VRILLE (VRI), whose transcription is activated by dCLK. The PER/TIM complex binds to dCLK and in this way reduces the activity of dCLK. The results of our simulations suggest that the positive and negative feedback loops of Pdp1 and vri are essential for the overall oscillations. Although self sustained oscillations can be obtained without per/tim, the model shows that the PER/TIM complex plays an important role in amplification and stabilization of the oscillations generated by the Pdp1/vri positive/negative feedback loops. We further show that in contrast to a single (per/tim) negative feedback loop oscillator, the interlocking-feedback loop model can readily account for the effect of gene dosages of per, vri, and Pdp1 on the period length. Calculations of phase resetting on a temperature compensated version of the model shows good agreement with experimental phase response curves for high and low temperature pulses. Also, the partial losses of temperature compensation in perS and perL mutants can be described, which are related to decreased stabilities of the PER/TIM complex in perS and the stronger/more stable inhibitory complex between dCLK and PER/TIM in perL, respectively. The model shows (somewhat surprisingly) poor entrainment properties, especially under extended light/dark (L/D) cycles, which suggests that parts of the L/D tracking or sensing system are not well represented.

Temperature dependency and temperature compensation in a model of yeast glycolytic oscillations

Temperature sensitivities and conditions for temperature compensation have been investigated in a model for yeast glycolytic oscillations. The model can quantitatively simulate the experimental observation that the period length of glycolytic oscillations decreases with increasing temperature. Temperature compensation is studied by using control coefficients describing the effect of rate constants on oscillatory frequencies. Temperature compensation of the oscillatory period is observed when the positive contributions to the sum of products between control coefficients and activation energies balance the corresponding sum of the negative contributions. The calculations suggest that by changing the activation energies for one or several of the processes, i.e. by mutations, it could be possible to obtain temperature compensation in the yeast glycolytic oscillator.

Biological timing and the clock metaphor: oscillatory and hourglass mechanisms

Living organisms have developed a multitude of timing mechanisms--"biological clocks." Their mechanisms are based on either oscillations (oscillatory clocks) or unidirectional processes (hourglass clocks). Oscillatory clocks comprise circatidal, circalunidian, circadian, circalunar, and circannual oscillations--which keep time with environmental periodicities--as well as ultradian oscillations, ovarian cycles, and oscillations in development and in the brain, which keep time with biological timescales. These clocks mainly determine time points at specific phases of their oscillations. Hourglass clocks are predominantly found in development and aging and also in the brain. They determine time intervals (duration). More complex timing systems combine oscillatory and hourglass mechanisms, such as the case for cell cycle, sleep initiation, or brain clocks, whereas others combine external and internal periodicities (photoperiodism, seasonal reproduction). A definition of a biological clock may be derived from its control of functions external to its own processes and its use in determining temporal order (sequences of events) or durations. Biological and chemical oscillators are characterized by positive and negative feedback (or feedforward) mechanisms. During evolution, living organisms made use of the many existing oscillations for signal transmission, movement, and pump mechanisms, as well as for clocks. Some clocks, such as the circadian clock, that time with environmental periodicities are usually compensated (stabilized) against temperature, whereas other clocks, such as the cell cycle, that keep time with an organismic timescale are not compensated. This difference may be related to the predominance of negative feedback in the first class of clocks and a predominance of positive feedback (autocatalytic amplification) in the second class. The present knowledge of a compensated clock (the circadian oscillator) and an uncompensated clock (the cell cycle), as well as relevant models, are briefly re viewed. Hourglass clocks are based on linear or exponential unidirectional processes that trigger events mainly in the course of development and aging. An important hourglass mechanism within the aging process is the limitation of cell division capacity by the length of telomeres. The mechanism of this clock is briefly reviewed. In all clock mechanisms, thresholds at which "dependent variables" are triggered play an important role.

The Teorell membrane oscillator--a complete nerve model

The membrane oscillator discovered by T. Teorell in 1954 (10) is one of the most remarkable kinetic systems exhibiting spontaneous periodic behaviour under constant environmental conditions. It can be shown and demonstrated experimentally that the intrinsic reason for the occurrence of oscillations in the Teorell oscillator, like in other physicochemical and biological oscillatory systems, is an appropriate antagonistic action of a labilizing positive and a recovering stabilizing negative feedback. Each kind of feedback causes a group of characteristic temporal phenomena, which are observed in all oscillatory systems including the living excitable nerve such as: instability, bistability, excitability, propagation of exitation and recovery, refractoriness, abolition, accommodation etc..