Clock In Organisms Research Articles

The Evolutionary Pathways of the Circadian Rhythms through Phylogenetical Analysis of Basal Circadian Genes

Circadian rhythm is the endogenous clock in organisms that regulates the performance of various physiological and metabolic events in accordance with the periodic oscillating changes in the environment, especially the periodic light-dark cycle. The clock has endowed organisms with the ability in anticipating environmental changes allowing them to adjust their survival strategies accordingly, promoting their selective fitness. However, the evolutionary path and the emergence of such an intricate and vital system remain elusive. The article aims to analyse the molecular architecture and components of the circadian clock among three kingdoms of plants, animals, fungi, and their unicellular ancestors, revealing the possible emergence of the circadian clock from the primordial circadian rhythm of prokaryotes to complicated rhythms seen in multicellular organisms. In comparative genetic analyses of the circadian clocks, researchers have identified homologs in the circadian genes of multicellular organisms with their unicellular ancestors, indicating prior emergence of the circadian clock than multicellularity. In addition, comparative genetic studies among fungi, animal, and plant circadian clocks implied that the emergence of circadian rhythms across the kingdoms resulted from convergent evolution due to the significant selective advantages concomitant with the circadian clock. Furthermore, the article also reviewed methods of gene transferring laterally, including horizontal gene transfer and endosymbiotic gene transfer, which may explain the overall similarities in the transcription-translation feedback mechanism among the many circadian rhythms. However, while genetic transfer among distantly related organisms enhanced biodiversity and biological innovations in nature, whether the horizontal changes of genetic materials contribute to the similar feedback loop of the circadian clock still requires further research to determine.

To be or not to be rhythmic? A review of studies on organisms inhabiting constant environments

Circadian clocks are endogenous time keeping mechanisms that drive near 24-h behavioural, physiological and metabolic rhythms in organisms. It is thought that organisms possess circadian clocks to facilitate coordination of essential biological events to the external day and night (extrinsic advantage) so as to enhance Darwinian fitness. However, on Earth, there are a number of habitats that are not subject to such robust daily cycling of geo-physical factors. Do organisms living under such conditions exhibit rhythmic behaviours that are driven by endogenous circadian clocks? We attempt to critically survey studies of rhythms (or the lack of them) in organisms living in a range of constant environments. Many such organisms do show rhythms in behaviour and/or physiological variables. We suggest that such presence of rhythms may be indicative of an underlying clock that facilitates, (a) internal synchrony among rhythms, and (b) temporal partitioning of incompatible cellular processes (intrinsic advantage). We then highlight reasons that limit our interpretations about the presence (or absence) of clocks in such organisms living under constant conditions, and suggest possible methods to conclusively test whether or not rhythms in these organisms are driven by endogenous circadian clocks with the hope that it may enhance our understanding of circadian clocks in organisms under constant environments.

The influence of day/night cycles on biomass yield and composition of Neochloris oleoabundans

BackgroundDay/night cycles regulate the circadian clock of organisms to program daily activities. Many species of microalgae have a synchronized cell division when grown under a day/night cycle, and synchronization might influence biomass yield and composition. Therefore, the aim of this study was to study the influence of day/night cycle on biomass yield and composition of the green microalgae Neochloris oleoabundans. Hence, we compared continuous turbidostat cultures grown under continuous light with cultures grown under simulated day/night cycles.ResultsUnder day/night cycles, cultures were synchronized as cell division was scheduled in the night, whereas under continuous light cell division occurred randomly synchronized cultures were able to use the light 10–15% more efficiently than non-synchronized cultures. Our results indicate that the efficiency of light use varies over the cell cycle and that synchronized cell division provides a fitness benefit to microalgae. Biomass composition under day/night cycles was similar to continuous light, with the exception of starch content. The starch content was higher in cultures under continuous light, most likely because the cells never had to respire starch to cover for maintenance during dark periods. Day/night cycles were provided in a ‘block’ (continuous light intensity during the light period) and in a ‘sine’ (using a sine function to simulate light intensities from sunrise to sunset). There were no differences in biomass yield or composition between these two ways of providing light (in a ‘block’ or in a ‘sine’).ConclusionsThe biomass yield and composition of N. oleoabundans were influenced by day/night cycles. These results are important to better understand the relations between research done under continuous light conditions and with day/night cycle conditions. Our findings also imply that more research should be done under day/night cycles.

Non-transcriptional/translational regulations of the circadian system

Circadian clocks in organisms drive physiology and behavior, helping with adjustment to earth’s environment and human society. The generation and regulation mechanisms of circadian rhythms are starting to be understood. The transcriptional/post-transcriptional delayed feedback loop has been widely studied as the main regulation mechanism. But it cannot fully account for all circadian rhythms in cells. It has been reported that the “proto-clock” may have been a cytosolic metabolic oscillation and that the transcriptional translational regulation system, which provides robustness and amplifies circadian outputs, was developed during evolution. Research on circadian rhythms in cyanobacteria Synechococcus elongatus, algae Ostreococcus tauri, and human red blood cells in the absence of transcription and translation indicates the existence of a non-transcriptional/translational regulation mechanism, in addition to the classical transcriptional/translational regulation mechanism. It revealed a close link between the two regulation systems of circadian rhythms, in which they might complement each other. And NAD, involved in energy metabolism, may be involved in their interaction.

Chaotic dynamics and diffusion in a piecewise linear equation.

Genetic interactions are often modeled by logical networks in which time is discrete and all gene activity states update simultaneously. However, there is no synchronizing clock in organisms. An alternative model assumes that the logical network is preserved and plays a key role in driving the dynamics in piecewise nonlinear differential equations. We examine dynamics in a particular 4-dimensional equation of this class. In the equation, two of the variables form a negative feedback loop that drives a second negative feedback loop. By modifying the original equations by eliminating exponential decay, we generate a modified system that is amenable to detailed analysis. In the modified system, we can determine in detail the Poincaré (return) map on a cross section to the flow. By analyzing the eigenvalues of the map for the different trajectories, we are able to show that except for a set of measure 0, the flow must necessarily have an eigenvalue greater than 1 and hence there is sensitive dependence on initial conditions. Further, there is an irregular oscillation whose amplitude is described by a diffusive process that is well-modeled by the Irwin-Hall distribution. There is a large class of other piecewise-linear networks that might be analyzed using similar methods. The analysis gives insight into possible origins of chaotic dynamics in periodically forced dynamical systems.

Circadian rhythms. Decoupling circadian clock protein turnover from circadian period determination.

The mechanistic basis of eukaryotic circadian oscillators in model systems as diverse as Neurospora, Drosophila, and mammalian cells is thought to be a transcription-and-translation-based negative feedback loop, wherein progressive and controlled phosphorylation of one or more negative elements ultimately elicits their own proteasome-mediated degradation, thereby releasing negative feedback and determining circadian period length. The Neurospora crassa circadian negative element FREQUENCY (FRQ) exemplifies such proteins; it is progressively phosphorylated at more than 100 sites, and strains bearing alleles of frq with anomalous phosphorylation display abnormal stability of FRQ that is well correlated with altered periods or apparent arrhythmicity. Unexpectedly, we unveiled normal circadian oscillations that reflect the allelic state of frq but that persist in the absence of typical degradation of FRQ. This manifest uncoupling of negative element turnover from circadian period length determination is not consistent with the consensus eukaryotic circadian model.

Defining necessary circadian clock elements

Circadian Rhythms The circadian clock in organisms as diverse as fungi and humans have a rather similar structure: Timing depends on daily cycles of transcription in circuits in which feedback loops control the timing of oscillations. A critical role has been ascribed to negative elements, which

Using circadian entrainment to find cryptic clocks.

Three properties are most often attributed to the circadian clock: a ca. 24-h free-running rhythm, temperature compensation of the circadian rhythm, and its entrainment to zeitgeber cycles. Relatively few experiments, however, are performed under entrainment conditions. Rather, most chronobiology protocols concern constant conditions. We have turned this paradigm around and used entrainment to study the circadian clock in organisms where a free-running rhythm is weak or lacking. We describe two examples therein: Caenorhabditis elegans and Saccharomyces cerevisiae. By probing the system with zeitgeber cycles that have various structures and amplitudes, we can demonstrate the establishment of systematic entrained phase angles in these organisms. We conclude that entrainment can be utilized to discover hitherto unknown circadian clocks and we discuss the implications of using entrainment more broadly, even in model systems that show robust free-running rhythms.

How to get Oscillators in a Multicellular Clock to Agree on the Right Period

Circadian clocks generate nearly 24-h rhythms that regulate many physiological behaviors of organisms throughout the kingdoms of life. A clock’s complexity varies with the complexity of the organism. For simple organisms, rhythms are generated by a gene regulatory network within a single cell. For higher organisms (such as mammals and flies), the clockworks reside in multiple cells: each cell contains a genetic oscillator and intercellular signaling synchronizes the cellular rhythms, forming coherent, high-amplitude oscillations. Clocks in organisms at all levels of complexity have at their core a negative feedback loop. They differ in many details, such as the number of genes, the mechanisms involved in the regulation, and posttranslational modifications. Kim et al. (1) have identified the negative regulation term as key to clock functionality and provide an explanation as to why unicellular and multicellular clocks rely on different mechanisms. They do so by connecting protein sequestration within each cell to the emergent behavior of the synchronized multicellular oscillator in the mammalian clock. In mammals, the gene regulatory network within each cell is relatively well understood (2) and it has been fruitful to develop mechanistic mathematical models of the network that capture both the mRNA and protein interactions within each cell and the effects of intercellular signaling (3,4). Model analyses are helping us to understand how it is possible for a network of weak, heterogeneous oscillators to form a reliable clock. For example, it has been shown that tissues are more likely to synchronize if they are composed of single cells that operate close to a bifurcation boundary (5) and that networks with weak oscillators at network hubs are more easily synchronized than those with strong oscillators at hubs (3). Further, the phenomenon of amplitude expansion allows for cells with low amplitude to collectively increase their amplitudes and become less sensitive to external perturbations (6). In addition to understanding how the circadian clock achieves high-amplitude synchrony, we want to know how the period of the population is determined by the periods of the constituent cells (7). Experimental data show that the period of the synchronized clock is close to the mean intrinsic periods of its cells (8,9). Kim et al. (1) address the question of period-determination, in particular of how the population period ends up being very close to the mean of the individual periods. They construct a clear chain of mathematical reasoning that leads us from a particular mechanism within a cell to emergent behavior at the population level—that of the period of oscillation (see Fig. 1). They identify the expression controlling transcriptional regulation as key (10), show that protein sequestration is the appropriate mechanism, relate it to the alternative (and more popular) Hill kinetics, and explain the response of the transcription rate to the regulators. They then relate the transcription rate’s response to the phase response. Using the phase response and techniques from the theory of weakly connected neural networks (11), they derive formulae for predicting the period of the population. They simulate a simple (three-equation) model to demonstrate the accuracy of their predictions and show that their reasoning does not depend on the specific choice of parameters. This is important, because it suggests that their observations apply to broader contexts. Figure 1 Tracing the effects of protein sequestration as the mechanism for transcriptional regulation to the period of the synchronized network of oscillators in Kim et al. (1). (A) Within each cell, a key gene is downregulated when the activator (A) and ... Connecting individual cell properties to network-level behavior is complicated—not only does the behavior of oscillators affect the network, but the network affects the oscillators. In other words, context is critical. Do insights drawn from the model of Kim et al. (1) extend to models of multicellular clocks that are more complex, and, more importantly, do they explain the mechanisms in vivo? Previous modeling work has shown that the traditional Hill kinetics for transcriptional regulation tends to predict population periods that differ from the mean intrinsic periods of the constituent cells (12–14). However, in the future, it will be necessary to conduct formal analyses of models involving more processes to see if those additional processes, such as posttranslational modification, in some way compensate for or negate the effects of the term controlling transcriptional regulation. It will also be important to determine whether Kim et al. (1) have uncovered an evolutionary principle: Have multicellular organisms evolved to include protein-sequestration-based regulation as a critical modulator of circadian clock function? If so, we now know why.

A Role for Protein Kinase Casein Kinase2 α-Subunits in the Arabidopsis Circadian Clock

Circadian rhythms are autoregulatory, endogenous rhythms with a period of approximately 24 h. A wide variety of physiological and molecular processes are regulated by the circadian clock in organisms ranging from bacteria to humans. Phosphorylation of clock proteins plays a critical role in generating proper circadian rhythms. Casein Kinase2 (CK2) is an evolutionarily conserved serine/threonine protein kinase composed of two catalytic α-subunits and two regulatory β-subunits. Although most of the molecular components responsible for circadian function are not conserved between kingdoms, CK2 is a well-conserved clock component modulating the stability and subcellular localization of essential clock proteins. Here, we examined the effects of a cka1a2a3 triple mutant on the Arabidopsis (Arabidopsis thaliana) circadian clock. Loss-of-function mutations in three nuclear-localized CK2α subunits result in period lengthening of various circadian output rhythms and central clock gene expression, demonstrating that the cka1a2a3 triple mutant affects the pace of the circadian clock. Additionally, the cka1a2a3 triple mutant has reduced levels of CK2 kinase activity and CIRCADIAN CLOCK ASSOCIATED1 phosphorylation in vitro. Finally, we found that the photoperiodic flowering response, which is regulated by circadian rhythms, was reduced in the cka1a2a3 triple mutant and that the plants flowered later under long-day conditions. These data demonstrate that CK2α subunits are important components of the Arabidopsis circadian system and their effects on rhythms are in part due to their phosphorylation of CIRCADIAN CLOCK ASSOCIATED1.

Modeling Light Adaptation in Circadian Clock: Prediction of the Response That Stabilizes Entrainment

Periods of biological clocks are close to but often different from the rotation period of the earth. Thus, the clocks of organisms must be adjusted to synchronize with day-night cycles. The primary signal that adjusts the clocks is light. In Neurospora, light transiently up-regulates the expression of specific clock genes. This molecular response to light is called light adaptation. Does light adaptation occur in other organisms? Using published experimental data, we first estimated the time course of the up-regulation rate of gene expression by light. Intriguingly, the estimated up-regulation rate was transient during light period in mice as well as Neurospora. Next, we constructed a computational model to consider how light adaptation had an effect on the entrainment of circadian oscillation to 24-h light-dark cycles. We found that cellular oscillations are more likely to be destabilized without light adaption especially when light intensity is very high. From the present results, we predict that the instability of circadian oscillations under 24-h light-dark cycles can be experimentally observed if light adaptation is altered. We conclude that the functional consequence of light adaptation is to increase the adjustability to 24-h light-dark cycles and then adapt to fluctuating environments in nature.

The intelligent clock and the Rube Goldberg clock

Circadian rhythms are generated by cell-autonomous molecular clocks in organisms ranging from cyanobacteria to humans. Recent research on the mechanisms of molecular clocks call for a reflection on the cause and necessity of complexity in biological systems.