Circadian systems: different levels of complexity

Bioluminescence and Photoreception in Unicellular Organisms: Light-Signalling in a Bio-Communication Perspective

Bioluminescence, the emission of light catalysed by luciferases, has evolved in many taxa from bacteria to vertebrates and is predominant in the marine environment. It is now well established that in animals possessing a nervous system capable of integrating light stimuli, bioluminescence triggers various behavioural responses and plays a role in intra- or interspecific visual communication. The function of light emission in unicellular organisms is less clear and it is currently thought that it has evolved in an ecological framework, to be perceived by visual animals. For example, while it is thought that bioluminescence allows bacteria to be ingested by zooplankton or fish, providing them with favourable conditions for growth and dispersal, the luminous flashes emitted by dinoflagellates may have evolved as an anti-predation system against copepods. In this short review, we re-examine this paradigm in light of recent findings in microorganism photoreception, signal integration and complex behaviours. Numerous studies show that on the one hand, bacteria and protists, whether autotrophs or heterotrophs, possess a variety of photoreceptors capable of perceiving and integrating light stimuli of different wavelengths. Single-cell light-perception produces responses ranging from phototaxis to more complex behaviours. On the other hand, there is growing evidence that unicellular prokaryotes and eukaryotes can perform complex tasks ranging from habituation and decision-making to associative learning, despite lacking a nervous system. Here, we focus our analysis on two taxa, bacteria and dinoflagellates, whose bioluminescence is well studied. We propose the hypothesis that similar to visual animals, the interplay between light-emission and reception could play multiple roles in intra- and interspecific communication and participate in complex behaviour in the unicellular world.

Desynchronised times? Chronobiology, (bio)medicalisation and the rhythms of life itself

This paper takes a critical look at the role of chronobiology in society today, with particular reference to its entanglements with health and medicine and whether or not this amounts to the (bio)medicalisation of our bodily rhythms. What we have here, we show, is a complex unfolding storyline, within and beyond medicine. On the one hand, the promises and problems of these circadian, infradian and ultradian rhythms for our health and well-being are now increasingly emphasised. On the other hand, a variety of new rhythmic interventions and forms of governance are now emerging within and beyond medicine, from chronotherapies and chronopharmacology to biocompatible school and work schedules, and from chronodiets to the optimisation of all we do according to our 'chronotypes'. Conceptualising these developments, we suggest challenges us to think within and beyond medicalisation to wider processes of biomedicalisation and the biopolitics of our body clocks: a vital new strand of chronopolitics today indeed which implicates us all in sickness and in health as the very embodiment of these rhythms of life itself. The paper concludes with a call for further research on these complex unfolding relations between chronobiology, health and society in these desynchronised times of ours.

Temperature-sensitive and circadian oscillators of Neurospora crassa share components

In Neurospora crassa, the interactions between products of the frequency (frq), frequency-interacting RNA helicase (frh), white collar-1 (wc-1), and white collar-2 (wc-2) genes establish a molecular circadian clockwork, called the FRQ-WC-Oscillator (FWO), which is required for the generation of molecular and overt circadian rhythmicity. In strains carrying nonfunctional frq alleles, circadian rhythms in asexual spore development (conidiation) are abolished in constant conditions, yet conidiation remains rhythmic in temperature cycles. Certain characteristics of these temperature-synchronized rhythms have been attributed to the activity of a FRQ-less oscillator (FLO). The molecular components of this FLO are as yet unknown. To test whether the FLO depends on other circadian clock components, we created a strain that carries deletions in the frq, wc-1, wc-2, and vivid (vvd) genes. Conidiation in this ΔFWO strain was still synchronized to cyclic temperature programs, but temperature-induced rhythmicity was distinct from that seen in single frq knockout strains. These results and other evidence presented indicate that components of the FWO are part of the temperature-induced FLO.

Clocks in the green lineage: comparative functional analysis of the circadian architecture of the picoeukaryote ostreococcus

Biological rhythms that allow organisms to adapt to the solar cycle are generated by endogenous circadian clocks. In higher plants, many clock components have been identified and cellular rhythmicity is thought to be driven by a complex transcriptional feedback circuitry. In the small genome of the green unicellular alga Ostreococcus tauri, two of the master clock genes Timing of Cab expression1 (TOC1) and Circadian Clock-Associated1 (CCA1) appear to be conserved, but others like Gigantea or Early-Flowering4 are lacking. Stably transformed luciferase reporter lines and tools for gene functional analysis were therefore developed to characterize clock gene function in this simple eukaryotic system. This approach revealed several features that are comparable to those in higher plants, including the circadian regulation of TOC1, CCA1, and the output gene Chlorophyll a/b Binding under constant light, the relative phases of TOC1/CCA1 expression under light/dark cycles, arrhythmic overexpression phenotypes under constant light, the binding of CCA1 to a conserved evening element in the TOC1 promoter, as well as the requirement of the evening element for circadian regulation of TOC1 promoter activity. Functional analysis supports TOC1 playing a central role in the clock, but repression of CCA1 had no effect on clock function in constant light, arguing against a simple TOC1 /CCA1 one-loop clock in Ostreococcus. The emergence of functional genomics in a simple green cell with a small genome may facilitate increased understanding of how complex cellular processes such as the circadian clock have evolved in plants.

Synergy between the light-induced acute response and the circadian cycle: a new mechanism for the synchronization of the Phaseolus vulgaris clock to light

PvLHY and Lhcb expression has been studied in primary bean leaves after exposure of etiolated leaves to two or three white light-pulses and under different photoperiods. Under the tested photoperiods, the steady-state mRNA levels exhibit diurnal oscillations with zenith in the morning between ZT21 and 4 for PvLHY and between ZT4 and 6 for Lhcb. Nadir is in the evening between ZT12 and 18 for PvLHY and ZT18 and 24 for Lhcb. Light-pulses to etiolated seedlings induce a differentiated acute response that is reciprocally correlated with the amplitude of the following circadian cycle. In addition, the clock modulates the duration of the acute response (descending part of the curve included), which according to the phase of the rhythm at light application extends from 7 to 18 h. This constitutes the response dynamics of the Phaseolus clock to light. Similarly, the waveform of PvLHY and Lhcb expression during the day of different photoperiods resembles in induction capability (accomplishment of peak after lights-on) and duration (from lights-on phase to trough) the phase-dependent progression of acute response in etiolated seedlings. Consequently, the peak of Lhcb (all tested photoperiods) and PvLHY (in LD 18:6) attained in the photophase corresponds to the acute response peak, while the peak of PvLHY during the scotophase (in LD 12:12 and 6:18) corresponds to the circadian peak. Thus, the effect of the response dynamics in the photoperiod determines the coincidence of the peak with the photo- or scotophase, respectively. This represents a new model mechanism for the adaptation of the Phaseolus clock to light.

Assessing physiological complexity

Physiologists both admire and fear complexity, but we have made relatively few attempts to understand it. Inherently complex systems are more difficult to study and less predictable. However, a deeper understanding of physiological systems can be achieved by modifying experimental design and analysis to account for complexity. We begin this essay with a tour of some mathematical views of complexity. After briefly exploring chaotic systems, information theory and emergent behavior, we reluctantly conclude that, while a mathematical view of complexity provides useful perspectives and some narrowly focused tools, there are too few generally practical take-home messages for physiologists studying complex systems. Consequently, we attempt to provide guidelines as to how complex systems might be best approached by physiologists. After describing complexity based on the sum of a physiological system's structures and processes, we highlight increasingly refined approaches based on the pattern of interactions between structures and processes. We then provide a series of examples illustrating how appreciating physiological complexity can improve physiological research, including choosing experimental models, guiding data collection, improving data interpretations and constructing more rigorous system models. Finally, we conclude with an invitation for physiologists, applied mathematicians and physicists to collaborate on describing, studying and learning from studies of physiological complexity.

Experimental determination of the periodicity of incremental features in enamel

Vital labelling of hard tissues was used to examine the periodicity of features of dental enamel microstructure. Fluorescent labels were administered pre- and postnatally to developing macaques (Macaca nemestrina), which were identified histologically in dentine and related to accentuated lines in enamel, allowing for counts of features within known-period intervals. This study demonstrates that cross-striations represent a daily rhythm in enamel secretion, and suggests that intradian lines are the result of a similar 12-h rhythm. Retzius lines were found to have a regular periodicity within individual dentitions, and laminations appear to represent a daily rhythm that also shows 12-h subdivisions. The inclusion of intradian lines and laminations represents the first empirical evidence for their periodicities in primates; these features frequently complicate precise measurements of secretion rate and Retzius line periodicity, which are necessary for determination of crown formation time. The biological basis of incremental feature formation is not completely understood; long-period features may result from interactions between short-period rhythms, although this does not explain the known range of Retzius line periodicities within humans or among primates. Studies of the genetic, neurological and hormonal basis of incremental feature formation are needed to provide more insight into their physiological and structural basis.

Circuit topology and the evolution of robustness in two-gene circadian oscillators

Many parameters driving the behavior of biochemical circuits vary extensively and are thus not fine-tuned. Therefore, the topology of such circuits (the who-interacts-with-whom) is key to understanding their central properties. I here explore several hundred different topologies of a simple biochemical model of circadian oscillations to ask two questions: Do different circuits differ dramatically in their robustness to parameter change? If so, can a process of gradual molecular evolution find highly robust topologies when starting from less robust topologies? I find that the distribution of robustness among different circuit topologies is highly skewed: Most show low robustness, whereas very few topologies are highly robust. To address the second evolutionary question, I define a topology graph, each of whose nodes corresponds to one circuit topology that shows circadian oscillations. Two nodes in this graph are connected if they differ by only one regulatory interaction within the circuit. For the circadian oscillator I study, most topologies are connected in this graph, making evolutionary transitions from low to high robustness easy. A similar approach has been used to study the evolution of robustness in biological macromolecules, with similar results. This suggests that the same principles govern the evolution of robustness on different levels of biological organization. The regulatory interlocking of several oscillating gene products in biological circadian oscillators may exist because it provides robustness.

PCC1: a merging point for pathogen defence and circadian signalling in Arabidopsis

Using a cDNA-array we identified expressed sequence tag 163B24T7 as rapidly up-regulated in Arabidopsis thaliana (L.) Heynh. after pathogen exposure. Detailed expression analysis revealed that the corresponding gene is up-regulated not only after exposure to avirulent Pseudomonas syringae pv. tomato but also to virulent strains. This up-regulation is dependent on functional salicylic acid defence-signalling pathways. Moreover, we found the gene was circadian-regulated, showing peaks of expression at the end of the day. Using plants overexpressing the clock component CCA1, we showed that the PCC1 gene is regulated by the inner clock of Arabidopsis. Accordingly, we named the gene PCC1, for pathogen and circadian controlled. PCC1 is a member of a novel family of six small polypeptides in Arabidopsis. A functional role for PCC1 in plant defence was demonstrated since plants overexpressing PCC1 are resistant against normally virulent oomycetes. Thus, PCC1 demonstrates a potential interrelationship between pathogen and circadian signalling pathways.

The circular topology of rhythm in asynchronous random Boolean networks

The analysis of previously evolved rhythmic asynchronous random Boolean networks [Biosystems 59 (2001) 185] reveals common topological characteristics indicating that rhythm originates from a circular functional structure. The rhythm generating core of the network has the form of a closed ring which operates as a synchronisation substrate by supporting a travelling wave of state change; the size of the ring corresponds well with the period of oscillation. The remaining nodes in the network are either stationary or follow the activity of the ring without feeding back into it so as to form a coherent whole. Rings are typically formed early on in the evolutionary search process. Alternatively, long chains of nodes are favoured before they close upon themselves to stabilize. Analysis of asynchronous networks with de-correlated (non-rhythmic, non-stationary) attractors reveals no such common topological characteristics. These results have been obtained using statistical analysis and a specifically developed bottom-up pruning algorithm. This algorithm works from local interactions to global configuration by eliminating redundant links. The suitability of the algorithm has been confirmed by both numerical and single lesion analysis. The ring topology solution for the generation of rhythm implies that it will be harder to evolve rhythmic networks for big sizes and small periods and for bigger number of connections per node. These trends are confirmed empirically. Finally, the identified mechanisms are utilised to handcraft rhythmic networks of different periods showing that a low number of connections suffices for a large variety of rhythms. Random asynchronous update forces the evolved solutions to be highly robust maintaining their performance in the presence of intrinsic noise. The biological implications of such robust designs for molecular clocks are discussed.

A PERIOD inhibitor buffer introduces a delay mechanism for CLK/CYC-activated transcription

We investigated the functions of clock genes period (per) and timeless (tim) in establishing negative feedback on circadian transcription factors clock/cycle (Clk/cyc) in Drosophila. We show that PER protein persists for several hours after rapid degradation of TIM in the morning. We observed in cell culture that isolated PER inhibits CLK/CYC-activated transcription in the absence of TIM and we further demonstrated for the first time in vivo that PER accumulation in a tim loss-of-function mutant background causes efficient inhibition of CLK/CYC-dependent transcription. These results identify PER to be the main inhibitor for CLK/CYC and they suggest a delay mechanism during early morning, when PER protein, after degradation of TIM, forms an inhibitor buffer for CLK/CYC that attenuates the restart of the next cycle of CLK/CYC-activated transcription. While TIM likely enhances the inhibition of CLK/CYC by PER in the dark, our results suggest a reduction of PER-mediated inhibition by TIM in light.

Loss of circadian rhythmicity in aging mPer1-/-mCry2-/- mutant mice

The mPer1, mPer2, mCry1, and mCry2 genes play a central role in the molecular mechanism driving the central pacemaker of the mammalian circadian clock, located in the suprachiasmatic nuclei (SCN) of the hypothalamus. In vitro studies suggest a close interaction of all mPER and mCRY proteins. We investigated mPER and mCRY interactions in vivo by generating different combinations of mPer/mCry double-mutant mice. We previously showed that mCry2 acts as a nonallelic suppressor of mPer2 in the core clock mechanism. Here, we focus on the circadian phenotypes of mPer1/mCry double-mutant animals and find a decay of the clock with age in mPer1-/- mCry2-/- mice at the behavioral and the molecular levels. Our findings indicate that complexes consisting of different combinations of mPER and mCRY proteins are not redundant in vivo and have different potentials in transcriptional regulation in the system of autoregulatory feedback loops driving the circadian clock.

Life before the clock: modeling circadian evolution

A feedback loop that functions via transcription and translation is thought to be the mechanistic core of circadian rhythmicity. Numerous modeling efforts incorporate the identified components and their modifications to recreate the circadian clock in computer simulations. Several issues remain problematic, including the lack of precise quantitative kinetics and the likely existence of additional, as-yet-undiscovered components. Even without these complications, models and flow charts of the circadian system have reached high complexity. They attempt to reconcile all observations without violating current views and concepts. In this article, the authors consider the mechanisms that may have preceded the circadian system in evolution. Given that cellular metabolism and biochemistry were presumably already interconnected in cascading feedback reactions prior to the appendage of the transcription/translation feedback loop, a coordinated response to exogenous changes would be advantageous over unsystematic responses. The authors hypothesize that those mechanisms that allowed synchronization in spite of metabolic complexity form the basis for the evolution of circadian properties and are as fundamental to the circadian system as the transcriptional/translational feedback loop.

Cellular signalling and the complexity of biological timing: insights from the ultradian clock of Schizosaccharomyces pombe

The molecular bases of circadian clocks are complex and cannot be sufficiently explained by the relatively simple feedback loops, based on transcription and translation, of current models. The existence of additional oscillators has been demonstrated experimentally, but their mechanism(s) have so far resisted elucidation and any universally conserved clock components have yet to be identified. The fission yeast, Schizosaccharomyces pombe, as a simple and well-characterized eukaryote, is a useful model organism in the investigation of many aspects of cell regulation. In fast-growing cells of the yeast an ultradian clock operates, which can serve as a model system to analyse clock complexity. This clock shares strict period homeostasis and efficient entrainment with circadian clocks but, because of its short period of 30 min, mechanisms other than a transcription/translation-based feedback loop must be working. An initial systematic screen involving over 200 deletion mutants has shown that major cellular signalling pathways (calcium/phosphoinositide, mitogen-activated protein kinase and cAMP/protein kinase A) are crucial for the normal functioning of this ultradian clock. A comparative examination of the role of cellular signalling pathways in the S.pombe ultradian clock and in the circadian timekeeping of different eukaryotes may indicate common principles in biological timing processes that are universally conserved amongst eukaryotes.

Genetic interactions between clock mutations in Neurospora crassa: can they help us to understand complexity?

Recent work on circadian clocks in Neurospora has primarily focused on the frequency (frq) and white-collar (wc) loci. However, a number of other genes are known that affect either the period or temperature compensation of the rhythm. These include the period (no relationship to the period gene of Drosophila) genes and a number of genes that affect cellular metabolism. How these other loci fit into the circadian system is not known, and metabolic effects on the clock are typically not considered in single-oscillator models. Recent evidence has pointed to multiple oscillators in Neurospora, at least one of which is predicted to incorporate metabolic processes. Here, the Neurospora clock-affecting mutations will be reviewed and their genetic interactions discussed in the context of a more complex clock model involving two coupled oscillators: a FRQ/WC-based oscillator and a 'frq-less' oscillator that may involve metabolic components.

Flies, clocks and evolution

The negative feedback model for gene regulation of the circadian mechanism is described for the fruitfly, Drosophila melanogaster. The conservation of function of clock molecules is illustrated by comparison with the mammalian circadian system, and the apparent swapping of roles between various canonical clock gene components is highlighted. The role of clock gene duplications and divergence of function is introduced via the timeless gene. The impressive similarities in clock gene regulation between flies and mammals could suggest that variation between more closely related species within insects might be minimal. However, this is not borne out because the expression of clock molecules in the brain of the giant silk moth, Antheraea pernyi, is not easy to reconcile with the negative feedback roles of the period and timeless genes. Variation in clock gene sequences between and within fly species is examined and the role of co-evolution between and within clock molecules is described, particularly with reference to adaptive functions of the circadian phenotype.

Picking out parallels: plant circadian clocks in context

Molecular models have been described for the circadian clocks of representatives of several different taxa. Much of the work on the plant circadian system has been carried out using the thale cress, Arabidopsis thaliana, as a model. We discuss the roles of genes implicated in the plant circadian system, with special emphasis on Arabidopsis. Plants have an endogenous clock that regulates many aspects of circadian and photoperiodic behaviour. Despite the discovery of components that resemble those involved in the clocks of animals or fungi, no coherent model of the plant clock has yet been proposed. In this review, we aim to provide an overview of studies of the Arabidopsis circadian system. We shall compare these with results from different taxa and discuss them in the context of what is known about clocks in other organisms.

The Neurospora circadian clock: simple or complex?

The fungus Neurospora crassa is being used by a number of research groups as a model organism to investigate circadian (daily) rhythmicity. In this review we concentrate on recent work relating to the complexity of the circadian system in this organism. We discuss: the advantages of Neurospora as a model system for clock studies; the frequency (frq), white collar-1 and white collar-2 genes and their roles in rhythmicity; the phenomenon of rhythmicity in null frq mutants and its implications for clock mechanisms; the study of output pathways using clock-controlled genes; other rhythms in fungi; mathematical modelling of the Neurospora circadian system; and the application of new technologies to the study of Neurospora rhythmicity. We conclude that there may be many gene products involved in the clock mechanism, there may be multiple interacting oscillators comprising the clock mechanism, there may be feedback from output pathways onto the oscillator(s) and from the oscillator(s) onto input pathways, and there may be several independent clocks coexisting in one organism. Thus even a relatively simple lower eukaryote can be used to address questions about a complex, networked circadian system.