Evidence for a central role of transcription in the timing mechanism of a circadian clock

Metabolic rhythms: A framework for coordinating cellular function

Circadian clocks are widespread among eukaryotes and generally involve feedback loops coupled with metabolic processes and redox balance. The organising power of these oscillations has not only allowed organisms to anticipate day-night cycles, but also acts to temporally compartmentalise otherwise incompatible processes, enhance metabolic efficiency, make the system more robust to noise and propagate signals among cells. While daily rhythms and the function of the circadian transcription-translation loop have been the subject of extensive research over the past four decades, cycles of shorter period and respiratory oscillations, with which they are intertwined, have received less attention. Here, we describe features of yeast respiratory oscillations, which share many features with daily and 12 hr cellular oscillations in animal cells. This relatively simple system enables the analysis of dynamic rhythmic changes in metabolism, independent of cellular oscillations that are a product of the circadian transcription-translation feedback loop. Knowledge gained from studying ultradian oscillations in yeast will lead to a better understanding of the basic mechanistic principles and evolutionary origins of oscillatory behaviour among eukaryotes.

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.

Cellular mechanisms of circadian pacemaking: beyond transcriptional loops

Circadian clocks drive the daily rhythms in our physiology and behaviour that adapt us to the 24-h solar and social worlds. Because they impinge upon every facet of metabolism, their acute or chronic disruption compromises performance (both physical and mental) and systemic health, respectively. Equally, the presence of such rhythms has significant implications for pharmacological dynamics and efficacy, because the fate of a drug and the state of its therapeutic target will vary as a function of time of day. Improved understanding of the cellular and molecular biology of circadian clocks therefore offers novel approaches for therapeutic development, for both clock-related and other conditions. At the cellular level, circadian clocks are pivoted around a transcriptional/post-translational delayed feedback loop (TTFL) in which the activation of Period and Cryptochrome genes is negatively regulated by their cognate protein products. Synchrony between these, literally countless, cellular clocks across the organism is maintained by the principal circadian pacemaker, the suprachiasmatic nucleus (SCN) of the hypothalamus. Notwithstanding the success of the TTFL model, a diverse range of experimental studies has shown that it is insufficient to account for all properties of cellular pacemaking. Most strikingly, circadian cycles of metabolic status can continue in human red blood cells, devoid of nuclei and thus incompetent to sustain a TTFL. Recent interest has therefore focused on the role of oscillatory cytosolic mechanisms as partners to the TTFL. In particular, cAMP- and Ca²⁺-dependent signalling are important components of the clock, whilst timekeeping activity is also sensitive to a series of highly conserved kinases and phosphatases. This has led to the view that the 'proto-clock' may have been a cytosolic, metabolic oscillation onto which evolution has bolted TTFLs to provide robustness and amplify circadian outputs in the form of rhythmic gene expression. This evolutionary ascent of the clock has culminated in the SCN, a true pacemaker to the innumerable clock cells distributed across the body. On the basis of findings from our own and other laboratories, we propose a model of the SCN pacemaker that synthesises the themes of TTFLs, intracellular signalling, metabolic flux and interneuronal coupling that can account for its unique circadian properties and pre-eminence.

Non-transcriptional oscillators in circadian timekeeping

Circadian clocks have evolved as an adaptation to life on a rotating planet, and orchestrate rhythmic changes in physiology to match the time of day. For decades, cellular circadian rhythms were considered to solely result from feedback between the products of rhythmically expressed genes. These transcriptional/translational feedback loops (TTFLs) have been ubiquitously studied, and explain the majority of circadian outputs. In recent years, however, non-transcriptional processes were shown to be major contributors to circadian rhythmicity. These key findings have profound implications on our understanding of the evolution and mechanistic basis of cellular circadian timekeeping. This review summarises and discusses these results and the experimental and theoretical evidence of a possible relation between non-transcriptional oscillator (NTO) mechanisms and TTFL oscillations.

Proteasome function is required for biological timing throughout the twenty-four hour cycle

Circadian clocks were, until recently, seen as a consequence of rhythmic transcription of clock components, directed by transcriptional/translational feedback loops (TTFLs). Oscillations of protein modification were then discovered in cyanobacteria. Canonical posttranslational signaling processes have known importance for clocks across taxa. More recently, evidence from the unicellular eukaryote Ostreococcus tauri revealed a transcription-independent, rhythmic protein modification shared in anucleate human cells. In this study, the Ostreococcus system reveals a central role for targeted protein degradation in the mechanism of circadian timing. The Ostreococcus clockwork contains a TTFL involving the morning-expressed CCA1 and evening-expressed TOC1 proteins. Cellular CCA1 and TOC1 protein content and degradation rates are analyzed qualitatively and quantitatively using luciferase reporter fusion proteins. CCA1 protein degradation rates, measured in high time resolution, feature a sharp clock-regulated peak under constant conditions. TOC1 degradation peaks in response to darkness. Targeted protein degradation, unlike transcription and translation, is shown to be essential to sustain TTFL rhythmicity throughout the circadian cycle. Although proteasomal degradation is not necessary for sustained posttranslational oscillations in transcriptionally inactive cells, TTFL and posttranslational oscillators are normally coupled, and proteasome function is crucial to sustain both.

Circadian rhythms persist without transcription in a eukaryote

Circadian rhythms are ubiquitous in eukaryotes, and coordinate numerous aspects of behaviour, physiology and metabolism, from sleep/wake cycles in mammals to growth and photosynthesis in plants. This daily timekeeping is thought to be driven by transcriptional-translational feedback loops, whereby rhythmic expression of 'clock' gene products regulates the expression of associated genes in approximately 24-hour cycles. The specific transcriptional components differ between phylogenetic kingdoms. The unicellular pico-eukaryotic alga Ostreococcus tauri possesses a naturally minimized clock, which includes many features that are shared with plants, such as a central negative feedback loop that involves the morning-expressed CCA1 and evening-expressed TOC1 genes. Given that recent observations in animals and plants have revealed prominent post-translational contributions to timekeeping, a reappraisal of the transcriptional contribution to oscillator function is overdue. Here we show that non-transcriptional mechanisms are sufficient to sustain circadian timekeeping in the eukaryotic lineage, although they normally function in conjunction with transcriptional components. We identify oxidation of peroxiredoxin proteins as a transcription-independent rhythmic biomarker, which is also rhythmic in mammals. Moreover we show that pharmacological modulators of the mammalian clock mechanism have the same effects on rhythms in Ostreococcus. Post-translational mechanisms, and at least one rhythmic marker, seem to be better conserved than transcriptional clock regulators. It is plausible that the oldest oscillator components are non-transcriptional in nature, as in cyanobacteria, and are conserved across kingdoms.

Lifetimes of mRNAs for Clock‐Regulated Proteins in a Dinoflagellate

Both pulsed and continuous applications of the RNA polymerase II inhibitor thiolutin cause a dramatic but reversible loss of bioluminescence and its overt rhythmicity in cells of the dinoflagellate Lingulodinium polyedrum (formerly Gonyaulax polyedra). Such cells remain alive, and the rhythm resumes after an interval, the length of which depends on the concentration of thiolutin used. The period and phase of the resumed rhythm were not systematically altered following such treatments, and the effects were not different at different circadian phases. For three different genes, luciferin binding protein (lbp), luciferase (lcf), and glyceraldehyde-3-phosphate dehydrogenase (gapdh), which are circadian-regulated at the level of translation, the amounts of their mRNAs were determined by Northern blots for times up to 12.5 h following the addition of 1.5 microM thiolutin. Consistent with previous reports that their abundances do not change with circadian time, their levels remained high for several hours after thiolutin addition, but then did diminish.

Circadian regulation of a transcription factor, ApC/EBP, in the eye of Aplysia californica

The transcription factor, ApC/EBP (Aplysia CCAAT enhancer-binding protein) is an immediate early gene that is rapidly induced by serotonin and the cAMP signaling pathway. ApC/EBP acts as an important link following the activation of protein kinase A (PKA) in the consolidation of long-term memory in Aplysia californica. In this study, we report that levels of ApC/EBP mRNA in the eye of Aplysia are modulated by serotonin or light. These responses of ApC/EBP to serotonin and light are mimicked by analogs of cAMP and cGMP. Expression of ApC/EBP in the eye is also under the control of the circadian oscillator with circadian rhythms of ApC/EBP mRNA present under constant dark conditions. Therefore, ApC/EBP is a candidate gene for a circadian transcription factor to mediate circadian responses activated by the cAMP and cGMP second messenger signaling pathways.

A novel mechanism for the control of circadian clock period by light

The free-running period expressed by circadian clocks in constant environmental conditions is history dependent, and one effect of entrainment of circadian clocks by light cycles is to cause long-lasting changes in the free-running period that are termed aftereffects. It has been suggested that aftereffects are a consequence of the particular phase relationships among constituent oscillators of the circadian system that are established by the entrainment. In a test of this hypothesis, it is shown that aftereffects of entrainment of the free-running rhythm of nerve impulse activity from the eye of Bulla gouldiana are completely unaffected by treatment with 12-, 24-, or 48-h pulses of the translation inhibitor cycloheximide or with 24-h pulses of the transcription inhibitor DRB (5,6-dichlorobenzimidazole riboside). These treatments reset the phase of circadian oscillators generally and those in the eye of B. gouldiana specifically. The absence of any effect of the treatments indicates that aftereffects are independent of oscillator phase. These results suggest that history-dependent changes in period result from a novel, long-lasting, and previously unrecognized mechanism of action of light on the circadian pacemaking system. Furthermore, the data indicate that aftereffects can persist in the absence of translation, transcription, or the continued cycling of the circadian system.

Cellular circadian clocks in the pineal

Daily rhythms are a fundamental feature of all living organisms; most are synchronized by the 24 hr light/dark (LD) cycle. In most species, these rhythms are generated by a circadian system, and free run under constant conditions with a period close to 24 hr. To function properly the system needs a pacemaker or clock, an entrainment pathway to the clock, and one or more output signals. In vertebrates, the pineal hormone melatonin is one of these signals which functions as an internal time-keeping molecule. Its production is high at night and low during day. Evidence indicates that each melatonin producing cell of the pineal constitutes a circadian system per se in non-mammalian vertebrates. In addition to the melatonin generating system, they contain the clock as well as the photoreceptive unit. This is despite the fact that these cells have been profoundly modified from fish to birds. Modifications include a regression of the photoreceptive capacities, and of the ability to transmit a nervous message to the brain. The ultimate stage of this evolutionary process leads to the definitive loss of both the direct photosensitivity and the clock, as observed in the pineal of mammals. This review focuses on the functional properties of the cellular circadian clocks of non-mammalian vertebrates. How functions the clock? How is the photoreceptive unit linked to it and how is the clock linked to its output signal? These questions are addressed in light of past and recent data obtained in vertebrates, as well as invertebrates and unicellulars.

Keeping an eye on retinal clocks

Circadian pacemakers that drive rhythmicity in retinal function are found in both invertebrates and vertebrates. They have been localized to photoreceptors in molluscs, amphibians, and mammals. Like other circadian pacemakers, they entrain to light, oscillate based on a negative feedback between transcription and translation of clock genes, and control a variety of physiological and behavioral rhythms that often includes rhythmic melatonin production. As a highly organized and accessible tissue, the retina is particularly well suited for the study of the input-output pathways and the mechanism for rhythm generation. Impressive advances can now be expected as researchers apply new molecular techniques toward looking into the eye's clock.

Aging affects the ocular circadian pacemaker of Aplysia californica

The eye of Aplysia has been used to explore various aspects of circadian rhythms. The authors discovered that age has profound effects on the circadian rhythm of nerve impulses from the eye. With age, there was a significant decrease in the amplitude of the rhythm. The decrease appeared to be continuous over the life span of the animal and was observed both in vitro and in vivo. The free-running period and phase angle of the rhythm steadily increased with age, indicating that the pacemaker itself was affected by age. Rates of transcription and translation were significantly increased with age, suggesting that age-associated alterations of the pacemaker may occur through changes in macromolecular synthesis. Interestingly, eyes from some older (> or = 10 months) animals had "cloudy" lenses (cataracts). Highly damped or arrhythmic rhythms always were seen in eyes with cloudy lenses. Morphology of eyes with cloudy lenses indicated severe retinal degeneration. No such degeneration was observed in eyes with clear lenses that were used in the analysis of the rhythm with age.

Effects of cyclin-dependent kinase inhibitors on transcription and ocular circadian rhythm of Aplysia

Cyclin-dependent kinases (CDKs) mediate cell-cycle phase transitions. Recently, CDKs have been associated with non-cell-cycle roles such as DNA repair, transcription, and phosphate metabolism in yeast. The cyclical processes, circadian rhythms and the eukaryotic cell cycle, are similar in many respects. It is possible that a kinase like CDK is involved in the control of circadian rhythms. In this study, the effects of CDK inhibitors (olomoucine, roscovitine, and butyrolactone I) on the Aplysia ocular circadian rhythm were investigated. Continuous treatments with olomoucine (10 microM) lengthened the free-running period of the rhythm, and pulse treatments of olomoucine (6 h, 100 microM) delayed the rhythm. The effects of olomoucine on the rhythm were qualitatively similar to those of a reversible inhibitor of transcription, 5,6-dichloro-beta-1-ribobenzimidazole. Subsequently, olomoucine was found to inhibit RNA synthesis in the eye of Aplysia and Bulla. All of the other CDK inhibitors used in this study also inhibited transcription in the eye of Aplysia, and their effects on transcription correlated with their effects on the circadian rhythm. This study adds substantial evidence to that previously obtained by using 5,6-dichloro-beta-1-ribobenzimidazole for a role of transcription in the mechanism responsible for circadian rhythmicity in the eye of Aplysia. Also, these results indicate that caution is warranted in interpreting results obtained by using CDK inhibitors, because these drugs appear to inhibit transcription as well as CDKs.

Inhibitors of messenger RNA and protein synthesis affect differently serotonin arylalkylamine N-acetyltransferase activity in clock-controlled and non clock-controlled fish pineal

The pineal organ of fish contains photoreceptor cells. In some species (e.g., pike) each photoreceptor is a cellular circadian system which contains a photoreceptive unit, the clock and an output unit. In others (e.g., trout) the clock is lacking. The main rhythmic output of the pineal photoreceptor is melatonin, an internal 'zeitgeber' of the organisms. The nocturnal rise in melatonin secretion results from an increase in the activity of the arylalkylamine-N-acetyltransferase (AA-NAT) which converts serotonin to N-acetylserotonin. In the present study we investigated the effects of transcription and translation inhibitors on AA-NAT activity in pike and trout pineal organs in culture. Cycloheximide, anisomycin, and puromycin inhibited the rise in AA-NAT activity observed during the first 2, 4 or 6 h of the dark phase, in both species. Actinomycin D was active only in the pike. Six hours of treatment during the first half of the night induced inhibition of AA-NAT activity, providing that forskolin (an adenylyl cyclase stimulator) was present in the culture medium. When the treatment was run for 3, 6 or 12 h, starting at midday of a 12L/12D cycle, basal and forskolin-stimulated AA-NAT activity (measured at midnight) were dramatically reduced. Such a treatment had no effect on trout AA-NAT activity. It is concluded that: (1) the dark-induced rise in AA-NAT activity and melatonin secretion are dependent on newly synthesized protein in both pike and trout pineal; (2) AA-NAT regulation takes place at the translational and post-translational levels in both species; (3) AA-NAT regulation occurs also at the transcriptional level in the pike, but not in the trout; and (4) the cAMP-dependent activation of AA-NAT requires transcription in the pike, not in the trout. The presence of a cell population acting as a circadian clock in the pike pineal, but not in the trout pineal, can explain the difference between these two species. Thus, we suggest that the clock mechanism operates at the genetic level in these cells. Further comparative studies between clock-controlled and non-clock-controlled pineals might prove interesting to demonstrate the difference between these two regulatory pathways.