Flies and fish: birds of a feather

Comparative Analysis of Vertebrate Diurnal/Circadian Transcriptomes

From photosynthetic bacteria to mammals, the circadian clock evolved to track diurnal rhythms and enable organisms to anticipate daily recurring changes such as temperature and light. It orchestrates a broad spectrum of physiology such as the sleep/wake and eating/fasting cycles. While we have made tremendous advances in our understanding of the molecular details of the circadian clock mechanism and how it is synchronized with the environment, we still have rudimentary knowledge regarding its connection to help regulate diurnal physiology. One potential reason is the sheer size of the output network. Diurnal/circadian transcriptomic studies are reporting that around 10% of the expressed genome is rhythmically controlled. Zebrafish is an important model system for the study of the core circadian mechanism in vertebrate. As Zebrafish share more than 70% of its genes with human, it could also be an additional model in addition to rodent for exploring the diurnal/circadian output with potential for translational relevance. Here we performed comparative diurnal/circadian transcriptome analysis with established mouse liver and other tissue datasets. First, by combining liver tissue sampling in a 48h time series, transcription profiling using oligonucleotide arrays and bioinformatics analysis, we profiled rhythmic transcripts and identified 2609 rhythmic genes. The comparative analysis revealed interesting features of the output network regarding number of rhythmic genes, proportion of tissue specific genes and the extent of transcription factor family expression. Undoubtedly, the Zebrafish model system will help identify new vertebrate outputs and their regulators and provides leads for further characterization of the diurnal cis-regulatory network.

Circadian rhythmicity and photic plasticity of myosin gene transcription in fast skeletal muscle of Atlantic cod (Gadus morhua)

The circadian rhythm is a fundamental adaptive mechanism to the daily environmental changes experienced by many organisms, including fish. Myosins constitute a large family of contractile proteins that are essential functional components of skeletal muscle. They are known to display thermal plasticity but the influence of light on myosin expression remains to be investigated in fish. In the present study, we have examined the circadian rhythmicity and photoperiodic plasticity of myosin gene transcription in Atlantic cod (Gadus morhua) fast skeletal muscle. In silico mining of the Atlantic cod genome resulted in the identification of 76 myosins representing different classes, many of which were hitherto uncharacterized. Among the 23 fast skeletal muscle myosin genes, myh_tc, myh_n1, myh_n4, myo18a_2, and myo18b_2 displayed circadian rhythmic expression and contained several circadian-related transcription factor binding sites (Creb, Mef2 and E-box motifs) within their putative promoter regions. Also, the circadian expression of these 5 myosins strongly correlated with the transcription pattern of clock genes in fast skeletal muscle. Under ex vivo conditions, myosin transcript levels lost their circadian rhythmicity. Nonetheless, different photoperiod regimes influenced the mRNA levels of myh_n4, myo18a_2 and myo18b_2 in fast skeletal muscle explants. Photoperiod manipulation in Atlantic cod juveniles revealed that continuous light significantly elevated mRNA levels of several myosins in fast skeletal muscle when compared to natural photoperiod. The daily rhythmicity observed in some fast skeletal muscle myosin genes suggests that they may be under circadian clock regulation. In addition, the influence of photoperiod on their expression implies that myosins may be involved in the photic plasticity of muscle growth observed in Atlantic cod.

Light Reaches the Very Heart of the Zebrafish Clock

Zebrafish are typically used as a model system to study various aspects of developmental biology, largely as a consequence of their ex vivo development, high degree of transparency, and, of course, ability to perform forward genetic mutant screens. More recently, zebrafish have been developed as a model system with which to study circadian clocks. Cell lines generated from early-stage zebrafish embryos contain clocks that are directly light-responsive. We describe recent experiments using single-cell luminescent imaging approaches to study clock function in this novel cell line system. Furthermore, studies examining the process of entrainment to light pulses within this cell population are described in this review, as are experiments examining light-responsiveness of early-stage zebrafish embryos.

Evidence for differential photic regulation of pineal melatonin synthesis in teleosts

The aim of this study was to compare the circadian control of melatonin production in teleosts. To do so, the effects of ophthalmectomy on circulating melatonin rhythms were studied along with ex vivo pineal culture in six different teleosts. Results strongly suggested that the circadian control of melatonin production could have dramatically changed with at least three different systems being present in teleosts when one considers the photic regulation of pineal melatonin production. First, salmonids presented a decentralized system in which the pineal gland responds directly to light independently of the eyes. Then, in seabass and cod both the eyes and the pineal gland are required to sustain full night-time melatonin production. Finally, a third type of circadian control of melatonin production is proposed in tilapia and catfish in which the pineal gland would not be light sensitive (or only slightly) and required the eyes to perceive light and inhibit melatonin synthesis. Further studies (anatomical, ultrastructural, retinal projections) are needed to confirm these results. Ex vivo experiments indirectly confirmed these results, as while the pineal gland responded normally to day-night rhythms in salmonids, seabass and cod, only very low levels were obtained at night in tilapia and no melatonin could be measured from isolated pineal glands in catfish. Together, these findings suggest that mechanisms involved in the perception of light and the transduction of this signal through the circadian axis has changed in teleosts possibly as a reflection of the photic environment in which they have evolved in.

Organization of cell and tissue circadian pacemakers: a comparison among species

In most animal species, a circadian timing system has evolved as a strategy to cope with 24-hour rhythms in the environment. Circadian pacemakers are essential elements of the timing system and have been identified in anatomically discrete locations in animals ranging from insects to mammals. Rhythm generation occurs in single pacemaker neurons and is based on the interacting negative and positive molecular feedback loops. Rhythmicity in behavior and physiology is regulated by neuronal networks in which synchronization or coupling is required to produce coherent output signals. Coupling occurs among individual clock cells within an oscillating tissue, among functionally distinct subregions within the pacemaker, and between central pacemakers and the periphery. Recent evidence indicates that peripheral tissues can influence central pacemakers and contain autonomous circadian oscillators that contribute to the regulation of overt rhythmicity. The data discussed in this review describe coupling and synchronization mechanisms at the cell and tissue levels. By comparing the pacemaker systems of several multicellular animal species (Drosophila, cockroaches, crickets, snails, zebrafish and mammals), we will explore general organizational principles by which the circadian system regulates a 24-hour rhythmicity.

Light signaling to the zebrafish circadian clock by Cryptochrome 1a

Zebrafish tissues and cells have the unusual feature of not only containing a circadian clock, but also being directly light-responsive. Several zebrafish genes are induced by light, but little is known about their role in clock resetting or the mechanism by which this might occur. Here we show that Cryptochrome 1a (Cry1a) plays a key role in light entrainment of the zebrafish clock. Intensity and phase response curves reveal a strong correlation between light induction of Cry1a and clock resetting. Overexpression studies show that Cry1a acts as a potent repressor of clock function and mimics the effect of constant light to "stop" the circadian oscillator. Yeast two-hybrid analysis demonstrates that the Cry1a protein interacts directly with specific regions of core clock components, CLOCK and BMAL, blocking their ability to fully dimerize and transactivate downstream targets, providing a likely mechanism for clock resetting. A comparison of entrainment of zebrafish cells to complete versus skeleton photoperiods reveals that clock phase is identical under these two conditions. However, the amplitude of the core clock oscillation is much higher on a complete photoperiod, as are the levels of light-induced Cry1a. We believe that Cry1a acts on the core clock machinery in both a continuous and discrete fashion, leading not only to entrainment, but also to the establishment of a high-amplitude rhythm and even stopping of the clock under long photoperiods.

Seasonal variation and the immune response: a fish perspective

The environment in which an animal lives affects the physiology and psychology of that animal. The greater the distance from the equator the more profound this influence becomes, as the environment becomes more variable over the years. Temperature, photoperiod, precipitation and other environmental conditions, which are directly or indirectly controlled by the season, can affect an animal. It is becoming apparent that these conditions may impact on the immune system, and this can affect animal health. This review looks at the known mechanisms for transducing environmental cues and how these can affect immune parameters and function. The main focus is fish, especially in relation to aquaculture and the associated disease risks. Work on other animal classes is included for comparison.

Zebrafish circadian clocks: cells that see light

In the classical view of circadian clock organization, the daily rhythms of most organisms were thought to be regulated by a central, ‘master’ pacemaker, usually located within neural structures of the animal. However, with the results of experiments performed in zebrafish, mammalian cell lines and, more recently, mammalian tissues, this view has changed to one where clock organization is now seen as being highly decentralized. It is clear that clocks exist in the peripheral tissues of animals as diverse as Drosophila, zebrafish and mammals. In the case of Drosophila and zebrafish, these tissues are also directly light-responsive. This light sensitivity and direct clock entrainability is also true for zebrafish cell lines and early-stage embryos. Using luminescent reporter cell lines containing clock gene promoters driving the expression of luciferase and single-cell imaging techniques, we have been able to show how each cell responds rapidly to a single light pulse by being shifted to a common phase, equivalent to the early day. This direct light sensitivity might be related to the requirement for light in these cells to activate the transcription of genes involved in DNA repair. It is also clear that the circadian clock in zebrafish regulates the timing of the cell cycle, demonstrating the wide impact that this light sensitivity and daily rhythmicity has on the biology of zebrafish.

Imaging of single light-responsive clock cells reveals fluctuating free-running periods

Zebrafish tissues and cell lines contain circadian clocks that respond directly to light. Using fluorescence-activated cell sorting, we have isolated clonal cell lines that contain the reporter construct, zfperiod4-luciferase. Bioluminescent assays show that oscillations within cell populations are dampened in constant darkness. However, single-cell imaging reveals that individual cells continue to oscillate, but with widely distributed phases and marked stochastic fluctuations in free-running period. Because these cells are directly light responsive, we can easily follow phase shifts to single light pulses. Here we show that light acts to reset desynchronous cellular oscillations to a common phase, as well as stabilize the subsequent free-running period.

Homeobox-clock protein interaction in zebrafish. A shared mechanism for pineal-specific and circadian gene expression

In non-mammalian vertebrates, the pineal gland is photoreceptive and contains an intrinsic circadian oscillator that drives rhythmic production and secretion of melatonin. These features require an accurate spatiotemporal expression of an array of specific genes in the pineal gland. Among these is the arylalkylamine N-acetyltransferase, a key enzyme in the melatonin production pathway. In zebrafish, pineal specificity of zfaanat2 is determined by a region designated the pineal-restrictive downstream module (PRDM), which contains three photoreceptor conserved elements (PCEs) and an E-box, elements that are generally associated with photoreceptor-specific and rhythmic expression, respectively. Here, by using in vivo and in vitro approaches, it was found that the PCEs and E-box of the PRDM mediate a synergistic effect of the photoreceptor-specific homeobox OTX5 and rhythmically expressed clock protein heterodimer, BMAL/CLOCK, on zfaanat2 expression. Furthermore, the distance between the PCEs and the E-box was found to be critical for PRDM function, suggesting a possible physical feature of this synergistic interaction. OTX5-BMAL/CLOCK may act through this mechanism to simultaneously control pineal-specific and rhythmic expression of zfaanat2 and possibly also other pineal and retinal genes.

Effects of photoperiod on the development of the central glutamate system in tilapia, Oreochromis mossambicus

The effect of photoperiod (light/dark cycle) on the development of the central glutamate system was investigated in tilapia, Oreochromis mossambicus. Tilapia, at 0, 5, and 10 days posthatching were respectively divided into three equal groups to be kept in different photoperiods: 12/12 h, 24/0 h (full day), and 0/24 h (full night). Neither the full-day nor the full-night photoperiod showed any influence on the development of the central glutamate system, including glutamate content and mRNA expression of glutamate receptor 3 alpha, in the developing tilapia brain. These results suggest that neither constant light nor dark photoperiods affected the influence of the central glutamate system on brain sex differentiation in tilapia during the early developing period.

Periodic dip of lipidperoxidation in humans: a redox signal to synchronize peripheral circadian clocks?

The output generated by the endogenous circadian clock to control circadian functions and temporal organization in metazoans is unknown. Redox state perturbations generated by reactive oxygen species (ROS) and antioxidants are known to influence the expression of a number of genes and signal transduction pathways. Evidence has been recently provided that the reduced redox cofactors NAD and NADP both regulate clock gene activity in the suprachiasmatic nucleus (SCN) and are induced by it. Significant periodic variations of lipidperoxidation in human blood with a dip at 04.00 h have been previously reported. Such variations could be expected to alter the cellular redox state, thus possibly functioning as periodic redox signals from the master clock. To verify the existence of the mentioned variations the serum levels of malondialdehyde (MDA), a marker of lipidperoxidation, were monitored by High-Performance Liquid Chromatography in 39 healthy subjects at 3-h intervals over a 24-h period. Throughout the test period, only biological noise could be detected in all test persons. However, the normalized MDA levels at 03.00 h were significantly lower (p < 0.05 to < 0.00005) in 38 (97%) of the cases and showed a significantly lower standard deviation (p < 0.004) than at any of the other 3-h intervals, indicating a periodic dip of lipidperoxidation (PDL) in diurnal active subjects. We hypothesize that the PDL, on the basis of its time of appearance, its frequency and its potential influence on cellular redox state, represents a periodic systemic redox output of the SCN, in terms of a relatively short and sudden interruption of the daily oxidative noise. According to recent research, it could be the result of redox alterations induced by the SCN activity and at the same time the pathway by which the master clock resets and synchronizes peripheral oscillators to the light/dark cycle. Additionally, the antioxidative function of the pineal gland activity postulated elsewhere could play a part in generating the described phenomenon. The PDL could be useful as a circadian phase marker in research dealing with treatment of jet lag and other sleep disorders.

Chemical discovery and global gene expression analysis in zebrafish

The zebrafish (Danio rerio) provides an excellent model for studying vertebrate development and human disease because of its ex utero, optically transparent embryogenesis and amenability to in vivo manipulation. The rapid embryonic developmental cycle, large clutch sizes and ease of maintenance at large numbers also add to the appeal of this species. Considerable genomic data has recently become publicly available that is aiding the construction of zebrafish microarrays, thus permitting global gene expression analysis. The zebrafish is also suitable for chemical genomics, in part as a result of the permeability of its embryos to small molecules and consequent avoidance of external confounding maternal effects. Finally, there is increasing characterization and analysis of zebrafish models of human disease. Thus, the zebrafish offers a high-quality, high-throughput bioassay tool for determining the biological effect of small molecules as well as for dissecting biological pathways.