Studying the Evolution of the Vertebrate Circadian Clock: The Power of Fish as Comparative Models.

The utility of any model species cannot be judged solely in terms of the tools and approaches it provides for genetic analysis. A fundamental consideration is also how its biology has been shaped by the environment and the ecological niche which it occupies. By comparing different species occupying very different habitats we can learn how molecular and cellular mechanisms change during evolution in order to optimally adapt to their environment. Such knowledge is as important as understanding how these mechanisms work. This is illustrated by the use of fish models for studying the function and evolution of the circadian clock. In this review we outline our current understanding of how fish clocks sense and respond to light and explain how this differs fundamentally from the situation with mammalian clocks. In addition, we present results from comparative studies involving two species of blind cavefish, Astyanax mexicanus and Phreatichthys andruzzii. This work reveals the consequences of evolution in perpetual darkness for the circadian clock and its regulation by light as well as for other mechanisms such as DNA repair, sleep, and metabolism which directly or indirectly are affected by regular exposure to sunlight. Major differences in the cave habitats inhabited by these two cavefish species have a clear impact on shaping the molecular and cellular adaptations to life in complete darkness.

Relaxed selective constraints drove functional modifications in peripheral photoreception of the cavefish P. andruzzii and provide insight into the time of cave colonization.

The genetic basis of phenotypic changes in extreme environments is a key but rather unexplored topic in animal evolution. Here we provide an exemplar case of evolution by relaxed selection in the Somalian cavefish Phreatichthys andruzzii that has evolved in the complete absence of light for at least 2.8 million years. This has resulted in extreme degenerative phenotypes, including complete eye loss and partial degeneration of the circadian clock. We have investigated the molecular evolution of the nonvisual photoreceptor melanopsin opn4m2, whose mutation contributes to the inability of peripheral clocks to respond to light. Our intra- and inter-species analyses suggest that the 'blind' clock in P. andruzzii evolved because of the loss of selective constraints on a trait that was no longer adaptive. Based on this change in selective regime, we estimate that the functional constraint on cavefish opn4m2 was relaxed at ∼5.3 Myr. This implies a long subterranean history, about half in complete isolation from the surface. The visual photoreceptor rhodopsin, expressed in the brain and implicated in photophobic behavior, shows similar evolutionary patterns, suggesting that extreme isolation in darkness led to a general weakening of evolutionary constraints on light-responsive mechanisms. Conversely, the same genes are still conserved in Garra barreimiae, a cavefish from Oman, that independently and more recently colonized subterranean waters and evolved troglomorphic traits. Our results contribute substantially to the open debate on the genetic bases of regressive evolution.

Demographic history and adaptation account for clock gene diversity in humans.

Circadian clocks give rise to daily oscillations in behavior and physiological functions that often anticipate upcoming environmental changes generated by the Earth rotation. In model organisms a relationship exists between several genes affecting the circadian rhythms and latitude. We investigated the allele distributions at 116 000 single-nucleotide polymorphisms (SNPs) of 25 human clock and clock-related genes from the 1000Genomes Project, and at a reference data set of putatively neutral polymorphisms. The global genetic structure at the clock genes did not differ from that observed at the reference data set. We then tested for evidence of local adaptation searching for FST outliers under both an island and a hierarchical model, and for significant association between allele frequencies and environmental variables by a Bayesian approach. A total of 230 SNPs in 23 genes, or 84 SNPs in 19 genes, depending on the significance thresholds chosen, showed signs of local adaptation, whereas a maximum of 190 SNPs in 23 genes had significant covariance with one or more environmental variables. Only two SNPs from two genes (NPAS2 and AANAT) exhibit both elevated population differentiation and covariance with at least one environmental variable. We then checked whether the SNPs emerging from these analyses fall within a set of candidate SNPs associated with different chronotypes or sleep disorders. Correlation of five such SNPs with environmental variables supports a selective role of latitude or photoperiod, but certainly not a major one.

Light and feeding entrainment of the molecular circadian clock in a marine teleost (Sparus aurata).

Daily light and feeding cycles act as powerful synchronizers of circadian rhythmicity. Ultimately, these external cues entrain the expression of clock genes, which generate daily rhythmic behavioral and physiological responses in vertebrates. In the present study, we investigated clock genes in a marine teleost (gilthead sea bream). Partial cDNA sequences of key elements from both positive (Bmal1, Clock) and negative (Per2, Cry1) regulatory loops were cloned before studying how feeding time affects the daily rhythms of locomotor activity and clock gene expression in the central (brain) and peripheral (liver) oscillators. To this end, all fish were kept under a light-dark (LD) cycle and were divided into three experimental groups, depending on the time of their daily meal: mid-light (ML), mid-darkness (MD), or at random (RD) times. Finally, the existence of circadian control on gene expression was investigated in the absence of external cues (DD + RD). The behavioral results showed that seabream fed at ML or RD displayed a diurnal activity pattern (>91% of activity during the day), whereas fish fed at MD were nocturnal (89% of activity during the night). Moreover, seabream subjected to regular feeding cycles (ML and MD groups) showed food-anticipatory activity (FAA). Regardless of the mealtime, the daily rhythm of clock gene expression in the brain peaked close to the light-dark transition in the case of Bmal1 and Clock, and at the beginning of the light phase in the case of Per2 and Cry1, showing the existence of phase delay between the positive and negative elements of the molecular clock. In the liver, however, the acrophases of the daily rhythms differed depending on the feeding regime: the maximum expression of Bmal1 and Clock in the ML and RD groups was in antiphase to the expression pattern observed in the fish fed at MD. Under constant conditions (DD + RD), Per2 and Cry1 showed circadian rhythmicity in the brain, whereas Bmal1, Clock, and Per2 did in the liver. Our results indicate that the seabream clock gene expression is endogenously controlled and in liver it is strongly entrained by food signals, rather than by the LD cycle, and that scheduled feeding can shift the phase of the daily rhythm of clock gene expression in a peripheral organ (liver) without changing the phase of these rhythms in a central oscillator (brain), suggesting uncoupling of the light-entrainable oscillator (LEO) from the food-entrainable oscillator (FEO). These findings provide the basis and new tools for improving our knowledge of the circadian system and entraining pathways of this fish species, which is of great interest for the Mediterranean aquaculture.

Daily variations of serum lipids in Ovis aries under different lighting and feeding conditions.

The aim of this study was to discriminate the impact of lighting and feeding conditions on the regulation of lipid metabolism in Ovis aries. Six clinically healthy female Comisana ewes, not pregnant and not lactating were kept under different environmental conditions: 12:12 light-dark (LD) cycle, constant darkness and fasting. Blood samples were collected at the end of each period of treatment every 4 h for a 24-h period. Blood concentration of triglycerides, total cholesterol and non-esterified fatty acid showed robust daily rhythmicity in ewes maintained under 12:12 LD cycle and fed ad libitum. Conversely, either constant darkness or fasting had a deep impact on all lipid parameters investigated. Our results suggest that lighting and feeding conditions have an impact on daily variations in lipid metabolism in ewes.

A sky polarization compass in lizards: the central role of the parietal eye.

The present study first examined whether ruin lizards Podarcis sicula are able to orientate using the e-vector direction of polarized light. Ruin lizards were trained and tested indoors, inside a hexagonal Morris water maze, positioned under an artificial light source producing plane polarized light with a single e-vector, which provided an axial cue. Lizards were subjected to axial training by positioning two identical goals in contact with the centre of two opposite side walls of the Morris water maze. Goals were invisible because they were placed just beneath the water surface, and water was rendered opaque. The results showed that the directional choices of lizards meeting learning criteria were bimodally distributed along the training axis, and that after 90 deg rotation of the e-vector direction of polarized light the lizards directional choices rotated correspondingly, producing a bimodal distribution which was perpendicular to the training axis. The present results confirm in ruin lizards results previously obtained in other lizard species showing that these reptiles can use the e-vector direction of polarized light in the form of a sky polarization compass. The second step of the study aimed at answering the still open question of whether functioning of a sky polarization compass would be mediated by the lizard parietal eye. To test this, ruin lizards meeting learning criteria were tested inside the Morris water maze under polarized light after their parietal eyes were painted black. Lizards with black-painted parietal eyes were completely disoriented. Thus, the present data show for the first time that the parietal eye plays a central role in mediating the functioning of a putative sky polarization compass of lizards.

Seasonal variations in daily rhythms of activity in athletic horses.

Circadian rhythms reflect extensive programming of biological activity that meets and exploits the challenges and opportunities offered by the periodic nature of the environment. In the present investigation, we recorded the total activity of athletic horses kept at four different times of the year (vernal equinox, summer solstice, autumn equinox and winter solstice), to evaluate the presence of seasonal variations of daily activity rhythms. Athletic Thoroughbred horses were kept in individual boxes with paddock. Digitally integrated measure of total activity of each mare was continuously recorded by actigraphy-based data loggers. Horse total activities were not evenly distributed over the day, but they were mainly diurnal during the year. Daily activity rhythms showed clear seasonal variations, with the highest daily amount of activity during the vernal equinox and the lowest during the winter solstice. Interestingly, the amount of activity during either photophase or scotophase changed significantly throughout the year. Circadian analysis of horse activities showed that the acrophase, the estimated time at which the peak of the rhythm occurs, did not change during the year, it always occurred in the middle of the photoperiod. Analysing the time structure of long-term and continuously measured activity and feeding could be a useful method to critically evaluate athletic horse management systems in which spontaneous locomotor activity and feeding are severely limited. Circadian rhythms are present in several elements of sensory motor and psychomotor functions and these would be taken into consideration to plan the training schedules and competitions in athletic horses.

Photoperiod affects amplitude but not duration of in vitro melatonin production in the ruin lizard (Podarcis sicula).

The pineal gland and its major output signal melatonin have been demonstrated to play a central role in the seasonal organization of the ruin lizard Podarcis sicula. Seasonal variations in the amplitude of the nocturnal melatonin signal, with high values in spring as compared to low values in summer and autumn, have been found in vivo. The authors examined whether the pineal gland of the ruin lizard contains autonomous circadian oscillators controlling melatonin synthesis and whether previously described seasonal variations of in vivo melatonin production can also be found in isolated cultured pineal glands obtained from ruin lizards in summer and winter. In vitro melatonin release from isolated pineal glands of the ruin lizard persisted for 4 days in constant conditions. Cultured explanted pineal glands obtained from animals in winter and summer showed similar circadian rhythms of melatonin release, characterized by damping of the amplitude of the melatonin rhythm. Although different photoperiodic conditions were imposed on ruin lizards before explantation of pineal glands, the authors did not find any indication for corresponding differences in the duration of elevated melatonin in vitro. Differences were found in the amplitude of in vitro melatonin production in light/dark conditions and, to a lesser degree, in constant conditions. The presence of a circadian melatonin rhythm in vitro in winter, although such a rhythm is absent in vivo in winter, suggests that pineal melatonin production is influenced by an extrapineal oscillator in the intact animal that may either positively or negatively modulate melatonin production in summer and winter, respectively.

The circadian system of reptiles: a multioscillatory and multiphotoreceptive system.

Many parameters exhibited by organisms show daily fluctuations that may persist when the organisms are held in constant environmental conditions. Rhythms that persist in constant conditions with a period close to 24 h are called circadian. Although nowadays most research in this field is focused on the molecular and genetic aspects--and therefore mostly on two animal models (Drosophila and mouse)--the study of alternative animal models still represent a useful approach to understanding how the vertebrate circadian system is organized, and how this fascinating time-keeping system has changed throughout the evolution of vertebrates. The present paper summarizes the current knowledge of the circadian organization of Reptiles. The circadian organization of reptiles is multioscillatory in nature. The retinas, the pineal, and the parietal eye (and, possibly, the suprachiasmatic nuclei of the hypothalamus, SCN) contain circadian clocks. Of particular interest is the observation that the role these structures play in the circadian organization varies considerably among species and within the same species in different seasons. Another remarkable feature of this class is the redundancy of circadian photoreceptors: retinas of the lateral eyes, pineal, parietal eye, and the brain all contain photoreceptors.

Temperature cycles induce a bimodal activity pattern in ruin lizards: masking or clock-controlled event? A seasonal problem.

The daily locomotor activity pattern of Ruin lizards in the field is mainly unimodal, except for summer months when soil temperatures exceed 40 degrees C to 42 degrees C around midday. In such a situation, lizards reduce their locomotor activity around midday to avoid overheating, and thus their daily activity pattern becomes bimodal. The bimodal pattern expressed in the field is usually retained in the free-running rhythm under constant temperature and DD for a couple of weeks, after which the bimodal pattern changes into a unimodal pattern. In the present study, the authors examined whether 24-h temperature cycles (TCs) would change lizard activity from a unimodal to a bimodal pattern. Administration of TCs to unimodal lizards free-running in DD is able to entrain locomotor rhythms and to induce a bimodal pattern both in summer and autumn-winter. There are, however, striking seasonal differences in the effectiveness with which TCs achieve bimodality: (a) Numbers of lizards rendered bimodal are significantly higher in summer than in autumn-winter; (b) TCs require less time to achieve bimodality in summer than autumn-winter; (c) bimodality is retained as an aftereffect in the postentrainment free-run in summer, but not in autumn-winter; (d) TCs change activity duration in summer, but not in autumn-winter. All this demonstrates the existence of seasonal changes in responsiveness of the circadian oscillators controlling activity to the external factors inducing bimodality. Oscillators' responsiveness is high in summer, when bimodality is the survival strategy of Ruin lizards to avoid overheating around midday in open fields, and low in autumn-winter, when bimodality has no recognizable adaptive significance.

Role of suprachiasmatic nuclei in circadian and light-entrained behavioral rhythms of lizards.

To establish whether the suprachiasmatic nuclei (SCN) of the Ruin lizard (Podarcis sicula) play a role in entrainment of circadian rhythms to light, we examined the effects of exposure to 24-h light-dark (LD) cycles on the locomotor behavior of lizards with SCN lesions. Lizards became arrhythmic in response to complete SCN lesion under constant temperature and constant darkness (DD), and they remained arrhythmic after exposure to LD cycles. Remnants of SCN tissue in other lesioned lizards were sufficient to warrant entrainment to LD cycles. Hence, the SCN of Ruin lizards are essential both to maintain locomotor rhythmicity and to mediate entrainment of these rhythms to light. We also asked whether light causes expression of Fos-like immunoreactivity (Fos-LI) in the SCN. Under LD cycles, the SCN express a daily rhythm in Fos-LI. Because Fos-LI is undetectable in DD, the rhythm seen in LD cycles is caused by light. We further showed that unilateral SCN lesions in DD induce dramatic period changes. Altogether, the present data support the existence of a strong functional similarity between the SCN of lizards and the SCN of mammals.

Seasonality and role of SCN in entrainment of lizard circadian rhythms to daily melatonin injections.

To establish whether the capability of daily melatonin injections to entrain circadian rhythms varies with season, we examined in constant conditions the locomotor behavior of lizards Podarcis sicula collected and subjected to daily melatonin injections at different times of the year. Although in summer locomotor rhythms of both pineal-intact and pinealectomized lizards became entrained to the 24-h injection period, in the other seasons their rhythms did not entrain to the injection period. To establish whether the suprachiasmatic nuclei (SCN) mediate summer entrainment of locomotor rhythms to melatonin, we examined the behavioral effects of daily melatonin injections in lizards subjected to either bilateral (SCN-X) or unilateral (USCN-X) ablation of the SCN. SCN-X lizards became behaviorally arrhythmic, and daily melatonin injections did not restore rhythmicity. USCN-X lizards remained rhythmic, and their locomotor rhythms did entrain to the injections. Besides demonstrating for the first time in a vertebrate that daily melatonin injections are capable of entraining circadian rhythmicity in only one season (summer), the present results support the view that the SCN (and not the pineal gland) are the primary target sites of melatonin in the circadian system of P. sicula.

Pineal transplantation to the brain of pinealectomized lizards: effects on circadian rhythms of locomotor activity.

Pinealectomized lizards (Podarcis sicula) whose locomotor rhythms were recorded in constant temperature (29 degrees C) and darkness were subdivided into 2 groups of hosts: Each belonging to the 1st group (experimentals) received from a donor a pineal gland, and each belonging to the 2nd one (controls) received a piece of cerebellum. Pineal transplantation induced drastic changes in the free-running period (tau) of locomotor rhythms, which were significantly greater than the tau changes induced by cerebellum transplantation. Either application or removal of melatonin implants left the locomotor rhythms of the controls completely undisturbed, showing that in absence of melatonin rhythms (pinealectomy alone abolishes blood-borne melatonin rhythms) melatonin implants are ineffective. Melatonin rhythms, however, had to be present in the experimentals, because the circadian system reacts to melatonin implants by changing tau (as if melatonin rhythms had been suppressed) and to removal of the implants by again changing tau (as if melatonin rhythms had been restored).

Assignment of the hyperfine-shifted 1H-NMR signals of the heme in the oxygen sensor FixL from Rhizobium meliloti.

BACKGROUND: [corrected] The Rhizobial oxygen sensor FixL is a hemoprotein with kinase activity. On binding of strong-field ligands, a change of the ferrous or ferric heme iron from high to low spin reversibly inactivates the kinase. This spin-state change and other information on the heme pocket have been inferred from enzymatic assays, absorption spectra and mutagenesis studies. We set out to investigate the spin-state of the FixL heme and to identify the hyperfine-shifted heme-proton signals by NMR spectroscopy. RESULTS: Using one-dimensional NMR we directly observed the high- and low-spin nature of the met- and cyanomet-FixL heme domain, respectively. We determined the hyperfine-shifted 1H-NMR signals of the heme and the proximal histidine by one- and two-dimensional spectroscopy and note the absence of distal histidine signals. CONCLUSIONS: These findings support the spin-state mechanism of FixL regulation. They establish that the site of heme coordination is a histidine residue and strongly suggest that a distal histidine is absent. With a majority of the heme resonances identified, one- and two-dimensional NMR techniques can be extended to provide structural and mechanistic information about the residues that line the heme pocket.

Seasonal variations of pineal involvement in the circadian organization of the ruin lizard Podarcis sicula

To establish whether the effects of pinealectomy on circadian locomotor rhythmicity vary with season, we examined, in constant temperature and darkness, the locomotor behaviour of ruin lizards Podarcis sicula collected and subjected to pinealectomy at different times of the year. Changes in the freerunning period in response to pinealectomy were found to be significantly greater in summer than in winter, spring and autumn. Circadian activity time changed significantly in response to pinealectomy only in spring and summer. Furthermore, while pinealectomy was effective in altering the locomotor rhythms of all individual lizards tested in summer, the same surgery was found to leave locomotor rhythmicity of many lizards tested in autumn and winter completely undisturbed. These results demonstrate for the first time in a non-mammalian vertebrate that the pineal gland is centrally involved in determining circadian organization in some seasons and is only marginally involved in others.

Electrolytic lesions to the optic chiasm affect circadian locomotor rhythms in lizards.

Electrolytic lesions to 85-95% of both optic nerves at the level of the optic chiasm (OC-X) induce a significant shortening of the free-running period (tau) of locomotor rhythms in Podarcis sicula held in constant temperature (29 degrees C) and constant darkness. Together with previous data in P. sicula, showing that retinalectomy (RET-X) in constant darkness also mostly induces a shortening of tau, the present results demonstrate that the retinae play a central role in the control of behavioural circadian rhythmicity independently of light perception. The fact that OC-X and RET-X affect locomotor rhythms in the same way (mostly by shortening tau), strongly supports the contention that the influence of the retinae on the circadian system is neurally mediated.