Molecular Correlates of Circadian Clocks in Fruit Fly Drosophila melanogaster Populations Exhibiting early and late Emergence Chronotypes

Molecular circadian rhythms are robust in marine annelids lacking rhythmic behavior

The circadian clock controls behavior and metabolism in various organisms. However, the exact timing and strength of rhythmic phenotypes can vary significantly between individuals of the same species. This is highly relevant for rhythmically complex marine environments where organismal rhythmic diversity likely permits the occupation of different microenvironments. When investigating circadian locomotor behavior of Platynereis dumerilii, a model system for marine molecular chronobiology, we found strain-specific, high variability between individual worms. The individual patterns were maintained for several weeks. A diel head transcriptome comparison of behaviorally rhythmic versus arrhythmic wild-type worms showed that 24-h cycling of core circadian clock transcripts is identical between both behavioral phenotypes. While behaviorally arrhythmic worms showed a similar total number of cycling transcripts compared to their behaviorally rhythmic counterparts, the annotation categories of their transcripts, however, differed substantially. Consistent with their locomotor phenotype, behaviorally rhythmic worms exhibit an enrichment of cycling transcripts related to neuronal/behavioral processes. In contrast, behaviorally arrhythmic worms showed significantly increased diel cycling for metabolism- and physiology-related transcripts. The prominent role of the neuropeptide pigment-dispersing factor (PDF) in Drosophila circadian behavior prompted us to test for a possible functional involvement of Platynereis pdf. Differing from its role in Drosophila, loss of pdf impacts overall activity levels but shows only indirect effects on rhythmicity. Our results show that individuals arrhythmic in a given process can show increased rhythmicity in others. Across the Platynereis population, rhythmic phenotypes exist as a continuum, with no distinct "boundaries" between rhythmicity and arrhythmicity. We suggest that such diel rhythm breadth is an important biodiversity resource enabling the species to quickly adapt to heterogeneous or changing marine environments. In times of massive sequencing, our work also emphasizes the importance of time series and functional tests.

What have we learned about sleep from selective breeding strategies?

Selective breeding is a classic technique that enables an experimenter to modify a heritable target trait as desired. Direct selective breeding for extreme sleep and circadian phenotypes in flies successfully alters these behaviors, and sleep and circadian perturbations emerge as correlated responses to selection for other traits in mice, rats, and dogs. The application of sequencing technologies to the process of selective breeding identifies the genetic network impacting the selected trait in a holistic way. Breeding techniques preserve the extreme phenotypes generated during selective breeding, generating community resources for further functional testing. Selective breeding is thus a unique strategy that can explore the phenotypic limits of sleep and circadian behavior, discover correlated responses of traits having shared genetic architecture with the target trait, identify naturally-occurring genomic variants and gene expression changes that affect trait variability, and pinpoint genes with conserved roles.

Intrinsic individual variation in daily activity onset and plastic responses on temporal but not spatial scales in female great tits

In a variety of species, individuals appear to be consistent in the daily timing of their activity onset. Such consistent among-individual differences can result from both intrinsic factors, as individuals may e.g. differ genetically, and extrinsic factors, as the environment may vary on spatial and temporal scales. However, previous studies typically did not differentiate between their respective contributions on individual variation in the timing of activities. Here, we repeatedly measured the onset of activity in female great tits (Parus major) on consecutive days during the egg laying phase of the breeding season in four consecutive years. Subsequently, we used a variance partitioning analysis in order to determine which part of the total variation could be attributed to intrinsic (female identity) and extrinsic (nest box identity) factors. Overall, 27% of the total variation could be attributed to female identity. In addition, we found temporal variation in the activity onset, indicating that individuals can plastically adjust their timing. Yet despite their general ability to change the timing of activities over time, spatial environmental factors did not contribute significantly to the observed variation. Individuals may choose a habitat that matches the preferred timing of activities, or might not benefit from adjusting their timing to environmental factors that might vary on spatial scales.

Evidence for Co-Evolution of Masking With Circadian Phase in Drosophila Melanogaster

Heritable variation in the timing of rhythmic events with respect to daily time cues gives rise to chronotypes. Despite its importance, the mechanisms (clock or non-clock) regulating chronotypes remain elusive. Using artificial laboratory selection for divergent phasing of emergence of adults from pupae, our group has derived populations of Drosophila melanogaster which are early and late chronotypes for eclosion rhythm. Several circadian rhythm characteristics of these populations have since been described. We hypothesized that our selection protocol has inadvertently resulted in selection for masking, a non-clock phenomenon, in the early chronotype due to the placement of our selection window (which includes the lights-ON transition). We designed experiments to discriminate between enhanced masking to light versus circadian clock mediated changes in determining enhanced emergence in the morning window in our early chronotypes. Using a series of phase-shift protocols, LD-DD transition, and T-cycle experiments, we find that our early chronotypes have evolved positive masking, and their apparent entrained phases are largely contributed by masking. Through skeleton T-cycle experiments, we find that in addition to the evolution of greater masking, our early chronotypes have also evolved advanced phase of entrainment. Furthermore, our study systematically outlines experimental approaches to examine relative contributions of clock versus non-clock control of an entrained behavior. Although it has previously been suggested that masking may confer an adaptive advantage to organisms, here we provide experimental evidence for the evolution of masking as a means of phasing that can complement clock control of an entrained behavior.

Responses of activity rhythms to temperature cues evolve in Drosophila populations selected for divergent timing of eclosion

Even though the rhythms in adult emergence and locomotor activity are two different phenomena that occur at distinct life stages of the fly life cycle, previous studies have hinted at similarities in certain aspects of the organisation of the circadian clock driving these two rhythms. For instance, the period gene plays an important regulatory role in both rhythms. In an earlier study, we have shown that selection on timing of adult emergence behaviour in populations of Drosophila melanogaster leads to the co-evolution of temperature sensitivity of circadian clocks driving eclosion. In this study, we investigated whether temperature sensitivity of the locomotor activity rhythm evolved in our populations separately from the adult emergence rhythm, with the goal of understanding the extent of similarity (or lack thereof) in circadian organisation underlying the two rhythms. We found that in response to simulated jetlag with temperature cycles, late chronotypes (populations selected for predominant emergence during dusk) indeed re-entrained faster than early chronotypes (populations selected for predominant emergence during dawn) to 6 h phase delays, thereby indicating enhanced sensitivity of the activity/rest clock to temperature cues in these stocks (entrainment is the synchronisation of internal rhythms to cyclic environmental time cues). Additionally, we found that late chronotypes show higher plasticity of phases across regimes, day-to-day stability in phases and amplitude of entrainment, all indicative of enhanced temperature-sensitive activity/rest rhythms. Our results highlight remarkably similar organisation principles between circadian clocks regulating emergence and activity/rest rhythms.

Waveform Plasticity under Entrainment to 12-h T-cycles in Drosophila melanogaster: Behavior, Neuronal Network, and Evolution

A crucial property of circadian clocks is the ability to regulate the shape of an oscillation over its cycle length (waveform) appropriately, thus enhancing Darwinian fitness. Many studies over the past decade have revealed interesting ways in which the waveform of rodent behavior could be manipulated, one of which is that the activity bout bifurcates under environments that have 2 light/dark cycles within one 24-h day (LDLD). It has been observed that such unique, although unnatural, environments reveal acute changes in the circadian clock network. However, although adaptation of waveforms to different photoperiods is well studied, modulation of waveforms under LDLD has received relatively less attention in research on insect rhythms. Therefore, we undertook this study to ask the following questions: what is the extent of waveform plasticity that Drosophila melanogaster exhibits, and what are the neuronal underpinnings of such plasticity under LDLD? We found that the activity/rest rhythms of wild-type flies do not bifurcate under LDLD. Instead, they show similar but significantly different behavior from that under a long-day LD cycle. This behavior is accompanied by differences in the organization of the circadian neuronal network, which include changes in waveforms of a core clock component and an output molecule. In addition, to understand the functional significance of such variations in the waveform, we examined laboratory selected populations that exhibit divergent eclosion chronotypes (and therefore, waveforms). We found that populations selected for predominant eclosion in an evening window (late chronotypes) showed reduced amplitude plasticity and increased phase plasticity of activity/rest rhythms. This, we argue, is reflective of divergent evolution of circadian neuronal network organization in our laboratory selected flies.

Hydrogen peroxide modulates clock gene expression via PRX2-STAT3-REV-ERBα/β pathway

The circadian rhythm is a widespread physiological phenomenon present in almost all forms of life and is constituted by a system of interlocked transcriptional/translational feedback loops (TTFLs). External zeitgebers regulate biological rhythms through the direct or indirect regulation of circadian genes. Oxidative stress is involved in many diseases and injuries, such as ageing, diabetes, Alzheimer's disease, and cancer. Despite an increasing number of studies on circadian rhythm disorders caused by oxidative stress, little is known about the effects of oxidants on clock gene expression and the underlying mechanism. In this study, we found that the protein expression of circadian genes Clock, Bmal1, Per1/2, and Cry1/2 in NIH3T3 cells was upregulated by hydrogen peroxide (H2O2), an important mediator of oxidative stress. In addition, H2O2 modulated the circadian rhythm of Bmal1-luciferase via RORα, REV-ERBα (NR1D1), and REV-ERBβ (NR1D2). Further studies showed that H2O2 regulated biological rhythm by PRX2-STAT3-REV-ERBα/β pathway. These findings provide an accessory loop-related mechanism by which non-transcriptional oscillation interplays with TTFLs.

Selection for Timing of Eclosion Results in Co-evolution of Temperature Responsiveness in Drosophila melanogaster

Circadian rhythms in adult eclosion of Drosophila are postulated to be regulated by a pair of coupled oscillators: one is the master clock that is light sensitive and temperature compensated and the other that is a slave oscillator whose period is temperature sensitive and whose phase is reflected in the overt behavior. Within this framework, we reasoned that in populations of Drosophila melanogaster that have been artificially selected for highly divergent phases of eclosion rhythm, there may be changes in this network of the master-slave oscillator system, via changes in the temperature-sensitive oscillator and/or the coupling of the light- and temperature-sensitive oscillators. We used light/dark cycles in conjunction with different constant ambient temperatures and 2 different amplitudes of temperature cycles in an overall cool or warm temperature and analyzed phases, gate width, and normalized amplitude of the rhythms in each of these conditions. We found that the populations selected for eclosion in the morning ( early flies) do not vary their phases with change in temperature regimes, whereas the populations selected for eclosion in the evening ( late flies) show phase lability of up to ~5 h. Our results imply a genetic correlation between timing of behavior and temperature sensitivity of the circadian clock.

Variation in chronotype is associated with migratory timing in a songbird

Like many organisms, birds exhibit daily (circadian) and seasonal biological rhythms, and within populations both daily and seasonal timing often vary among individuals. Because photoperiod interacts with the circadian rhythms of many organisms to induce seasonal changes in behaviour and physiology, it is hypothesized that differences in daily timing, called chronotypes, underpin differences among individuals in the timing of seasonal events. For seasonal events stimulated by increasing daylength, this hypothesis predicts a positive relationship between the timing of daily and seasonal activities of individuals, with advanced chronotypes expressing events earlier in the year. The few previous tests of this hypothesis have focused on seasonal reproductive timing in birds. However, the hypothesis predicts that this relationship should extend to other photoinduced seasonal events. Therefore, we tested whether variation in chronotype was associated with variation in spring migratory timing in a captive songbird model, the pine siskin (Spinus pinus). We found that pine siskins expressing migratory restlessness exhibited repeatable chronotypes in their timing of nocturnal activity. Further, chronotype was significantly associated with the onset date of migratory behaviour, consistent with the hypothesized relationship between chronotype and seasonal timing.

Non-Pleiotropic Coupling of Daily and Seasonal Temporal Isolation in the European Corn Borer

Speciation often involves the coupling of multiple isolating barriers to produce reproductive isolation, but how coupling is generated among different premating barriers is unknown. We measure the degree of coupling between the daily mating time and seasonal mating time between strains of European corn borer (Ostrinia nubilalis) and evaluate the hypothesis that the coupling of different forms of allochrony is due to a shared genetic architecture, involving genes with pleiotropic effects on both timing phenotypes. We measure differences in gene expression at peak mating times and compare these genes to previously identified candidates that are associated with changes in seasonal mating time between the corn borer strains. We find that the E strain, which mates earlier in the season, also mates 2.7 h earlier in the night than the Z strain. Earlier daily mating is correlated with the differences in expression of the circadian clock genes cycle, slimb, and vrille. However, different circadian clock genes associate with daily and seasonal timing, suggesting that the coupling of timing traits is maintained by natural selection rather than pleiotropy. Juvenile hormone gene expression was associated with both types of timing, suggesting that circadian genes activate common downstream modules that may impose constraint on future evolution of these traits.

Two sides of a coin: ecological and chronobiological perspectives of timing in the wild

Most processes within organisms, and most interactions between organisms and their environment, have distinct time profiles. The temporal coordination of such processes is crucial across levels of biological organization, but disciplines differ widely in their approaches to study timing. Such differences are accentuated between ecologists, who are centrally concerned with a holistic view of an organism in relation to its external environment, and chronobiologists, who emphasize internal timekeeping within an organism and the mechanisms of its adjustment to the environment. We argue that ecological and chronobiological perspectives are complementary, and that studies at the intersection will enable both fields to jointly overcome obstacles that currently hinder progress. However, to achieve this integration, we first have to cross some conceptual barriers, clarifying prohibitively inaccessible terminologies. We critically assess main assumptions and concepts in either field, as well as their common interests. Both approaches intersect in their need to understand the extent and regulation of temporal plasticity, and in the concept of 'chronotype', i.e. the characteristic temporal properties of individuals which are the targets of natural and sexual selection. We then highlight promising developments, point out open questions, acknowledge difficulties and propose directions for further integration of ecological and chronobiological perspectives through Wild Clock research.This article is part of the themed issue 'Wild Clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals'.

The influence of pro-longevity gene Gclc overexpression on the age-dependent changes in Drosophila transcriptome and biological functions

Background

Transcriptional changes that contribute to the organism’s longevity and prevent the age-dependent decline of biological functions are not well understood. Here, we overexpressed pro-longevity gene encoding glutamate-cysteine ligase catalytic subunit (Gclc) and analyzed age-dependent changes in transcriptome that associated with the longevity, stress resistance, locomotor activity, circadian rhythmicity, and fertility.

Results

Here we reproduced the life extension effect of neuronal overexpression of the Gclc gene and investigated its influence on the age-depended dynamics of transcriptome and biological functions such as fecundity, spontaneous locomotor activity and circadian rhythmicity, as well as on the resistance to oxidative, proteotoxic and osmotic stresses. It was shown that Gclc overexpression reduces locomotor activity in the young and middle ages compared to control flies. Gclc overexpression slowed down the age-dependent decline of locomotor activity and circadian rhythmicity, and resistance to stress treatments. Gclc level demonstrated associations with the expression of genes involved in a variety of cellular processes including Jak-STAT, MAPK, FOXO, Notch, mTOR, TGF-beta signaling pathways, translation, protein processing in endoplasmic reticulum, proteasomal degradation, glycolysis, oxidative phosphorylation, apoptosis, regulation of circadian rhythms, differentiation of neurons, synaptic plasticity and transmission.

Conclusions

Our study revealed that Gclc overexpression induces transcriptional changes associated with the lifespan extension and uncovered pathways that may be associated with the age-dependent decline of biological functions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3356-0) contains supplementary material, which is available to authorized users.

Evolution of robust circadian clocks in Drosophila melanogaster populations reared in constant dark for over 330 generations

Robustness is considered to be an important feature of biological systems which may evolve when the functionality of a trait is associated with higher fitness across multiple environmental conditions. Thus, the ability to maintain stable biological phenotypes across environments is thought to be of adaptive value. Previously, we have reported higher intrinsic activity levels (activity levels of free-running rhythm in constant darkness) and power of rhythm (as assessed by amplitude of the periodogram) in Drosophila melanogaster populations (stocks) reared in constant darkness (DD stocks) as compared to those reared in constant light (LL stocks) and 12:12-h light-dark cycles (LD stocks) for over 19 years (∼330 generations). In the current study, we intended to examine whether the enhanced levels of activity observed in DD stocks persist under various environments such as photoperiods, ambient temperatures, non-24-h light-dark (LD) cycles, and semi-natural conditions (SN). We found that DD stocks largely retain their phenotype of enhanced activity levels across most of the above-mentioned environments suggesting the evolution of robust circadian clocks in DD stocks. Furthermore, we compared the peak activity levels of the three stocks across different environmental conditions relative to their peaks in constant darkness and found that the change in peak activity levels upon entrainment was not significantly different across the three stocks for any of the examined environmental conditions. This suggests that the enhancement of activity levels in DD stocks is not due to differential sensitivity to environment. Thus, these results suggest that rearing in constant darkness (DD) leads to evolution of robust circadian clocks suggesting a possible adaptive value of possessing such rhythms under constant dark environments.