Clocks do not tick in unison: isolation of Clock and vrille shed new light on the clockwork model of the sand fly Lutzomyia longipalpis

Daily rhythms in gene expression of the human parasite Schistosoma mansoni

Background

The consequences of the earth’s daily rotation have led to 24-h biological rhythms in most organisms. Even some parasites are known to have daily rhythms, which, when in synchrony with host rhythms, can optimise their fitness. Understanding these rhythms may enable the development of control strategies that take advantage of rhythmic vulnerabilities. Recent work on protozoan parasites has revealed 24-h rhythms in gene expression, drug sensitivity and the presence of an intrinsic circadian clock; however, similar studies on metazoan parasites are lacking. To address this, we investigated if a metazoan parasite has daily molecular oscillations, whether they reveal how these longer-lived organisms can survive host daily cycles over a lifespan of many years and if animal circadian clock genes are present and rhythmic. We addressed these questions using the human blood fluke Schistosoma mansoni that lives in the vasculature for decades and causes the tropical disease schistosomiasis.

Results

Using round-the-clock transcriptomics of male and female adult worms collected from experimentally infected mice, we discovered that ~ 2% of its genes followed a daily pattern of expression. Rhythmic processes included a stress response during the host’s active phase and a ‘peak in metabolic activity’ during the host’s resting phase. Transcriptional profiles in the female reproductive system were mirrored by daily patterns in egg laying (eggs are the main drivers of the host pathology). Genes cycling with the highest amplitudes include predicted drug targets and a vaccine candidate. These 24-h rhythms may be driven by host rhythms and/or generated by a circadian clock; however, orthologs of core clock genes are missing and secondary clock genes show no 24-h rhythmicity.

Conclusions

There are daily rhythms in the transcriptomes of adult S. mansoni, but they appear less pronounced than in other organisms. The rhythms reveal temporally compartmentalised internal processes and host interactions relevant to within-host survival and between-host transmission. Our findings suggest that if these daily rhythms are generated by an intrinsic circadian clock then the oscillatory mechanism must be distinct from that in other animals. We have shown which transcripts oscillate at this temporal scale and this will benefit the development and delivery of treatments against schistosomiasis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-01189-9.

VRILLE shows high divergence among Higher Diptera flies but may retain role as transcriptional repressor of clock

In the circadian system, the clock gene vrille (vri) is an essential component of the second feedback loop, being responsible in Drosophila for the rhythmicity of the Clock (Clk) gene transcription by its repression. Here we studied vri in a fruit fly pest, the Tephritidae Anastrepha fraterculus, aimingtoinvestigate its molecular evolution and expression patterns from whole-head extracts. We used a combination of transcriptomic, genomic and gene walking strategies to sequence and characterize Afravri in male and female head transcriptomes of A. fraterculus and detected two putative isoforms that may correspond to A and D vri isoforms of Drosophila. Both isoforms produced a full-length sequence that translates to 842 amino acids. While the protein sequence showed significant divergence to orthologous sequences from other organisms, the bZIP domain was highly conserved. Molecular evolutionary analyses showed that vri in higher Diptera flies has been evolving under positive selection. A more detailed analysis showed positive selection also in Tephritidae with 29 sites evolving under positive selection in comparison with Drosophilidae. Real time expression analysis in LD and DD conditions showed cyclic expression of Afravri mRNA with oscillation opposite to AfraClk, suggesting that VRI may also behave in Anastrepha as a transcriptional repressor of Clk, providing another indication that higher Diptera might share common interlocked transcript-translation feedback loops (TTFLs) mechanisms that differ from other insects in target genes.

Model and Non-model Insects in Chronobiology

The fruit fly Drosophila melanogaster is an established model organism in chronobiology, because genetic manipulation and breeding in the laboratory are easy. The circadian clock neuroanatomy in D. melanogaster is one of the best-known clock networks in insects and basic circadian behavior has been characterized in detail in this insect. Another model in chronobiology is the honey bee Apis mellifera, of which diurnal foraging behavior has been described already in the early twentieth century. A. mellifera hallmarks the research on the interplay between the clock and sociality and complex behaviors like sun compass navigation and time-place-learning. Nevertheless, there are aspects of clock structure and function, like for example the role of the clock in photoperiodism and diapause, which can be only insufficiently investigated in these two models. Unlike high-latitude flies such as Chymomyza costata or D. ezoana, cosmopolitan D. melanogaster flies do not display a photoperiodic diapause. Similarly, A. mellifera bees do not go into "real" diapause, but most solitary bee species exhibit an obligatory diapause. Furthermore, sociality evolved in different Hymenoptera independently, wherefore it might be misleading to study the social clock only in one social insect. Consequently, additional research on non-model insects is required to understand the circadian clock in Diptera and Hymenoptera. In this review, we introduce the two chronobiology model insects D. melanogaster and A. mellifera, compare them with other insects and show their advantages and limitations as general models for insect circadian clocks.

Functional analysis of Pdp1 and vrille in the circadian system of a cricket

Circadian rhythms are generated by a circadian clock for which oscillations are based on the rhythmic expression of the so-called clock genes. The present study investigated the role of Gryllus bimaculatus vrille (Gb'vri) and Par domain protein 1 (Gb'Pdp1) in the circadian clock of the cricket Gryllus bimaculatus. Structural analysis of Gb'vri and Gb'Pdp1 cDNAs revealed that they are a member of the bZIP transcription factors. Under light/dark cycles (LD) both genes were rhythmically expressed in the clock tissue, the optic lobes, whereas the rhythm diminished under constant darkness (DD). Gb'vri and Gb'Pdp1 mRNA levels were significantly reduced by RNA interference (RNAi) of Gb'Clk and Gb'cyc, suggesting they are controlled by Gb'CLK/Gb'CYC. RNAi of Gb'vri and Gb'Pdp1 had little effect on locomotor rhythms, although their effects became visible when treated together with Gb'cyc^RNAi. The average free-running period of Gb'vri^RNAi/Gb'cyc^RNAi crickets was significantly shorter than that of Gb'cyc^RNAi crickets. A similar period shortening was observed also when treated with Gb'Pdp1^RNAi/Gb'cyc^RNAi. Some Gb'Pdp1^RNAi/Gb'cyc^RNAi crickets showed rhythm splitting into two free-running components with different periods. Gb'vri^RNAi and Gb'Pdp1^RNAi treatments significantly altered the expression of Gb'Clk, Gb'cyc, and Gb'tim in LD. These results suggest that Gb'vri and Gb'Pdp1 play important roles in cricket circadian clocks.

Flies as models for circadian clock adaptation to environmental challenges

Life on earth is assumed to have developed in tropical regions that are characterized by regular 24 hr cycles in irradiance and temperature that remain the same throughout the seasons. All organisms developed circadian clocks that predict these environmental cycles and prepare the organisms in advance for them. A central question in chronobiology is how endogenous clocks changed in order to anticipate very different cyclical environmental conditions such as extremely short and long photoperiods existing close to the poles. Flies of the family Drosophilidae can be found all over the world-from the tropics to subarctic regions-making them unprecedented models for studying the evolutionary processes that underlie the adaptation of circadian clocks to different latitudes. This review summarizes our current understanding of these processes. We discuss evolutionary changes in the clock genes and in the clock network in the brain of different Drosophilids that may have caused behavioural adaptations to high latitudes.

Functional characterization of the circadian clock in the Antarctic krill, Euphausia superba

Antarctic krill (Euphausia superba) is a key species in Southern Ocean ecosystem where it plays a central role in the Antarctic food web. Available information supports the existence of an endogenous timing system in krill enabling it to synchronize metabolism and behavior with an environment characterized by extreme seasonal changes in terms of day length, food availability, and surface ice extent. A screening of our transcriptome database “KrillDB” allowed us to identify the putative orthologues of 20 circadian clock components. Mapping of conserved domains and phylogenetic analyses strongly supported annotations of the identified sequences. Luciferase assays and co-immunoprecipitation experiments allowed us to define the role of the main clock components. Our findings provide an overall picture of the molecular mechanisms underlying the functioning of the endogenous circadian clock in the Antarctic krill and shed light on their evolution throughout crustaceans speciation. Interestingly, the core clock machinery shows both mammalian and insect features that presumably contribute to an evolutionary strategy to cope with polar environment’s challenges. Moreover, despite the extreme variability characterizing the Antarctic seasonal day length, the conserved light mediated degradation of the photoreceptor EsCRY1 suggests a persisting pivotal role of light as a Zeitgeber.

Expanding the view of Clock and cycle gene evolution in Diptera

We expanded the view of Clock (Clk) and cycle (cyc) gene evolution in Diptera by studying the fruit fly Anastrepha fraterculus (Afra), a Brachycera. Despite the high conservation of clock genes amongst insect groups, striking structural and functional differences of some clocks have appeared throughout evolution. Clk and cyc nucleotide sequences and corresponding proteins were characterized, along with their mRNA expression data, to provide an evolutionary overview in the two major groups of Diptera: Lower Diptera and Higher Brachycera. We found that AfraCYC lacks the BMAL (Brain and muscle ARNT-like) C-terminus region (BCTR) domain and is constitutively expressed, suggesting that AfraCLK has the main transactivation function, which is corroborated by the presence of poly-Q repeats and an oscillatory pattern. Our analysis suggests that the loss of BCTR in CYC is not exclusive of drosophilids, as it also occurs in other Acalyptratae flies such as tephritids and drosophilids, however, but it is also present in some Calyptratae, such as Muscidae, Calliphoridae and Sarcophagidae. This indicates that BCTR is missing from CYC of all higher-level Brachycera and that it was lost during the evolution of Lower Brachycera. Thus, we can infer that CLK protein may play the main role in the CLK\CYC transcription complex in these flies, like in its Drosophila orthologues.