PER protein interactions and temperature compensation of a circadian clock in Drosophila

A protein linkage map of Escherichia coli bacteriophage T7

Genome sequencing projects are predicting large numbers of novel proteins, whose interactions with other proteins must mediate the function of cellular processes. To analyse these networks, we used the yeast two-hybrid system on a genome-wide scale to identify 25 interactions among the proteins of Escherichia coli bacteriophage T7. Among these is a set of six interactions connecting proteins that function in DNA replication and DNA packaging. Remarkably, two genes, arranged such that one entirely overlaps the other and uses a different reading frame, encode interacting proteins. Several of the interactions reflect intramolecular associations of different domains of the same polypeptide, suggesting that the two-hybrid assay may be useful in the analysis of protein folding. This global approach to protein-protein interactions may be applicable to the analysis of more complex genomes whose sequences are becoming available.

The basic helix-loop-helix/PAS factor Sim is associated with hsp90. Implications for regulation by interaction with partner factors

Sim is a Drosophila developmental basic helix-loop-helix (bHLH) transcription factor containing a Per-Arnt-Sim (PAS) region of homology. Here we demonstrate that Sim, in analogy to the structurally related bHLH/PAS dioxin receptor, was stably associated with the molecular chaperone hsp90. In the case of the dioxin receptor, release of hsp90 and derepression of receptor function appear to be regulated by ligand binding and dimerization with Arnt, a non-hsp90-associated bHLH/PAS factor. Dimerization with Arnt very efficiently disrupted Sim-hsp90 interaction, a process that required both the bHLH and PAS dimerization motifs of Arnt. Moreover, hsp90 was also released upon dimerization of Sim with the Drosophila PAS factor Per, whereas the hsp90-associated dioxin receptor failed to interact with Sim. These results indicate that hsp90 may play a role in conditional regulation of Sim function, and that Per and possibly bHLH/PAS partner factors may activate Sim by inducing release of hsp90 during the dimerization process.

Molecular genetic analysis of circadian rhythms in vertebrates and invertebrates

In recent years, there has been a flurry of activity directed towards identifying the molecular basis of circadian (approximately 24 h) rhythms. The past year has seen the isolation of the first clock mutations in a number of organisms (mice, Arabidopsis, cyanobacteria), the identification of a new circadian rhythm gene in Drosophila that interacts with the well known period gene, and considerable progress in the analysis of the 'clock genes', period and frequency. A combination of genetic, molecular and biochemical approaches is leading to an emerging picture of how molecular events enable organisms to keep time.

Positional cloning and sequence analysis of the Drosophila clock gene, timeless

The Drosophila genes timeless (tim) and period (per) interact, and both are required for production of circadian rhythms. Here the positional cloning and sequencing of tim are reported. The tim gene encodes a previously uncharacterized protein of 1389 amino acids, and possibly another protein of 1122 amino acids. The arrhythmic mutation tim01 is a 64-base pair deletion that truncates TIM to 749 amino acids. Absence of sequence similarity to the PER dimerization motif (PAS) indicates that direct interaction between PER and TIM would require a heterotypic protein association.

Isolation of timeless by PER protein interaction: defective interaction between timeless protein and long-period mutant PERL

The period (per) gene likely encodes a component of the Drosophila circadian clock. Circadian oscillations in the abundance of per messenger RNA and per protein (PER) are thought to arise from negative feedback control of per gene transcription by PER. A recently identified second clock locus, timeless (tim), apparently regulates entry of PER into the nucleus. Reported here are the cloning of complementary DNAs derived from the tim gene in a two-hybrid screen for PER-interacting proteins and the demonstration of a physical interaction between the tim protein (TIM) and PER in vitro. A restricted segment of TIM binds directly to a part of the PER dimerization domain PAS. PERL, a mutation that causes a temperature-sensitive lengthening of circadian period and a temperature-sensitive delay in PER nuclear entry, exhibits a temperature-sensitive defect in binding to TIM. These results suggest that the interaction between TIM and PER determines the timing of PER nuclear entry and therefore the duration of part of the circadian cycle.

Genes that control a temperature-compensated ultradian clock in Caenorhabditis elegans

Substantial progress has been made in understanding the genetic basis of temperature-compensated circadian clocks. Ultradian rhythms, with a period shorter than 24 h, are at least as widespread as circadian rhythms. We have initiated genetic analysis of defecation behavior, which is controlled by an ultradian clock in Caenorhabditis elegans. The defecation motor program is activated every 45 sec, and this rhythm is temperature compensated. We describe mutations in 12 genes that either shorten or lengthen the cycle period. We find that most of these mutations also disrupt temperature compensation, suggesting that this process is an integral part of the clock. These genes open the way for molecular genetic dissection of this ultradian clock.

Molecular control of circadian rhythms

Circadian rhythms are virtually ubiquitous in eukaryotes and have been shown to exist even in some prokaryotes. The generally accepted view is that these rhythms are generated by an endogenous clock. Recent progress, especially in the Drosophila, Neurospora and mouse systems, has revealed new clock components and mechanisms. These include the mouse clock gene, the Drosophila timeless gene, and the role of light in Neurospora.

A model for circadian oscillations in the Drosophila period protein (PER)

The mechanism of circadian oscillations in the period protein (PER) in Drosophila is investigated by means of a theoretical model. Taking into account recent experimental observations, the model for the circadian clock is based on multiple phosphorylation of PER and on the negative feedback exerted by PER on the transcription of the period (per) gene. This minimal biochemical model provides a molecular basis for circadian oscillations of the limit cycle type. During oscillations, the peak in per mRNA precedes by several hours the peak in total PER protein. The results support the view that multiple PER phosphorylation introduces times delays which strengthen the capability of negative feedback to produce oscillations. The analysis shows that the rhythm only occurs in a range bounded by two critical values of the maximum rate of PER degradation. A similar result is obtained with respect to the rate of PER transport into the nucleus. The results suggest a tentative explanation for the altered period of per mutants, in terms of variations in the rate of PER degradation.

Period protein from the giant silkmoth Antheraea pernyi functions as a circadian clock element in Drosophila melanogaster

Homologs of the Drosophila clock gene per have recently been cloned in Lepidopteran and Blattarian insect species. To assess the extent to which clock mechanisms are conserved among phylogenetically distant species, we determined whether PER protein from the silkmoth Antheraea pernyi can function in the Drosophila circadian timing system. When expressed in transgenic Drosophila, the silkmoth PER protein is detected in the expected neural cell types, with diurnal changes in abundance that are similar to those observed in wild-type fruitflies. Behavioral analysis demonstrates that the silkmoth protein can serve as a molecular element of the Drosophila clock system; expression of the protein shortens circadian period in a dose-dependent manner and restores pacemaker functions to arrhythmic per0 mutants. This comparative study also suggests that the involvement of PER in different aspects of circadian timing, such as period determination, strength of rhythmicity, and clock out-put, requires distinct molecular interactions.

Are competing intermolecular and intramolecular interactions of PERIOD protein important for the regulation of circadian rhythms in Drosophila?

Genetic analysis is revealing molecular components of circadian rhythms. The gene products of the period gene in Drosophila and the frequency gene in Neurospora oscillate with a circadian rhythm. A recent paper (1) has shown that the PERIOD protein can undergo both intermolecular and intramolecular interactions in vitro. The effects of temperature and two period mutations on these molecular interactions were compared to the effects of the mutations and temperature on the in vivo period length of circadian rhythms. The results suggest that the molecular interactions may compete to maintain a rhythm with a constant period over a wide temperature range.

Conformational study of the Thr-Gly repeat in the Drosophila clock protein, PERIOD

Recent results with the Drosophila melanogaster period gene suggest that the apparently conserved repetitive motif (Thr-Gly)n encoded by this gene may play an important role in the temperature compensation of the circadian clock. We have therefore initiated both a theoretical and experimental conformational analysis of (Thr-Gly)n peptides. By using a build-up method, it is clear that the hexapeptide (Thr-Gly)3 represents a 'conformational monomer' and generates a stable type II or type III beta-turn. Circular dichroism and nuclear magnetic resonance spectra of synthetic (Thr-Gly)3 and poly(Thr-Gly) peptides revealed that these peptides exhibit flexible conformations, especially in more polar environments and at higher temperatures. We speculate that this flexibility may illuminate our understanding of both the molecular mechanism of temperature compensation and the systematic geographical distribution within Europe of the Thr-Gly length polymorphism in D. melanogaster.

Tripping along the trail to the molecular mechanisms of biological clocks

Solving the mechanism of circadian clocks has become an important goal, in part because daily rhythms are running in such a wide variety of organisms, and contribute to many aspects of their well being. Systematic genetic approaches to studying 'the clock' were initiated in fruitflies more than 20 years ago as a novel means by which neural-pacemaking mysteries might be solved. Such chronogenetic investigations gained momentum when they spread to other species, and became molecular. However, the molecular studies were misleading, that is, until some elementary neuro-anatomical observations, involving the expression of a 'clock gene' in Drosophila, gave the experiments in this molecular-neurogenetic area of chronobiology a new direction. The initially neuro-descriptive studies led to the current investigations that involve negatively acting transcription factors and other clock molecules that are presumed to interact with them. In addition, new mutants and clones have been isolated in a timely manner. These mutations and molecules should permit chronogeneticists, working on a wide variety of organisms, to unravel further details of how the clock works, how environmental information finds its way to it, and how it sends information out into the organism's physiology, biochemistry and behavior.

Temporally regulated nuclear entry of the Drosophila period protein contributes to the circadian clock

The Drosophila period protein (PER) is a predominantly nuclear protein and a likely component of a circadian clock. PER is required for daily oscillations in the transcription of its own gene and thus participates in a circadian feedback loop. In this study, key pacemaker neurons of the Drosophila brain were examined to determine whether the subcellular distribution of PER changes with the time of day. Indeed, PER was found to accumulate in the cytoplasm for several hours before entering the nucleus during a narrow time window. Three long-period mutations (perL) cause a delay in the timing of nuclear translocation and a further delay at elevated temperature. The data indicate that regulation of PER nuclear entry is critical for circadian oscillations by providing a necessary temporal delay between PER synthesis and its effect on transcription.