Genetic dissection of the circadian clock: A timeless story

Different period gene repeats take 'turns' at fine-tuning the circadian clock

The repetitive region of the circadian clock gene period in Drosophila pseudoobscura consists predominantly of a pentapeptide sequence whose consensus is NSGAD. In D. melanogaster, this region is replaced by a dipeptide Thr-Gly repeat, which plays a role in the thermal stability of the circadian phenotype. The Thr-Gly repeat has been shown to form a type II or III beta-turn, whose conformational monomer is (Thr-Gly)3. Here we report, using conformational analyses, that both an NSGAD pentapeptide, and a polymer of the same sequence, form type II beta-turns. Thus two peptide sequences, whose amino-acid composition is very different, nevertheless form the same secondary structure. The implications of these structures for clock function are discussed.

Organization of the circadian system in insects

The circadian systems of different insect groups are summarized and compared. Emphasis is placed on the anatomical identification and characterization of circadian pacemakers, as well as on their entrainment, coupling, and output pathways. Cockroaches, crickets, beetles, and flies possess bilaterally organized pacemakers in the optic lobes that appear to be located in the accessory medulla, a small neuropil between the medulla and the lobula. Neurons that are immunoreactive for the peptide pigment-dispersing hormone (PDH) arborize in the accessory medulla and appear to be important components of the optic lobe pacemakers. The neuronal architecture of the accessory medulla with associated PDH-immunoreactive neurons is best characterized in cockroaches, while the molecular machinery of rhythm generation is best understood in fruit flies. One essential component of the circadian clock is the period protein (PER), which colocalizes with PDH in about half of the fruit fly's presumptive pacemaker neurons. PER is also found in the presumptive pacemaker neurons of beetles and moths, but appears to have different functions in these insects. In moths, the pacemakers are situated in the central brain and are closely associated with neuroendocrine functions. In the other insects, neurons associated with neuroendocrine functions also appear to be closely coupled to the optic lobe pacemakers. Some crickets and flies seem to possess central brain pacemakers in addition to their optic lobe pacemakers. With respect to neuronal organization, the circadian systems of insects show striking similarities to the vertebrate circadian system.

Light-induced resetting of a mammalian circadian clock is associated with rapid induction of the mPer1 transcript

To understand how light might entrain a mammalian circadian clock, we examined the effects of light on mPer1, a sequence homolog of Drosophila per, that exhibits robust rhythmic expression in the SCN. mPer1 is rapidly induced by short duration exposure to light at levels sufficient to reset the clock, and dose-response curves reveal that mPer1 induction shows both reciprocity and a strong correlation with phase shifting of the overt rhythm. Thus, in both the phasing of dark expression and the response to light mPer1 is most similar to the Neurospora clock gene frq. Within the SCN there appears to be localization of the induction phenomenon, consistent with the localization of both light-sensitive and light-insensitive oscillators in this circadian center.

Random mutagenesis screen for dominant behavioral mutations in mice

Large-scale mutagenesis and screening for altered phenotypes have been used effectively in many (lower) model organisms to identify mutations in genes that control biological processes. In the mouse, the cost of maintaining the large breeding colonies necessary to screen for recessive mutations makes it important to consider alternate approaches such as region-specific saturation mutagenesis or screening for mutations with a dominant mode of inheritance. In this article, a pilot screen for (semi)dominant visible and behavioral mutations in the mouse induced by a potent chemical mutagen, N-ethyl-N-nitrosourea (ENU), is described. An efficient protocol for ENU mutagenesis and strain-specific differences in the effect of mutagen on the sterility period and long-term survival are reported. In addition to a description of the screen for abnormal circadian wheel running activity that was used previously, the suitability of a high-throughput screen of mutagenized progeny in the Porsolt swim test, used to test the efficacy of antidepressant agents, and in the prepulse inhibition of the acoustic startle response, used to detect anomalies in sensorimotor gating, is tested. By demonstrating strain specific differences and prescreening 100 G1 progeny of mutagenized males, the feasibility of using these behavioral assays for a large-scale screen is illustrated. In this review, details of a mutagenesis screen for behavioral abnormalities are described and issues important in the initial characterization of novel ENU-induced mutations are considered.

Alternative initiation of translation and time-specific phosphorylation yield multiple forms of the essential clock protein FREQUENCY

The frequency (frq) gene encodes central components of the transcription/translation-based negative-feedback loop comprising the core of the Neurospora circadian oscillator; posttranscriptional regulation associated with FRQ is surprisingly complex. Alternative use of translation initiation sites gives rise to two forms of FRQ whose levels peak 4-6 hr following the peak of frq transcript. Each form of FRQ is progressively phosphorylated over the course of the day, thus providing a number of temporally distinct FRQ products. The kinetics of these regulatory processes suggest a view of the clock where relatively rapid events involving translational regulation in the synthesis of FRQ and negative feedback of FRQ on frq transcript levels are followed by slower posttranslational regulation, ultimately driving the turnover of FRQ and reactivation of the frq gene.

Thermally regulated translational control of FRQ mediates aspects of temperature responses in the neurospora circadian clock

Two forms of FRQ, a central component of the Neurospora circadian clock, arise through alternative in-frame initiation of translation. Either form alone suffices for a functional clock at some temperatures, but both are always necessary for robust rhythmicity. Temperature regulates the ratio of FRQ forms by favoring different initiation codons at different temperatures; when either initiation codon is eliminated, the temperature range permissive for rhythmicity is demonstrably reduced. This temperature-influenced choice of translation-initiation site represents a novel adaptive mechanism that extends the physiological temperature range over which clocks function. Additionally, a temperature-dependent threshold level of FRQ is required to establish the feedback loop comprising the oscillator. These data may explain how temperature limits permissive for rhythmicity are established, thus providing a molecular understanding for a basic characteristic of circadian clocks.

Neurospora wc-1 and wc-2: transcription, photoresponses, and the origins of circadian rhythmicity

Circadian rhythmicity is universally associated with the ability to perceive light, and the oscillators ("clocks") giving rise to these rhythms, which are feedback loops based on transcription and translation, are reset by light. Although such loops must contain elements of positive and negative regulation, the clock genes analyzed to date-frq in Neurospora and per and tim in Drosophila-are associated only with negative feedback and their biochemical functions are largely inferred. The white collar-1 and white collar-2 genes, both global regulators of photoresponses in Neurospora, encode DNA binding proteins that contain PAS domains and are believed to act as transcriptional activators. Data shown here suggest that wc-1 is a clock-associated gene and wc-2 is a clock component; both play essential roles in the assembly or operation of the Neurospora circadian oscillator. Thus DNA binding and transcriptional activation can now be associated with a clock gene that may provide a positive element in the feedback loop. In addition, similarities between the PAS-domain regions of molecules involved in light perception and circadian rhythmicity in several organisms suggest an evolutionary link between ancient photoreceptor proteins and more modern proteins required for circadian oscillation.

Rhythms of Drosophila period gene expression in culture

The Drosophila clock genes period (per) and timeless (tim) have been studied behaviorally and biochemically, but to date there has been no viable culture system for studying the cell biology of the Drosophila clock. We have cultured pupal ring glands attached to the central nervous system and observed rhythms of period gene expression in the prothoracic gland for 4-7 days. A daily rhythm of Per protein can be entrained by light in culture, even when neural activity is blocked by tetrodotoxin. In cultures maintained for a week in constant darkness, a per-luciferase reporter gene revealed circadian rhythms of bioluminescence. As the first circadian culture system from Drosophila, the prothoracic gland provides unique advantages for investigating the interactions between clock genes and cellular physiology.

Genetics and molecular analysis of circadian rhythms

The first part of this review summarizes the two best understood aspects of the two best understood circadian systems, the feedback oscillators of Neurospora and Drosophila, concentrating on what we know about the frequency (frq), period (per) and timeless (tim) genes. In the second part, the general circadian genetic and molecular literature is surveyed, with an eye to describing what is known from a variety of systems about input to the oscillator (entrainment), and how the oscillator might work and be temperature compensated, in emerging systems including Synechococcus, Gonyaulax, Arabidopsis, hamsters, and mice. Finally, the conversation of the molecular components of clocks is analyzed: both frq and per are widely conserved in their respective phylogenetic classes. Pharmacological data suggests that most other organisms use a day-phased oscillator of the type seen in Neurospora rather than a night-phased oscillator such as in Drosophila.

Circadian clock-controlled genes isolated from Neurospora crassa are late night- to early morning-specific

An endogenous circadian biological clock controls the temporal aspects of life in most organisms, including rhythmic control of genes involved in clock output pathways. In the fungus Neurospora crassa, one pathway known to be under control of the clock is asexual spore (conidia) development. To understand more fully the processes that are regulated by the N. crassa circadian clock, systematic screens were carried out for genes that oscillate at the transcriptional level. Time-of-day-specific cDNA libraries were generated and used in differential screens to identify six new clock-controlled genes (ccgs). Transcripts specific for each of the ccgs preferentially accumulate during the late night to early morning, although they vary with respect to steady-state mRNA levels and amplitude of the rhythm. Sequencing of the ends of the new ccg cDNAs revealed that ccg-12 is identical to N. crassa cmt encoding copper metallothionein, providing the suggestion that not all clock-regulated genes in N. crassa are specifically involved in the development of conidia. This was supported by finding that half of the new ccgs, including cmt(ccg-12), are not transcriptionally induced by developmental or light signals. These data suggest a major role for the clock in the regulation of biological processes distinct from development.

Regulation of the Drosophila protein timeless suggests a mechanism for resetting the circadian clock by light

Circadian behavioral rhythms in Drosophila depend on the appropriate regulation of at least two genes, period (per) and timeless (tim). Previous studies demonstrated that levels of PER and TIM RNA cycle with the same phase and that the PER and TIM proteins interact directly. Here we show the cyclic expression of TIM protein in adult heads and report that it lags behind peak levels of TIM RNA by several hours. We alsoshow that nuclear expression of TIM depends upon the expression of PER protein. Finally, we report that the expression of TIM, but not PER, is rapidly reduced by light, suggesting that TIM mediates light-induced resetting of the circadian clock. Since both PER and TIM RNA are unaffected by light treatment, the effects of light on TIM appear to be posttranscriptional.

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.