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Biomedical subjects

I Edery

Publications and source records attributed to I Edery.

At least 19 recordsLinked to original sources

Circadian rhythms in a nutshell.

Living organisms on this planet have adapted to the daily rotation of the earth on its axis. By means of endogenous circadian clocks that can be synchronized to the daily and seasonal changes in external time cues, most notably light and temperature, life forms anticipate environmental transitions, perform activities at biologically advantageous times during the day, and undergo characteristic seasonal responses. The effects of transmeridian flight and shift work are stark reminders that although modern technologies can create "cities that never sleep" we cannot escape the recalcitrance of endogenous clocks that regulate much of our physiology and behavior. Moreover, malfunctions in the human circadian timing system are implicated in several disorders, including chronic sleep disorders in the elderly, manic-depression, and seasonal affective disorders (SAD or winter depression). Recent progress in understanding the molecular mechanisms underlying circadian rhythms has been remarkable. In its most basic form, circadian clocks are comprised of a set of proteins that, by virtue of the design principles involved, generate a self-sustaining transcriptional-translational feedback loop with a free-running period of about 24 h. One or more of the clock components is acutely sensitive to light, resulting in an oscillator that can be synchronized to local time. This review provides an overview of the roles circadian clocks play in nature, how they might have arisen, human health concerns related to clock dysfunction, and mainly focuses on the clockworks found in Drosophila and mice, the two best studied animal model systems for understanding the biochemical and cellular bases of circadian rhythms.

Animals↗

dCLOCK is present in limiting amounts and likely mediates daily interactions between the dCLOCK-CYC transcription factor and the PER-TIM complex.

In Drosophila melanogaster four circadian clock proteins termed PERIOD (PER), TIMELESS (TIM), dCLOCK (dCLK), and CYCLE (CYC/dBMAL1) function in a transcriptional feedback loop that is a core element of the oscillator mechanism. dCLK and CYC are members of the basic helix-loop-helix (bHLH)/PAS (PER-ARNT-SIM) superfamily of transcription factors and are required for high-level expression of per and tim and repression of dClk, whereas PER and TIM inhibit dCLK-CYC-mediated transcription and lead to the activation of dClk. To understand further the dynamic regulation within the circadian oscillator mechanism, we biochemically characterized in vivo-produced CYC, determined the interactions of the four clock proteins, and calculated their absolute levels as a function of time. Our results indicate that throughout a daily cycle the majority of the dCLK present in adult heads stably interacts with CYC, indicating that CYC is the primary in vivo partner of dCLK. dCLK-CYC dimers are bound by PER and TIM during the late evening and early morning, suggesting the formation of a tetrameric complex with impaired transcriptional activity. Although dCLK is present in limiting amounts and CYC is by far the most abundant of the four clock proteins that have been examined, PER and TIM appear to interact preferentially with dCLK. Our results suggest that dCLK is the main component regulating the daily abundance of transcriptionally active dCLK-CYC complexes.

ARNTL Transcription Factors↗

How a circadian clock adapts to seasonal decreases in temperature and day length.

We show that a thermosensitive splicing event in the 3' untranslated region of the mRNA from the period (per) gene plays an important role in how a circadian clock in Drosophila adapts to seasonally cold days (low temperatures and short day lengths). The enhanced splicing of this intron at low temperatures advances the steady state phases of the per mRNA and protein cycles, events that significantly contribute to the preferential daytime activity of flies on cold days. Because the accumulation of PER is also dependent on the photosensitive TIMELESS (TIM) protein, long photoperiods partially counteract the cold-induced advances in the oscillatory mechanism by delaying the daily increases in the levels of TIM. Our findings also indicate that there is a temperature-dependent switch in the molecular logic governing cycles in per mRNA levels.

Adaptation, Physiological↗

PER and TIM inhibit the DNA binding activity of a Drosophila CLOCK-CYC/dBMAL1 heterodimer without disrupting formation of the heterodimer: a basis for circadian transcription.

The Drosophila CLOCK (dCLOCK) and CYCLE (CYC) (also referred to as dBMAL1) proteins are members of the basic helix-loop-helix PAS (PER-ARNT-SIM) superfamily of transcription factors and are required for high-level expression of the circadian clock genes period (per) and timeless (tim). Several lines of evidence indicate that PER, TIM, or a PER-TIM heterodimer somehow inhibit the transcriptional activity of a putative dCLOCK-CYC complex, generating a negative-feedback loop that is a core element of the Drosophila circadian oscillator. In this report we show that PER and/or TIM inhibits the binding of a dCLOCK-CYC heterodimer to an E-box-containing DNA fragment that is present in the 5' nontranscribed region of per and acts as a circadian enhancer element. Surprisingly, inhibition of this DNA binding activity by PER, TIM, or both is not accompanied by disruption of the association between dCLOCK and CYC. The results suggest that the interaction of PER, TIM, or both with the dCLOCK-CYC heterodimer induces a conformational change or masks protein regions in the heterodimer, leading to a reduction in DNA binding activity. Together with other findings, our results strongly suggest that daily cycles in the association of PER and TIM with the dCLOCK-CYC complex probably contribute to rhythmic expression of per and tim.

ARNTL Transcription Factors↗

Role of posttranscriptional regulation in circadian clocks: lessons from Drosophila.

Incredible progress has been made in the last few years in our understanding of the molecular mechanisms underlying circadian clocks. Many of the recent insights have been gained by the isolation and characterization of novel clock mutants and their associated gene products. As might be expected based on theoretical considerations and earlier studies that indicated the importance of temporally regulated macromolecular synthesis for the manifestation of overt rhythms, daily oscillations in the levels of "clock" RNAs and proteins are a pervasive feature of these timekeeping devices. How are these molecular rhythms generated and synchronized? Recent evidence accumulated from a wide variety of model organisms, ranging from bacteria to mammals, points toward an emerging trend; at the "heart" of circadian oscillators lies a cell autonomous transcriptional feedback loop that is composed of alternatively functioning positive and negative elements. Nonetheless, it is also clear that to bring this transcriptional feedback loop to "life" requires important contributions from posttranscriptional regulatory schemes. For one thing, there must be times in the day when the activities of negative-feedback regulators are separated from the activities of the positive regulators they act on, or else the oscillatory potential of the system will be dissipated, resulting in a collection of molecules at steady state. This review mainly summarizes the role of posttranscriptional regulation in the Drosophila melanogaster time-keeping mechanism. Accumulating evidence from Drosophila and other systems suggests that posttranscriptional regulatory mechanisms increase the dynamic range of circadian transcriptional feedback loops, overlaying them with appropriately timed biochemical constraints that not only engender these loops with precise daily periods of about 24 h, but also with the ability to integrate and respond rapidly to multiple environmental cues such that their phases are aligned optimally to the prevailing external conditions.

Animals↗

Heat-induced degradation of PER and TIM in Drosophila bearing a conditional allele of the heat shock transcription factor gene.

Heat pulses elicit dramatic and rapid decreases in the levels of the D. melanogaster period (per) and timeless (tim) proteins (i.e., PER and TIM). To investigate the possible role of the heat shock pathway in this response, we used Drosophila bearing a conditional allele of the hsf gene (termed hsf4), which encodes the heat shock transcription factor (HSF). At all times in a daily cycle, heat-induced decreases in the levels of PER and TIM were similar in wild-type and hsf4 mutant flies. The results strongly suggest that the heat shock pathway contributes little, if any, to the response of the Drosophila circadian clock to heat signals.

Alleles↗

The Drosophila CLOCK protein undergoes daily rhythms in abundance, phosphorylation, and interactions with the PER-TIM complex.

We report the in vivo characterization of the Drosophila CLOCK protein (dCLOCK), a transcription factor that is required for the expression of the circadian clock genes period (per) and timeless (tim). dCLOCK undergoes circadian fluctuations in abundance, is phosphorylated throughout a daily cycle, and interacts with PER, TIM, and/or the PER-TIM complex during the night but not during most of the day. Our results suggest that PER and TIM participate in transcriptional autoinhibition by physically interacting with dCLOCK or a dCLOCK-containing complex. Nevertheless, in the absence of PER or TIM, the levels of dCLOCK are constitutively low, indicating that PER and TIM also act as positive elements in the feedback loop by stimulating the production of dCLOCK.

Animals↗

Circadian regulation of a Drosophila homolog of the mammalian Clock gene: PER and TIM function as positive regulators.

The Clock gene plays an essential role in the manifestation of circadian rhythms (approximately 24 h) in mice and is a member of the basic helix-loop-helix (bHLH) PER-ARNT-SIM (PAS) superfamily of transcription factors. Here we report the characterization of a novel Drosophila bHLH-PAS protein that is highly homologous to mammalian CLOCK. (Similar findings were recently described by Allada et al. Cell 93:791-804, 1998, and Darlington et al., Science 280:1599-1603, 1998.) Transcripts from this putative Clock ortholog (designated dClock) undergo daily rhythms in abundance that are antiphase to the cycling observed for the RNA products from the Drosophila melanogaster circadian clock genes period (per) and timeless (tim). Furthermore, dClock RNA cycling is abolished and the levels are at trough values in the absence of either PER or TIM, suggesting that these two proteins can function as transcriptional activators, a possibility which is in stark contrast to their previously characterized role in transcriptional autoinhibition. Finally, the temporal regulation of dClock expression is quickly perturbed by shifts in light-dark cycles, indicating that this molecular rhythm is closely connected to the photic entrainment pathway. The isolation of a Drosophila homolog of Clock together with the recent discovery of mammalian homologs of per indicate that there is high structural conservation in the integral components underlying circadian oscillators in Drosophila and mammals. Nevertheless, because mammalian Clock mRNA is constitutively expressed, our findings are a further example of striking differences in the regulation of putative circadian clock orthologs in different species.

Amino Acid Sequence↗

Differential effects of light and heat on the Drosophila circadian clock proteins PER and TIM.

Circadian (approximately 24-h) rhythms are governed by endogenous biochemical oscillators (clocks) that in a wide variety of organisms can be phase shifted (i.e., delayed or advanced) by brief exposure to light and changes in temperature. However, how changes in temperature reset circadian timekeeping mechanisms is not known. To begin to address this issue, we measured the effects of short-duration heat pulses on the protein and mRNA products from the Drosophila circadian clock genes period (per) and timeless (tim). Heat pulses at all times in a daily cycle elicited dramatic and rapid decreases in the levels of PER and TIM proteins. PER is sensitive to heat but not light, indicating that individual clock components can markedly differ in sensitivity to environmental stimuli. A similar resetting mechanism involving delays in the per-tim transcriptional-translational feedback loop likely underlies the observation that when heat and light signals are administered in the early night, they both evoke phase delays in behavioral rhythms. However, whereas previous studies showed that the light-induced degradation of TIM in the late night is accompanied by stable phase advances in the temporal regulation of the PER and TIM biochemical rhythms, the heat-induced degradation of PER and TIM at these times in a daily cycle results in little, if any, long-term perturbation in the cycles of these clock proteins. Rather, the initial heat-induced degradation of PER and TIM in the late night is followed by a transient and rapid increase in the speed of the PER-TIM temporal program. The net effect of these heat-induced changes results in an oscillatory mechanism with a steady-state phase similar to that of the unperturbed control situation. These findings can account for the lack of apparent steady-state shifts in Drosophila behavioral rhythms by heat pulses applied in the late night and strongly suggest that stimulus-induced changes in the speed of circadian clocks can contribute to phase-shifting responses.

Animals↗

Drosophila melanogaster deficient in protein kinase A manifests behavior-specific arrhythmia but normal clock function.

Drosophila melanogaster bearing mutations in the DCO gene, which encodes the major catalytic subunit of cAMP-dependent protein kinase (PKA), displays arrhythmic locomotor activity strongly suggesting a role for PKA in the circadian timing system. This arrhythmicity might result from a requirement for PKA activity in photic resetting pathways, the timekeeping mechanism itself, or downstream effector pathways controlling overt behavioral rhythms. To address these possibilities, we examined the protein and mRNA products from the clock gene period (per) in PKA-deficient flies. The per protein (PER) and mRNA products undergo daily cycles in the heads and bodies of DCO mutants that are indistinguishable from those observed in control wild-type flies. These results indicate that PKA deficiencies affect the proper functioning of elements downstream of the Drosophila timekeeping mechanism. The requirement for PKA in the manifestation of rhythmic activity was preferentially greater in the absence of environmental cycles. However, PKA does not appear to play a universal role in output functions because the clock-controlled eclosion rhythm is normal in DCO mutants. Our results suggest that PKA plays a critical role in the flow of temporal information from circadian pacemaker cells to selective behaviors.

Animals↗

Resetting the Drosophila clock by photic regulation of PER and a PER-TIM complex.

Circadian clocks can be reset by light stimulation. To investigate the mechanism of this phase shifting, the effects of light pulses on the protein and messenger RNA products of the Drosophila clock gene period (per) were measured. Photic stimuli perturbed the timing of the PER protein and messenger RNA cycles in a manner consistent with the direction and magnitude of the phase shift. In addition, the recently identified clock protein TIM (for timeless) interacted with PER in vivo, and this association was rapidly decreased by light. This disruption of the PER-TIM complex in the cytoplasm was accompanied by a delay in PER phosphorylation and nuclear entry and disruption in the nucleus by an advance in PER phosphorylation and disappearance. These results suggest a mechanism for how a unidirectional environmental signal elicits a bidirectional clock response.

Animals↗

An efficient strategy to isolate full-length cDNAs based on an mRNA cap retention procedure (CAPture).

The ability to generate cDNA libraries is one of the most fundamental procedures in contemporary molecular biology. One of the major drawbacks of current methods is that most cDNAs present in any given library are incomplete, rendering the characterization of genes an inefficient and time-consuming task. We have developed an affinity selection procedure using a fusion protein containing the murine cap-binding protein (eukaryotic initiation factor 4E), coupled to a solid support matrix, that allows for the purification of mRNAs via the 5' cap structure. When combined with a single-strand-specific RNase digestion step, specific retention of complete cDNA-RNA duplexes following first-strand synthesis is achieved. This method can be used to generate cDNA libraries in which polyadenylated and nonpolyadenylated mRNAs are equally represented and to enrich for full-length or 5'-end clones, thus facilitating cDNA cloning and promoter mapping.

Amino Acid Sequence↗

Temporal phosphorylation of the Drosophila period protein.

The period gene (per) is required for Drosophila melanogaster to manifest circadian (congruent to 24 hr) rhythms. We report here that per protein (PER) undergoes daily oscillations in apparent molecular mass as well as abundance. The mobility changes are largely or exclusively due to multiple phosphorylation events. The temporal profile of the classic short-period form of PER (PERS) is altered in a manner consistent with the mutant strain's behavioral phenotype. As changes in abundance and phosphorylation persist under constant environmental conditions, they reflect or contribute to a free-running rhythm. We suggest that the phosphorylation status of PER is an important determinant in the Drosophila clock's time-keeping mechanism.

Animals↗

Phase shifting of the circadian clock by induction of the Drosophila period protein.

Virtually all organisms manifest circadian (24-hour) rhythms, governed by an ill-defined endogenous pacemaker or clock. Several lines of evidence suggest that the Drosophila melanogaster period gene product PER is a clock component. If PER were central to the time-keeping mechanism, a transient increase in its concentration would cause a stable shift in the phase of the clock. Therefore, transgenic flies bearing a heat-inducible copy of PER were subjected to temperature pulses. This treatment caused long-lasting phase shifts in the locomotor activity circadian rhythm, a result that supports the contention that PER is a bona fide clock component.

Animals↗

PAS is a dimerization domain common to Drosophila period and several transcription factors.

Mutations in the period gene product (PER) can shorten or lengthen the circadian rhythms of Drosophila melanogaster, but its biochemical activity has not been established. PER contains a motif of approximately 270 amino acids whose function is unknown (termed PAS) and which is also present in three transcription factors of the basic-helix-loop-helix (bHLH) type, in the D. melanogaster single-minded gene product (SIM), and in both subunits of the mammalian dioxin receptor complex. We show here that the PER PAS functions in vitro as a novel protein dimerization motif and that it can mediate associations between different members of the PAS protein family. The dimerization efficiency is decreased by several missense mutations in the PAS domain, including the original perL mutation, which lengthens circadian periods from 24 h to 29 h (ref. 1). The results indicate that the PAS domain may function as a dimerization domain in both SIM and the dioxin receptor complex, and that PER may regulate circadian gene transcription partly by interacting with the PAS domain of bHLH--PAS-containing transcription factors.

Amino Acid Sequence↗

The analysis of new short-period circadian rhythm mutants suggests features of D. melanogaster period gene function.

A number of new period gene (per) mutants were generated by in vitro mutagenesis and germ line transformation. Missense mutations were made at amino acid 589, which is altered in the 19 h short-period (per(s)) mutant, and insertion mutations were generated with peptides commonly used for epitope tagging. Most of these new per mutants had short behavioral rhythms. Flies with heteroallelic combinations of these new mutant per genes were found to have "hybrid" periods, i.e., they had values that were usually in between those of the individual alleles. These findings suggest that short-period per mutants are not unusual gain-of-function mutants but rather more traditional loss-of-function mutants that are unable to influence the circadian pacemaker in a proper manner. The data also suggest that the per protein may engage in important intermolecular interactions.

Animals↗

Multiple mRNAs encode the murine translation initiation factor eIF-4E.

All eukaryotic cellular mRNAs (except organellar) possess at their 5' end the structure m7GpppX (where X is any nucleotide) termed the "cap." The cap structure facilitates the melting of mRNA 5' secondary structure through the action of initiation factor-4F (eIF-4F) in conjunction with eIF-4B. eIF-4F consists of three subunits of which one, eIF-4E (eIF-4E has recently been designated eIF-4 alpha according to the Nomenclature Committee of the International Union of Biochemistry (NC-IUB) (Safer, B. (1989) Eur. J. Biochem. 186, 1-3)), contains the cap binding site. Several lines of evidence suggest that eIF-4E regulates the rate of translation initiation. Consequently, changes in cellular eIF-4E levels could control growth and differentiation. To investigate the possibility that eIF-4E expression is regulated, we studied the pattern of eIF-4E expression in several cell lines. Here, we show the existence of multiple mRNAs for eIF-4E that are generated by differential polyadenylation. In addition, we show tissue-specific differences in eIF-4E mRNA expression and utilization of polyadenylation sites.

Animals↗

Control of the interferon-induced 68-kilodalton protein kinase by the HIV-1 tat gene product.

The tat-responsive region (TAR) of the human immunodeficiency virus-1 (HIV-1) exhibits a trans-inhibitory effect on translation in vitro by activating the interferon-induced 68-kilodalton protein kinase (p68 kinase). Productive infection by HIV-1 was shown to result in a significant decrease in the amount of cellular p68 kinase. The steady-state amount of p68 kinase was also reduced in interferon-treated HeLa cell lines stably expressing tat, as compared to the amount of the kinase in interferon-treated control HeLa cells. Thus, the potential translational inhibitory effects of the TAR RNA region mediated by activation of p68 kinase may be downregulated by tat during productive HIV-1 infection.

2',5'-Oligoadenylate Synthetase↗