SEARCH · PubMed Health

Results for “CLOCK Proteins”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources

PubMed2001

Identification of a calcium/calmodulin-dependent protein kinase that phosphorylates the Neurospora circadian clock protein FREQUENCY.

Phosphorylation of circadian clock proteins represents a major regulatory step that controls circadian clocks. In Neurospora, the circadian clock protein FREQUENCY (FRQ) is progressively phosphorylated over time, and its level decreases when it is hyperphosphorylated. In this study, we showed that most of the kinase activity phosphorylating FRQ in vitro was calcium/calmodulin-dependent, and the endogenous FRQ in the Neurospora extracts was phosphorylated by a Ca/CaM-dependent kinase-like activity. From Neurospora cell extracts, an approximately 50-kDa Ca/CaM-dependent kinase (CAMK-1) that can specifically phosphorylate FRQ was purified. In vitro, this kinase accounts for near half of the FRQ kinase activity, and it can phosphorylate the FRQ region that contains the three known functionally important phosphorylation sites. To understand the function of camk-1 in vivo, it was disrupted in Neurospora by gene replacement. After germination from ascospores, the camk-1 null strains grew slowly, indicating that CAMK-1 plays an important role in growth and development of Neurospora. This phenotype was transient however, revealing redundancy in the system. Analysis of the camk-1 null strain revealed that the deletion of camk-1 affected phase, period, and light-induced phase shifting of the circadian conidiation rhythm. Taken together, our results suggest that multiple kinases may phosphorylate FRQ in vivo.

Amino Acid Sequence↗

PubMed2006

Hexamerization by the N-terminal domain and intersubunit phosphorylation by the C-terminal domain of cyanobacterial circadian clock protein KaiC.

Cyanobacterial clock protein KaiC has a hexagonal, pot-shaped structure composed of six identical dumbbell-shaped subunits. The opposing spherical regions of the dumbbell-shaped structures correspond to the N-terminal and C-terminal domains of KaiC. Previously, we hypothesized that the N-terminal domain of KaiC is responsible for the ATP-induced hexamerization of KaiC while the C-terminal domain is responsible for the phosphorylation of KaiC (Hayashi et al. 2004, J. Biol. Chem. 279, 52331-52337). Here, we tested that hypothesis using the purified protein of each domain. We prepared N-terminal and C-terminal domain proteins (KaiCN and KaiCC, respectively), examined their function by analyzing their ATP- or 5'-adenylylimidodiphosphate (AMPPNP; an unhydrolyzable ATP analog)-induced hexamerization, interactions with KaiA, and phosphorylation, and we demonstrated the following: (1) KaiCN had higher ATP- or AMPPNP-induced oligomerization activity than KaiCC. (2) KaiCc had phosphorylation activity as KaiCWT whereas KaiCN had no activity. (3) KaiCC interacted with KaiA whereas KaiCN did not. (4) The interactions of KaiCC with KaiA did not require that KaiC has a hexamer structure. (5) The interactions of KaiCC with KaiA enhanced the phosphorylation of KaiCC. Furthermore, we presented evidence for the intersubunit phosphorylation of KaiC. KaiCCatE2-, which lacks KaiC phosphorylation activity due to mutations of the catalytic Glu residues, was phosphorylated when it was co-incubated with KaiCC. We propose that the KaiC hexamer consists of a rigid ring structure formed by six N-terminal domains with hexamerization activity and a flexible structure formed by six C-terminal domains with intersubunit phosphorylation activity.

Amino Acid Sequence↗

PubMed2003

Fine distribution of CLOCK protein in hepatocytes of hibernating dormice.

CLOCK protein is a member of the bHLH-PAS family of transcription factors, it is expressed in several tissues including the liver and is essential for normal circadian rhythms. In this study we investigate the distribution of CLOCK protein in hepatocytes of euthermic and hibernating edible dormice Glis glis as well as in hepatocytes taken from the hibernating animals submitted in vitro to experimental conditions mimicking the arousal process. Our results demonstrate that CLOCK protein is expressed in all animals and is mostly located in the nucleus, in particular, on perichromatin fibrils and nucleoli. During deep hibernation CLOCK protein becomes more abundant but an intracellular redistribution occurs: the protein significantly decreases in all cellular compartments, but it accumulates in the amorphous bodies. These nuclear bodies, typical of the hibernating state, probably represent storage sites for CLOCK protein to be quickly used upon arousal. Accordingly, in hepatocytes submitted to in vitro conditions mimicking arousal CLOCK protein levels rapidly reach the euthermic values, while amorphous bodies disappear.

Animals↗

PubMed2004

Roles of two ATPase-motif-containing domains in cyanobacterial circadian clock protein KaiC.

Cyanobacterial clock protein KaiC has a hexagonal, pot-shaped structure composed of six identical dumbbell-shaped subunits. Each subunit has duplicated domains, and each domain has a set of ATPase motifs. The two spherical regions of the dumbbell are likely to correspond to two domains. We examined the role of the two sets of ATPase motifs by analyzing the in vitro activity of ATPgammaS binding, AMPPNP-induced hexamerization, thermostability, and phosphorylation of KaiC and by in vivo rhythm assays both in wild type KaiC (KaiCWT) and KaiCs carrying mutations in either Walker motif A or deduced catalytic Glu residues. We demonstrated that 1) the KaiC subunit had two types of ATP-binding sites, a high affinity site in N-terminal ATPase motifs and a low affinity site in C-terminal ATPase motifs, 2) the N-terminal motifs were responsible for hexamerization, and 3) the C-terminal motifs were responsible for both stabilization and phosphorylation of the KaiC hexamer. We proposed the following reaction mechanism. ATP preferentially binds to the N-terminal high affinity site, inducing the hexamerization of KaiC. Additional ATP then binds to the C-terminal low affinity site, stabilizing and phosphorylating the hexamer. We discussed the effect of these KaiC mutations on circadian bioluminescence rhythm in cells of cyanobacteria.

Adenosine Triphosphatases↗

PubMed2003

Non-cyclic and developmental stage-specific expression of circadian clock proteins during murine spermatogenesis.

The central circadian clock in mammals is housed in the brain and is based on cyclic transcription and translation of clock proteins. How the central clock regulates peripheral organ function is unclear. However, cyclic expression of circadian genes in peripheral tissues is well established, suggesting that these tissues have their own endogenous oscillators. Reproduction is a process influenced by circadian rhythms in many organisms, thus making the testis an attractive model for studying clock function in peripheral organs. However, results addressing cyclic expression of clock genes in the mammalian testis are inconsistent. To resolve this issue, RNA was extracted from testes of mice at various times of day. Expression of the circadian clock genes mPer1, mPer2, Bmal1, Clock, mCry1, and Npas2 was constant at all times. Immunohistochemical localization of mPER1 and CLOCK proteins revealed restricted expression only in cells at specific developmental stages of spermatogenesis. For mPER1, these stages are the spermatogonia and the condensing spermatids. In contrast, CLOCK expression was restricted to round spermatids, specifically within the developing acrosome. Expression of mPER1 and CLOCK was constant at all times of day. These results suggest that clock proteins have noncircadian functions in spermatogenesis. Noncircadian expression of clock genes was also found in the thymus, which, like the testis, is composed primarily of differentiating cells. We propose that cyclic expression of clock genes is suspended during cellular differentiation.

Acrosome↗

PubMed2003

Immunocytochemical analysis of the circadian clock protein in mouse hepatocytes.

Many biochemical, physiological, and behavioral processes in organisms ranging from prokaryotes to humans exhibit circadian rhythms, defined as cyclic oscillations of about 24 hours. The mechanism of the cellular circadian clock relies on interlocking positive and negative transcriptional/translational feedback loops based on the regulated expression of several genes. Clock is one of these genes and its transcript, CLOCK protein, is a transcription factor belonging to the bHLH-PAS family. In mammals the clock gene is expressed in several tissues, including the liver. In the present study, we analyzed by means of quali-quantitative immunoelectron microscopy the fine intracellular distribution of the CLOCK protein in mouse hepatocytes during the daily cycle. We demonstrated that CLOCK protein is mostly located in the cell nucleus, where it accumulates on perichromatin fibrils, representing the in situ form of nascent pre-mRNA, while condensed chromatin and nucleoli contain lower amounts of protein. Moreover, we found that CLOCK protein shows circadian oscillations in these nuclear compartments, peaking in late afternoon. At this time the hepatic transcriptional rate reaches the maximal level, thus suggesting an important role of CLOCK protein in the regulation of liver gene expression.

Animals↗

PubMed2006

Predicting regulation of the phosphorylation cycle of KaiC clock protein using mathematical analysis.

Abstract The cyanobacterial clock protein KaiC regulates the circadian cycle by exhibiting rhythms in transcription, translation, and phosphorylation. KaiC phosphorylation persists in circadian cycling even under transcription-less conditions and was reconstituted in vitro by incubating KaiC, KaiA, and KaiB. This presents a novel perspective for circadian oscillation occurring due to interactions between clock proteins. Using mathematical models, the authors investigated the mechanism for the transcription-less KaiC phosphorylation cycle. They developed a simple model based on the possible KaiC behavior, which is experimentally suggested by Kitayama et al. (2003, EMBO J, 22:2127-2134). They hypothesized that the KaiC-KaiA complex formation, followed by a decrease in free KaiA molecules, may attenuate the KaiC phosphorylation rate, and it acts as negative feedback in the system. However, this model was shown not to be adequate to generate the KaiC phosphorylation cycle. The authors developed the general version of the model and determined the necessary condition to generate the KaiC phosphorylation cycle. Linear stability analysis revealed that oscillations can occur when the distance of feedback between the recipient reaction and the effector is far enough. Furthermore, they classified negative feedback regulations in the closed system into 2 types: destabilizing inhibition and stabilizing inhibition. Based on this result, the authors predicted that, in addition to the identified states of KaiC, another unknown state must be present between KaiC phosphorylation and the complex formation. By incorporating the unknown state into the previous model, they realized the periodic pattern reminiscent of the KaiC phosphorylation cycle in computer simulation. This result implies that the KaiC-KaiA complex formation requires more than 1 step of posttranslational modification, including phosphorylation or conformational change of KaiC.

Algorithms↗

PubMed2002

The F-box protein slimb controls the levels of clock proteins period and timeless.

The Drosophila circadian clock is driven by daily fluctuations of the proteins Period and Timeless, which associate in a complex and negatively regulate the transcription of their own genes. Protein phosphorylation has a central role in this feedback loop, by controlling Per stability in both cytoplasmic and nuclear compartments as well as Per/Tim nuclear transfer. However, the pathways regulating degradation of phosphorylated Per and Tim are unknown. Here we show that the product of the slimb (slmb) gene--a member of the F-box/WD40 protein family of the ubiquitin ligase SCF complex that targets phosphorylated proteins for degradation--is an essential component of the Drosophila circadian clock. slmb mutants are behaviourally arrhythmic, and can be rescued by targeted expression of Slmb in the clock neurons. In constant darkness, highly phosphorylated forms of the Per and Tim proteins are constitutively present in the mutants, indicating that the control of their cyclic degradation is impaired. Because levels of Per and Tim oscillate in slmb mutants maintained in light:dark conditions, light- and clock-controlled degradation of Per and Tim do not rely on the same mechanisms.

Amino Acid Motifs↗

PubMed2005

Aging affects the distribution of the circadian CLOCK protein in rat hepatocytes.

Several biochemical, physiological, and behavioral processes exhibit cyclic oscillations of about 24 h, which have been defined as circadian rhythms. In mammals, the primary circadian pacemaker resides in the suprachiasmatic nuclei; however, cell-autonomous circadian oscillators occur also in extraneural tissues, including the liver. CLOCK protein is a transcription factor essential for normal circadian rhythms and recent studies have demonstrated that it undergoes intranuclear redistribution in hepatocytes, along the daily cycle. It is known that aging leads to a progressive deterioration of the circadian rhythm at the behavioral, physiological, and cellular levels; in addition, aging affects the organization of nuclear structural components involved in transcription and splicing. In this view, we carried out ultrastructural immunocytochemical analyses on hepatocytes of adult and old rats, so as to investigate possible qualitative and quantitative modifications of CLOCK protein, in relation to the aging process. Our observations demonstrated that most CLOCK protein was always located in the cell nucleus, where it accumulated on perichromatin fibrils (the sites of premRNA transcription and early splicing); in addition, CLOCK showed daily oscillations in the different nuclear compartments, but these oscillations differed significantly between adult and old animals. This unusual distribution of CLOCK protein during aging could be related to the prolonged diurnal activity of old animals and/or to altered nuclear pathways.

Aging↗

PubMed1999

A bioluminescence resonance energy transfer (BRET) system: application to interacting circadian clock proteins.

We describe a method for assaying protein interactions that offers some attractive advantages over previous assays. This method, called bioluminescence resonance energy transfer (BRET), uses a bioluminescent luciferase that is genetically fused to one candidate protein, and a green fluorescent protein mutant fused to another protein of interest. Interactions between the two fusion proteins can bring the luciferase and green fluorescent protein close enough for resonance energy transfer to occur, thus changing the color of the bioluminescent emission. By using proteins encoded by circadian (daily) clock genes from cyanobacteria, we use the BRET technique to demonstrate that the clock protein KaiB interacts to form homodimers. BRET should be particularly useful for testing protein interactions within native cells, especially with integral membrane proteins or proteins targeted to specific organelles.

Bacterial Proteins↗

PubMed2005

Nucleocytoplasmic shuttling of clock proteins.

The mammalian circadian clock in the neurons of suprachiasmatic nuclei (SCN) in the brain and in cells of peripheral tissues is driven by a self-sustained molecular oscillator, which generates rhythmic gene expression with a periodicity of about 24?h (Reppert and Weaver, 2002). This molecular oscillator is composed of interacting positive and negative transcription/translation feedback loops in which the heterodimeric transcription activator CLOCK?BMAL1 promotes the transcription of E-box containing Cryptochrome (Cry1 and Cry2) and Period (Per1 and Per2) genes, as well as clock-controlled output genes. After being synthesized in the cytoplasm, CRY and PER proteins feedback in the nucleus to inhibit the transactivation mediated by positive regulators. The mPER2 protein acts at the interphase between positive and negative feedback loops by indirectly promoting the circadian transcription of the Bmal1 gene (through RevErbalpha) (Preitner et al., 2002; Shearman et al., 2000) and by interacting with mCRY proteins (Kume et al., 1999; Yagita et al., 2002) (for a detailed review, see Reppert and Weaver, 2002). In addition to cyclic transcription of clock genes, immunohistochemical studies on SCN neurons have revealed that mCRY1, mCRY2, mPER1, and mPER2 proteins undergo near synchronous circadian patterns of nuclear abundance (Field et al., 2000). The delay of approximately 6h between the peak in clock mRNA production and maximal levels of protein expression in the nucleus is believed to originate from posttranslational modification steps involving phosphorylation, ubiquitination, and proteosomal degradation. Thus, the timing of entry, as well as the residence time of core clock proteins into the nucleus, is a critical step in maintaining the correct pace of the circadian clock. Several clock proteins have been shown to contain nuclear export signal, sequences, on top of nuclear import signals, that facilitate their cellular trafficking (Chopin-Delannoy et al., 2003; Miyazaki et al., 2001; Yagita et al., 2002). This type of dynamic intracellular movement not only regulates protein localization, but also often affects functions by determining interactive partners and protein turnover. Because most of the clock genes have been identified by genetic screening in Drosophila and by gene knockdown in mammals, the development of innovative cellular techniques is essential in learning the structure-function and regulation of the corresponding proteins. This article discusses approaches, limitations, and applicable protocols to study the regulation of cellular localization of mammalian clock proteins, with a particular focus on mammalian CRY1 and PER2 proteins.

Animals↗

PubMed2006

The circadian protein Clock localizes to the sarcomeric Z-disk and is a sensor of myofilament cross-bridge activity in cardiac myocytes.

In the mammalian heart, the circadian protein Clock regulates glucose and fatty acid metabolism. In this study, we determined some of the factors that regulate Clock expression and subcellular distribution in myocytes. Using immunochemistry and biochemical subcellular fractionation, we have shown that Clock localizes to the Z-disk of the myofilaments. Increasing calcium and cross-bridge cycling with 10 microM phenylephrine for 48 h resulted in a threefold increase in Clock and a translocation of the protein to the nucleus. When myofilament cross-bridge cycling was inhibited with 10 microM verapamil or 7.5mM butanedione monoxime for 48 h, both significantly reduced the presence of Clock in the nucleus and cytoskeleton. These results suggest that the expression and subcellular distribution of Clock can be altered by changes in cross-bridge cycling, a major source of energy expenditure in myocytes. We suggest that the circadian Clock protein may help coordinate the sensing of energy expenditure with energy supply.

Actin Cytoskeleton↗

PubMed2000

Circadian clock-protein expression in cyanobacteria: rhythms and phase setting.

The cyanobacterial gene cluster kaiABC encodes three essential circadian clock proteins: KaiA, KaiB and KaiC. The KaiB and KaiC protein levels are robustly rhythmical, whereas the KaiA protein abundance undergoes little if any circadian oscillation in constant light. The level of the KaiC protein is crucial for correct functioning of the clock because induction of the protein at phases when the protein level is normally low elicits phase resetting. Titration of the effects of the inducer upon phase resetting versus KaiC level shows a direct correlation between induction of the KaiC protein within the physiological range and significant phase shifting. The protein synthesis inhibitor chloramphenicol prevents the induction of KaiC and blocks phase shifting. When the metabolism is repressed by either translational inhibition or constant darkness, the rhythm of KaiC abundance persists; therefore, clock protein expression has a preferred status under a variety of conditions. These data indicate that rhythmic expression of KaiC appears to be a crucial component of clock precession in cyanobacteria.

Bacterial Proteins↗

PubMed2002

Structure and function from the circadian clock protein KaiA of Synechococcus elongatus: a potential clock input mechanism.

In the cyanobacterium Synechococcus elongatus (PCC 7942) the proteins KaiA, KaiB, and KaiC are required for circadian clock function. We deduced a circadian clock function for KaiA from a combination of biochemical and structural data. Both KaiA and its isolated carboxyl-terminal domain (KaiA180C) stimulated KaiC autophosphorylation and facilitated attenuation of KaiC autophosphorylation by KaiB. An amino-terminal domain (KaiA135N) had no function in the autophosphorylation assay. NMR structure determination showed that KaiA135N is a pseudo-receiver domain. We propose that this pseudo-receiver is a timing input-device that regulates KaiA stimulation of KaiC autophosphorylation, which in turn is essential for circadian timekeeping.

Bacterial Proteins↗

PubMed2003

Comparative analysis of avian BMAL1 and CLOCK protein sequences: a search for features associated with owl nocturnal behaviour.

Animals differ widely in the phasing of their daily rhythms with respect to daily environmental rhythms. While birds are predominantly day-active, nocturnal activity is a characteristic feature of the order Strigiformes (owls). To study the evolution of owl night-activity cDNA sequences encoding the circadian core oscillator (CCO) proteins BMAL1 and CLOCK were obtained from barn owl (Tyto alba). The predicted proteins showed high sequence identity with their Galliform homologues (BMAL1: 99%; CLOCK: 95.6%). A computer-predicted chicken BMAL1 casein kinase-1 phosphorylation site is absent from T. alba BMAL1, but also absent from homologues of other six bird species (5 orders) (night-active (n=2), day-active (n=4)) indicating no evolutionary association with night activity. Sequence differences between T. alba and Galliform CLOCK frequently involved serine and threonine residues suggesting potential differences in their phosphorylation. The length of a poly-glutamine string in the CLOCK C-terminus varied between and within 25 species (6 orders) examined, however, no discernible feature distinguishing day and night active species was found. No differences were found between day (n=5) and night (n=7)-active species (12 species, 6 orders) in a region of the PER2 protein implicated in altered rhythm phasing in humans. In conclusion the avian CCO components examined showed strong evolutionary conservation. Molecular evolution associated with owl night-activity may have involved alterations in the CCO relationship with 'output' genes rather than in the molecular structure of the CCO itself.

Amino Acid Sequence↗

PubMed2005

Homeobox-clock protein interaction in zebrafish. A shared mechanism for pineal-specific and circadian gene expression.

In non-mammalian vertebrates, the pineal gland is photoreceptive and contains an intrinsic circadian oscillator that drives rhythmic production and secretion of melatonin. These features require an accurate spatiotemporal expression of an array of specific genes in the pineal gland. Among these is the arylalkylamine N-acetyltransferase, a key enzyme in the melatonin production pathway. In zebrafish, pineal specificity of zfaanat2 is determined by a region designated the pineal-restrictive downstream module (PRDM), which contains three photoreceptor conserved elements (PCEs) and an E-box, elements that are generally associated with photoreceptor-specific and rhythmic expression, respectively. Here, by using in vivo and in vitro approaches, it was found that the PCEs and E-box of the PRDM mediate a synergistic effect of the photoreceptor-specific homeobox OTX5 and rhythmically expressed clock protein heterodimer, BMAL/CLOCK, on zfaanat2 expression. Furthermore, the distance between the PCEs and the E-box was found to be critical for PRDM function, suggesting a possible physical feature of this synergistic interaction. OTX5-BMAL/CLOCK may act through this mechanism to simultaneously control pineal-specific and rhythmic expression of zfaanat2 and possibly also other pineal and retinal genes.

Animals↗

PubMed2002

Circadian formation of clock protein complexes by KaiA, KaiB, KaiC, and SasA in cyanobacteria.

Physical interactions among clock-related proteins KaiA, KaiB, KaiC, and SasA are proposed to be important for circadian function in the cyanobacterium Synechococcus elongatus PCC 7942. Here we show that the Kai proteins and SasA form heteromultimeric protein complexes dynamically in a circadian fashion. KaiC forms protein complexes of approximately 350 and 400-600 kDa during the subjective day and night, respectively, and serves as a core of the circadian protein complexes. This change in the size of the KaiC-containing complex is accompanied by nighttime-specific interaction of KaiA and KaiB with KaiC. In various arrhythmic mutants that lack each functional Kai protein or SasA, circadian rhythms in formation of the clock protein complex are abolished, and the size of the protein complexes is dramatically affected. Thus, circadian-regulated formation of the clock protein complexes is probably a critical process in the generation of circadian rhythm in cyanobacteria.

Bacterial Proteins↗

PubMed2005

Degradation of the Neurospora circadian clock protein FREQUENCY through the ubiquitin-proteasome pathway.

Phosphorylation of the Neurospora circadian clock protein FREQUENCY (FRQ) promotes its degradation through the ubiquitin-proteasome pathway. Ubiquitination of FRQ requires FWD-1 (F-box/WD-40 repeat-containing protein-1), which is the substrate-recruiting subunit of an SCF (SKP/Cullin/F-box)-type ubiquitin ligase. In the fwd-1 mutant strains, FRQ degradation is defective, resulting in the accumulation of hyperphosphorylated FRQ and the loss of the circadian rhythmicities. The CSN (COP9 signalosome) promotes the function of SCF complexes in vivo. But in vitro, deneddylation of cullins by CSN inhibits SCF activity. In Neurospora, the disruption of the csn-2 subunit impairs FRQ degradation and compromises the normal circadian functions. These defects are due to the dramatically reduced levels of FWD-1 in the csn-2 mutant, a result of its rapid degradation. Other components of the SCF(FWD-1) complex, SKP-1 and CUL-1 are also unstable in the mutant. These results establish important roles for SCF(FWD-1) and CSN in the circadian clock of Neurospora and suggest that they are conserved components of the eukaryotic circadian clocks. In addition, these findings resolve the CSN paradox and suggest that the major function of CSN is to maintain the stability of SCF ubiquitin ligases in vivo.

Biological Clocks↗