1
|
Cai YD, Chow GK, Hidalgo S, Liu X, Jackson KC, Vasquez CD, Gao ZY, Lam VH, Tabuloc CA, Zheng H, Zhao C, Chiu JC. Alternative splicing of clock transcript mediates the response of circadian clocks to temperature changes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593646. [PMID: 38766142 PMCID: PMC11100826 DOI: 10.1101/2024.05.10.593646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Circadian clocks respond to temperature changes over the calendar year, allowing organisms to adjust their daily biological rhythms to optimize health and fitness. In Drosophila, seasonal adaptations and temperature compensation are regulated by temperature-sensitive alternative splicing (AS) of period (per) and timeless (tim) genes that encode key transcriptional repressors of clock gene expression. Although clock (clk) gene encodes the critical activator of clock gene expression, AS of its transcripts and its potential role in temperature regulation of clock function have not been explored. We therefore sought to investigate whether clk exhibits AS in response to temperature and the functional changes of the differentially spliced transcripts. We observed that clk transcripts indeed undergo temperature-sensitive AS. Specifically, cold temperature leads to the production of an alternative clk transcript, hereinafter termed clk-cold, which encodes a CLK isoform with an in-frame deletion of four amino acids proximal to the DNA binding domain. Notably, serine 13 (S13), which we found to be a CK1α-dependent phosphorylation site, is among the four amino acids deleted in CLK-cold protein. Using a combination of transgenic fly, tissue culture, and in vitro experiments, we demonstrated that upon phosphorylation at CLK(S13), CLK-DNA interaction is reduced, thus decreasing CLK occupancy at clock gene promoters. This is in agreement with our findings that CLK occupancy at clock genes and transcriptional output are elevated at cold temperature, which can be explained by the higher amounts of CLK-cold isoforms that lack S13 residue. This study provides new insights into the complex collaboration between AS and phospho-regulation in shaping temperature responses of the circadian clock.
Collapse
Affiliation(s)
- Yao D. Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Gary K. Chow
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Sergio Hidalgo
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Xianhui Liu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Kiya C. Jackson
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Cameron D. Vasquez
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Zita Y. Gao
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Vu H. Lam
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Christine A. Tabuloc
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Haiyan Zheng
- Biological Mass Spectrometry Facility, Robert Wood Johnson Medical School and Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Caifeng Zhao
- Biological Mass Spectrometry Facility, Robert Wood Johnson Medical School and Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Joanna C. Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| |
Collapse
|
2
|
Madenli O, Akarsu C, Adigüzel AO, Altuntepe A, Zan R, Deveci EÜ. Synthesis of graphite/rGO-modified fungal hyphae for chromium (VI) bioremediation process. ENVIRONMENTAL TECHNOLOGY 2024; 45:811-826. [PMID: 36152299 DOI: 10.1080/09593330.2022.2128892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Bioremediation is a promising technology that can eliminate the drawbacks of conventional treatment methods in removing harmful toxic metals including chromium(VI). Therefore, in this study, fungal hyphae modified with graphite and reduced graphene oxide were synthesized and assessed for their potential to bioremediate heavy metals for the first time in the literature. The effects of the carbon-based materials on microbial structure were characterized using scanning electron microscopy analysis. Thermogravimetric, RAMAN, X-ray diffraction, and enzymatic analyzes were performed to determine the role of functional groups. In addition, batch adsorption experiments utilizing response surface methodology were conducted to optimize operating parameters such as time (1-11 h), chromium (10-50 mg/L), and graphite/reduced graphene oxide (0.1-1 g/L). The maximum adsorption capacity with the graphene fungal hyphae was determined to be 568 mg.g-1, which is 9.7 times that of the crude fungal hyphae. The Cr(VI) removal for fungal hyphae-graphite and fungal hyphae-reduced graphene oxide biocomposites was 98.25% and 98.49%, respectively. The isothermal and kinetic results perfectly matched the 2nd order pseudo-model and Langmuir model in terms of the nature of the adsorption process. The laboratory scale test results indicate that fungal hyphae modified with graphite and reduced graphene oxide have a high adsorption capacity, suitable for the removal of chromium (VI) from wastewater.
Collapse
Affiliation(s)
- Ozgecan Madenli
- Niğde Ömer Halisdemir University, Enviromental Engineering Deparment, Niğde, Turkey
| | - Ceyhun Akarsu
- Istanbul University-Cerrahpasa, Department of Environmental Engineering, Istanbul, Turkey
| | - Ali Osman Adigüzel
- Ondokuz Mayıs University, Moleculer Biology and Genetics, Samsun, Turkey
| | - Ali Altuntepe
- Niğde Ömer Halisdemir University, Nanotechnology Research Center, Niğde, Turkey
| | - Recep Zan
- Niğde Ömer Halisdemir University, Nanotechnology Research Center, Niğde, Turkey
- Niğde Ömer Halisdemir University, Faculty of Arts and Sciences Department, Niğde, Turkey
| | - Ece Ümmü Deveci
- Niğde Ömer Halisdemir University, Enviromental Engineering Deparment, Niğde, Turkey
| |
Collapse
|
3
|
Liu W, Ma R, Sun C, Xu Y, Liu Y, Hu J, Ma Y, Wang D, Wen D, Yu Y. Implications from proteomic studies investigating circadian rhythm disorder-regulated neurodegenerative disease pathology. Sleep Med Rev 2023; 70:101789. [PMID: 37253318 DOI: 10.1016/j.smrv.2023.101789] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 06/01/2023]
Abstract
Neurodegenerative diseases (NDs) affect 15% of the world's population and are becoming an increasingly common cause of morbidity and mortality worldwide. Circadian rhythm disorders (CRDs) have been reported to be involved in the pathogenic regulation of various neurologic diseases, including Alzheimer's disease, Parkinson's disease, Huntington's disease, multiple sclerosis and amyotrophic lateral sclerosis. Proteomic technology is helpful to explore treatment targets for CRDs in patients with NDs. Here, we review the key differentially expressed (DE) proteins identified in previous proteomic studies investigating NDs, CRDs and associated models and the related pathways identified by enrichment analysis. Furthermore, we summarize the advantages and disadvantages of the above studies and propose new proteomic technologies for the precise study of circadian disorder-mediated regulation of ND pathology. This review provides a theoretical and technical reference for the precise study of circadian disorder-mediated regulation of ND pathology.
Collapse
Affiliation(s)
- Weiwei Liu
- Health Sciences Institute, Key Laboratory of Obesity and Glucose/Lipid Associated Metabolic Diseases, China Medical University, Shenyang 110122, Liaoning, China
| | - Ruze Ma
- Health Sciences Institute, Key Laboratory of Obesity and Glucose/Lipid Associated Metabolic Diseases, China Medical University, Shenyang 110122, Liaoning, China; Department of Gerontology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, China
| | - Chen Sun
- Health Sciences Institute, Key Laboratory of Obesity and Glucose/Lipid Associated Metabolic Diseases, China Medical University, Shenyang 110122, Liaoning, China; Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China
| | - Yingxi Xu
- Health Sciences Institute, Key Laboratory of Obesity and Glucose/Lipid Associated Metabolic Diseases, China Medical University, Shenyang 110122, Liaoning, China
| | - Yang Liu
- Health Sciences Institute, Key Laboratory of Obesity and Glucose/Lipid Associated Metabolic Diseases, China Medical University, Shenyang 110122, Liaoning, China
| | - Jiajin Hu
- Health Sciences Institute, Key Laboratory of Obesity and Glucose/Lipid Associated Metabolic Diseases, China Medical University, Shenyang 110122, Liaoning, China
| | - Yanan Ma
- Health Sciences Institute, Key Laboratory of Obesity and Glucose/Lipid Associated Metabolic Diseases, China Medical University, Shenyang 110122, Liaoning, China; Department of Epidemiology and Health Statistics, School of Public Health, China Medical University, Shenyang, 110122, Liaoning, China
| | - Difei Wang
- Department of Gerontology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, China
| | - Deliang Wen
- Health Sciences Institute, Key Laboratory of Obesity and Glucose/Lipid Associated Metabolic Diseases, China Medical University, Shenyang 110122, Liaoning, China.
| | - Yang Yu
- Health Sciences Institute, Key Laboratory of Obesity and Glucose/Lipid Associated Metabolic Diseases, China Medical University, Shenyang 110122, Liaoning, China.
| |
Collapse
|
4
|
Hidalgo S, Anguiano M, Tabuloc CA, Chiu JC. Seasonal cues act through the circadian clock and pigment-dispersing factor to control EYES ABSENT and downstream physiological changes. Curr Biol 2023; 33:675-687.e5. [PMID: 36708710 PMCID: PMC9992282 DOI: 10.1016/j.cub.2023.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/05/2022] [Accepted: 01/05/2023] [Indexed: 01/28/2023]
Abstract
Organisms adapt to seasonal changes in photoperiod and temperature to survive; however, the mechanisms by which these signals are integrated in the brain to alter seasonal biology are poorly understood. We previously reported that EYES ABSENT (EYA) shows higher levels in cold temperature or short photoperiod and promotes winter physiology in Drosophila. Nevertheless, how EYA senses seasonal cues is unclear. Pigment-dispersing factor (PDF) is a neuropeptide important for regulating circadian output rhythms. Interestingly, PDF has also been shown to regulate seasonality, suggesting that it may mediate the function of the circadian clock in modulating seasonal physiology. In this study, we investigated the role of EYA in mediating the function of PDF on seasonal biology. We observed that PDF abundance is lower on cold and short days as compared with warm and long days, contrary to what was previously observed for EYA. We observed that manipulating PDF signaling in eya+ fly brain neurons, where EYA and PDF receptor are co-expressed, modulates seasonal adaptations in daily activity rhythm and ovary development via EYA-dependent and EYA-independent mechanisms. At the molecular level, altering PDF signaling impacted EYA protein abundance. Specifically, we showed that protein kinase A (PKA), an effector of PDF signaling, phosphorylates EYA promoting its degradation, thus explaining the opposite responses of PDF and EYA abundance to changes in seasonal cues. In summary, our results support a model in which PDF signaling negatively modulates EYA levels to regulate seasonal physiology, linking the circadian clock to the modulation of seasonal adaptations.
Collapse
Affiliation(s)
- Sergio Hidalgo
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Maribel Anguiano
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Christine A Tabuloc
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.
| |
Collapse
|
5
|
Tabuloc CA, Cai YD, Kwok RS, Chan EC, Hidalgo S, Chiu JC. CLOCK and TIMELESS regulate rhythmic occupancy of the BRAHMA chromatin-remodeling protein at clock gene promoters. PLoS Genet 2023; 19:e1010649. [PMID: 36809369 PMCID: PMC9983840 DOI: 10.1371/journal.pgen.1010649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/03/2023] [Accepted: 02/02/2023] [Indexed: 02/23/2023] Open
Abstract
Circadian clock and chromatin-remodeling complexes are tightly intertwined systems that regulate rhythmic gene expression. The circadian clock promotes rhythmic expression, timely recruitment, and/or activation of chromatin remodelers, while chromatin remodelers regulate accessibility of clock transcription factors to the DNA to influence expression of clock genes. We previously reported that the BRAHMA (BRM) chromatin-remodeling complex promotes the repression of circadian gene expression in Drosophila. In this study, we investigated the mechanisms by which the circadian clock feeds back to modulate daily BRM activity. Using chromatin immunoprecipitation, we observed rhythmic BRM binding to clock gene promoters despite constitutive BRM protein expression, suggesting that factors other than protein abundance are responsible for rhythmic BRM occupancy at clock-controlled loci. Since we previously reported that BRM interacts with two key clock proteins, CLOCK (CLK) and TIMELESS (TIM), we examined their effect on BRM occupancy to the period (per) promoter. We observed reduced BRM binding to the DNA in clk null flies, suggesting that CLK is involved in enhancing BRM occupancy to initiate transcriptional repression at the conclusion of the activation phase. Additionally, we observed reduced BRM binding to the per promoter in flies overexpressing TIM, suggesting that TIM promotes BRM removal from DNA. These conclusions are further supported by elevated BRM binding to the per promoter in flies subjected to constant light and experiments in Drosophila tissue culture in which the levels of CLK and TIM are manipulated. In summary, this study provides new insights into the reciprocal regulation between the circadian clock and the BRM chromatin-remodeling complex.
Collapse
Affiliation(s)
- Christine A. Tabuloc
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Yao D. Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Rosanna S. Kwok
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Elizabeth C. Chan
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Sergio Hidalgo
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| | - Joanna C. Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, California, United States of America
| |
Collapse
|
6
|
Thakkar N, Giesecke A, Bazalova O, Martinek J, Smykal V, Stanewsky R, Dolezel D. Evolution of casein kinase 1 and functional analysis of new doubletime mutants in Drosophila. Front Physiol 2022; 13:1062632. [PMID: 36589447 PMCID: PMC9794997 DOI: 10.3389/fphys.2022.1062632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Circadian clocks are timing devices that rhythmically adjust organism's behavior, physiology, and metabolism to the 24-h day-night cycle. Eukaryotic circadian clocks rely on several interlocked transcription-translation feedback loops, where protein stability is the key part of the delay between transcription and the appearance of the mature proteins within the feedback loops. In bilaterian animals, including mammals and insects, the circadian clock depends on a homologous set of proteins. Despite mostly conserved clock components among the fruit fly Drosophila and mammals, several lineage-specific differences exist. Here we have systematically explored the evolution and sequence variability of insect DBT proteins and their vertebrate homologs casein kinase 1 delta (CKIδ) and epsilon (CKIε), dated the origin and separation of CKIδ from CKIε, and identified at least three additional independent duplications of the CKIδ/ε gene in Petromyzon, Danio, and Xenopus. We determined conserved regions in DBT specific to Diptera, and functionally tested a subset of those in D. melanogaster. Replacement of Lysine K224 with acidic residues strongly impacts the free-running period even in heterozygous flies, whereas homozygous mutants are not viable. K224D mutants have a temperature compensation defect with longer free-running periods at higher temperatures, which is exactly the opposite trend of what was reported for corresponding mammalian mutants. All DBTs of dipteran insects contain the NKRQK motif at positions 220-224. The occurrence of this motif perfectly correlates with the presence of BRIDE OF DOUBLETIME, BDBT, in Diptera. BDBT is a non-canonical FK506-binding protein that physically interacts with Drosophila DBT. The phylogeny of FK506-binding proteins suggests that BDBT is either absent or highly modified in non-dipteran insects. In addition to in silico analysis of DBT/CKIδ/ε evolution and diversity, we have identified four novel casein kinase 1 genes specific to the Drosophila genus.
Collapse
Affiliation(s)
- Nirav Thakkar
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czechia,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czechia
| | - Astrid Giesecke
- Institute of Neuro- and Behavioral Biology, Westfälische Wilhelms University, Münster, Germany
| | - Olga Bazalova
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czechia
| | - Jan Martinek
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czechia
| | - Vlastimil Smykal
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czechia
| | - Ralf Stanewsky
- Institute of Neuro- and Behavioral Biology, Westfälische Wilhelms University, Münster, Germany,*Correspondence: Ralf Stanewsky, ; David Dolezel,
| | - David Dolezel
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, Ceske Budejovice, Czechia,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czechia,*Correspondence: Ralf Stanewsky, ; David Dolezel,
| |
Collapse
|
7
|
Ye J, Chen J, Wang J, Xia Z, Jia Y. Association of the Timeless Gene with Prognosis and Clinical Characteristics of Human Lung Cancer. Diagnostics (Basel) 2022; 12:2681. [PMID: 36359523 PMCID: PMC9688960 DOI: 10.3390/diagnostics12112681] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/22/2022] [Accepted: 10/27/2022] [Indexed: 07/24/2023] Open
Abstract
(1) Background: As the most common malignant tumor type worldwide, it is necessary to identify novel potential prognostic biomarkers to improve the poor prognosis of lung cancer. The Timeless gene, a circadian rhythm-related gene, is associated with several types of cancer. However, studies analyzing the clinical significance of the Timeless gene in patients with lung cancer are currently limited. (2) Methods: In the present study, the expression levels and prognostic potential of the Timeless gene and its co-expressed genes in different subtypes of lung cancer were explored using multiple bioinformatics approaches. The correlations between the Timeless gene and its co-expressed genes were validated using A549 and NCI-H226 cells by transfecting them with expression vectors and analyses using Western blot and reverse transcription-quantitative PCR. (3) Results: The Oncomine and GEPIA database analyses indicated that the expression of the Timeless gene was significantly higher in lung cancer as compared to that in the normal tissue. Using the UALCAN database, significant differences in Timeless gene expression were determined among different stages of lung cancer and between genders. A Kaplan-Meier plotter analysis indicated that high expression of the Timeless gene was associated with poor overall survival (OS) and progression-free survival (PFS) of patients with lung cancer. In the cBioPortal and GEPIA database analyses, extra spindle pole bodies like 1 (ESPL1) was the top correlated gene of Timeless in patients with lung cancer. Similar to the Timeless gene, high expression of the ESPL1 gene was also associated with poor OS and PFS. Of note, overexpression of the Timeless gene increased the expression level of ESPL1 at both the mRNA and protein levels. (4) Conclusion: The present study explored the clinical significance of the Timeless gene and its correlated gene ESPL1 in patients with lung cancer, thereby providing a potential therapeutic target for lung cancer.
Collapse
Affiliation(s)
- Jishi Ye
- Department of Pain, Renmin Hospital of Wuhan University, 99 Zhang Road, Wuhan 430060, China
| | - Jingli Chen
- Department of Pain, Renmin Hospital of Wuhan University, 99 Zhang Road, Wuhan 430060, China
- Department of Anesthesiology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430060, China
| | - Juan Wang
- Department of Pain, Renmin Hospital of Wuhan University, 99 Zhang Road, Wuhan 430060, China
| | - Zhongyuan Xia
- Department of Pain, Renmin Hospital of Wuhan University, 99 Zhang Road, Wuhan 430060, China
| | - Yifan Jia
- Department of Pain, Renmin Hospital of Wuhan University, 99 Zhang Road, Wuhan 430060, China
| |
Collapse
|
8
|
Joshi R, Cai YD, Xia Y, Chiu JC, Emery P. PERIOD Phosphoclusters Control Temperature Compensation of the Drosophila Circadian Clock. Front Physiol 2022; 13:888262. [PMID: 35721569 PMCID: PMC9201207 DOI: 10.3389/fphys.2022.888262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Ambient temperature varies constantly. However, the period of circadian pacemakers is remarkably stable over a wide-range of ecologically- and physiologically-relevant temperatures, even though the kinetics of most biochemical reactions accelerates as temperature rises. This thermal buffering phenomenon, called temperature compensation, is a critical feature of circadian rhythms, but how it is achieved remains elusive. Here, we uncovered the important role played by the Drosophila PERIOD (PER) phosphodegron in temperature compensation. This phosphorylation hotspot is crucial for PER proteasomal degradation and is the functional homolog of mammalian PER2 S478 phosphodegron, which also impacts temperature compensation. Using CRISPR-Cas9, we introduced a series of mutations that altered three Serines of the PER phosphodegron. While all three Serine to Alanine substitutions lengthened period at all temperatures tested, temperature compensation was differentially affected. S44A and S45A substitutions caused undercompensation, while S47A resulted in overcompensation. These results thus reveal unexpected functional heterogeneity of phosphodegron residues in thermal compensation. Furthermore, mutations impairing phosphorylation of the per s phosphocluster showed undercompensation, consistent with its inhibitory role on S47 phosphorylation. We observed that S47A substitution caused increased accumulation of hyper-phosphorylated PER at warmer temperatures. This finding was corroborated by cell culture assays in which S47A slowed down phosphorylation-dependent PER degradation at high temperatures, causing PER degradation to be excessively temperature-compensated. Thus, our results point to a novel role of the PER phosphodegron in temperature compensation through temperature-dependent modulation of the abundance of hyper-phosphorylated PER. Our work reveals interesting mechanistic convergences and differences between mammalian and Drosophila temperature compensation of the circadian clock.
Collapse
Affiliation(s)
- Radhika Joshi
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Yao D. Cai
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, United States
| | - Yongliang Xia
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Joanna C. Chiu
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, United States
| | - Patrick Emery
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| |
Collapse
|
9
|
Casein kinase 1 and disordered clock proteins form functionally equivalent, phospho-based circadian modules in fungi and mammals. Proc Natl Acad Sci U S A 2022; 119:2118286119. [PMID: 35217617 PMCID: PMC8892514 DOI: 10.1073/pnas.2118286119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2022] [Indexed: 02/02/2023] Open
Abstract
Circadian clocks rely on negative feedback loops. The core circadian inhibitors, FRQ in Neurospora and PERs in animals, are progressively hyperphosphorylated, inactivated, and degraded. CK1 is essential for these clocks. Despite our knowledge of the role of CK1, it is not known how many other kinases are required and how multisite phosphorylation might contribute to circadian timekeeping. We show here that CK1 alone is sufficient to slowly phosphorylate low-affinity sites in FRQ or PER2. The reaction is nearly temperature compensated, and the phosphorylation state of FRQ or PER2 corresponds to the time elapsed since the start of the reaction. Thus, CK1 and FRQ or PER2 form equivalent modules that are in principle capable of measuring time on a circadian scale. Circadian clocks are timing systems that rhythmically adjust physiology and metabolism to the 24-h day–night cycle. Eukaryotic circadian clocks are based on transcriptional–translational feedback loops (TTFLs). Yet TTFL-core components such as Frequency (FRQ) in Neurospora and Periods (PERs) in animals are not conserved, leaving unclear how a 24-h period is measured on the molecular level. Here, we show that CK1 is sufficient to promote FRQ and mouse PER2 (mPER2) hyperphosphorylation on a circadian timescale by targeting a large number of low-affinity phosphorylation sites. Slow phosphorylation kinetics rely on site-specific recruitment of Casein Kinase 1 (CK1) and access of intrinsically disordered segments of FRQ or mPER2 to bound CK1 and on CK1 autoinhibition. Compromising CK1 activity and substrate binding affects the circadian clock in Neurospora and mammalian cells, respectively. We propose that CK1 and the clock proteins FRQ and PERs form functionally equivalent, phospho-based timing modules in the core of the circadian clocks of fungi and animals.
Collapse
|
10
|
Zhang ZH, Xiong JM, Zhu YY, Zhang XD, Wu WJ, Zhou L, Zhuang JH, Xu XH. WNK3-PER1 interactions regulate the circadian rhythm in the suprachiasmatic nucleus in rats. Am J Transl Res 2022; 14:1001-1009. [PMID: 35273702 PMCID: PMC8902561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 07/08/2021] [Indexed: 06/14/2023]
Abstract
PER1 is a core component of the internal time-keeping system. In the suprachiasmatic nucleus, it serves as the primary circadian pacemaker in mammalian brains. PER1 functions with other clock components to generate a feedback loop involving the transcriptional repression of gene expression to produce a circadian rhythm with an approximately 24-hour cycle. Post-transcriptional modifications (PTMs) are a basic regulatory mechanism that both perpetuate self-sustained oscillations and interpret metabolic input into circadian physiology by affecting factors such as protein stability, interactions, localization, and activity. Here we examined whether the serine/threonine protein kinase WNK3, which is expressed in a circadian rhythm, can interact and colocalize with PER1 in the SCN. In rats, WNK3 knockdown in the SCN is associated with altered sleep patterns. Moreover, WNK3 can phosphorylate PER1 to promote its degradation and is associated with circadian oscillations when PER1 is expressed in vitro.
Collapse
Affiliation(s)
- Zhao-Huan Zhang
- School of Preclinical Medicine, Wannan Medical CollegeWuhu 241001, Anhui, China
- Department of Laboratory Medicine, Changzheng Hospital, Naval Medical UniversityShanghai 200003, China
| | - Jian-Mei Xiong
- Department of Neurology, Hainan Hospital, General Hospital of PLASanya 572014, Hainan, China
| | - Yun-Yi Zhu
- School of Life Sciences, Shanghai UniversityShanghai 200444, China
| | - Xiao-Dan Zhang
- School of Life Sciences, Shanghai UniversityShanghai 200444, China
| | - Wen-Jie Wu
- School of Life Sciences, Shanghai UniversityShanghai 200444, China
| | - Lin Zhou
- Department of Laboratory Medicine, Changzheng Hospital, Naval Medical UniversityShanghai 200003, China
| | - Jian-Hua Zhuang
- Department of Neurology, Changzheng Hospital, Naval Medical UniversityShanghai 200003, China
| | - Xiao-Hui Xu
- School of Preclinical Medicine, Wannan Medical CollegeWuhu 241001, Anhui, China
- School of Life Sciences, Shanghai UniversityShanghai 200444, China
| |
Collapse
|
11
|
Ahmadi SA, Tranmer JE, Ritonja JA, Flaten L, Topouza DG, Duan QL, Durocher F, Aronson KJ, Bhatti P. DNA methylation of circadian genes and markers of cardiometabolic risk in female hospital workers: An exploratory study. Chronobiol Int 2022; 39:735-746. [PMID: 35109725 DOI: 10.1080/07420528.2022.2032729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Night shift work has been linked to increased risk of cardiovascular disease (CVD); however, the underlying mechanisms remain unclear. A compelling yet understudied mechanism involves differential DNA methylation of circadian genes. To investigate the relevance of this mechanism, we conducted an exploratory cross-sectional study of 74 female hospital personnel (38 day workers, 36 night shift workers). Sociodemographic, lifestyle, and health characteristics as well as shift work status and history were determined through self-report. Fasting blood samples were collected to measure markers of cardiometabolic risk and DNA was extracted to measure DNA methylation of 1150 cytosine-guanine (CpG) sites across 22 circadian genes. Associations between methylation levels at individual CpG sites (β-values) and markers of cardiometabolic risk were analyzed while considering effect modification by shift work status. The false discovery rate was applied to account for multiple comparisons (q ≤ 0.20). Two CpG sites [cg06758649 (CRY1) and cg06899802 (CSNK1A1)] were differentially associated with waist circumference and body mass index by shift work status, and eight CpG sites [cg26103512 (CSNK1D), cg03941313 (CSNK1E), cg18217763 (CSNK1E), cg16682686 (DEC1), cg12061096 (RORA), cg10133825 (RORA), cg19652148 (RORA), and cg22904654 (RORA)] were differentially associated with LDL cholesterol concentration by shift work status (all q ≤ 0.20). Our findings suggest that the relationship between DNA methylation of circadian genes and cardiometabolic risk differs by day and night shift worker status, which may contribute to mechanisms of increased risk of CVD observed among night shift workers.
Collapse
Affiliation(s)
- Salman A Ahmadi
- Department of Public Health Sciences, Queen's University, Kingston, ON, Canada
| | - Joan E Tranmer
- Department of Public Health Sciences, Queen's University, Kingston, ON, Canada.,School of Nursing, Queen's University, Kingston, ON, Canada
| | - Jennifer A Ritonja
- Department of Public Health Sciences, Queen's University, Kingston, ON, Canada
| | - Lisa Flaten
- Department of Public Health Sciences, Queen's University, Kingston, ON, Canada
| | - Danai G Topouza
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Qing Ling Duan
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada.,School of Computing, Queen's University, Kingston, ON, Canada
| | - Francine Durocher
- Chu de Québec-Université Laval Research Center (Endocrinology and Nephrology Division), Université Laval Cancer Research Center and Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
| | - Kristan J Aronson
- Department of Public Health Sciences, Queen's University, Kingston, ON, Canada.,Division of Cancer Care and Epidemiology, Cancer Research Institute, Queen's University, Kingston, ON, Canada
| | - Parveen Bhatti
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
| |
Collapse
|
12
|
Marcogliese PC, Dutta D, Ray SS, Dang NDP, Zuo Z, Wang Y, Lu D, Fazal F, Ravenscroft TA, Chung H, Kanca O, Wan J, Douine ED, Network UD, Pena LDM, Yamamoto S, Nelson SF, Might M, Meyer KC, Yeo NC, Bellen HJ. Loss of IRF2BPL impairs neuronal maintenance through excess Wnt signaling. SCIENCE ADVANCES 2022; 8:eabl5613. [PMID: 35044823 PMCID: PMC8769555 DOI: 10.1126/sciadv.abl5613] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/30/2021] [Indexed: 05/12/2023]
Abstract
De novo truncations in Interferon Regulatory Factor 2 Binding Protein Like (IRF2BPL) lead to severe childhood-onset neurodegenerative disorders. To determine how loss of IRF2BPL causes neural dysfunction, we examined its function in Drosophila and zebrafish. Overexpression of either IRF2BPL or Pits, the Drosophila ortholog, represses Wnt transcription in flies. In contrast, neuronal depletion of Pits leads to increased wingless (wg) levels in the brain and is associated with axonal loss, whereas inhibition of Wg signaling is neuroprotective. Moreover, increased neuronal expression of wg in flies is sufficient to cause age-dependent axonal loss, similar to reduction of Pits. Loss of irf2bpl in zebrafish also causes neurological defects with an associated increase in wnt1 transcription and downstream signaling. WNT1 is also increased in patient-derived astrocytes, and pharmacological inhibition of Wnt suppresses the neurological phenotypes. Last, IRF2BPL and the Wnt antagonist, CKIα, physically and genetically interact, showing that IRF2BPL and CkIα antagonize Wnt transcription and signaling.
Collapse
Affiliation(s)
- Paul C. Marcogliese
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Debdeep Dutta
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Shrestha Sinha Ray
- The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Nghi D. P. Dang
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, AL 35294, USA
| | - Zhongyuan Zuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Yuchun Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Di Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Fatima Fazal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Thomas A. Ravenscroft
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Hyunglok Chung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - JiJun Wan
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Emilie D. Douine
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Undiagnosed Diseases Network
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, AL 35294, USA
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
- Precision Medicine Institute, University of Alabama, Birmingham, AL 35294, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Loren D. M. Pena
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stanley F. Nelson
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Matthew Might
- Precision Medicine Institute, University of Alabama, Birmingham, AL 35294, USA
| | - Kathrin C. Meyer
- The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Nan Cher Yeo
- Department of Pharmacology and Toxicology, University of Alabama, Birmingham, AL 35294, USA
- Precision Medicine Institute, University of Alabama, Birmingham, AL 35294, USA
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
13
|
Hirschhäuser A, van Cann M, Bogdan S. CK1α protects WAVE from degradation to regulate cell shape and motility in immune response. J Cell Sci 2021; 134:272700. [PMID: 34730182 PMCID: PMC8714073 DOI: 10.1242/jcs.258891] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/25/2021] [Indexed: 12/02/2022] Open
Abstract
The WAVE regulatory complex (WRC) is the main activator of the Arp2/3 complex, promoting lamellipodial protrusions in migrating cells. The WRC is basally inactive but can be activated by Rac1 and phospholipids, and through phosphorylation. However, the in vivo relevance of the phosphorylation of WAVE proteins remains largely unknown. Here, we identified casein kinase I alpha (CK1α) as a regulator of WAVE, thereby controlling cell shape and cell motility in Drosophila macrophages. CK1α binds and phosphorylates WAVE in vitro. Phosphorylation of WAVE by CK1α appears not to be required for activation but, rather, regulates its stability. Pharmacologic inhibition of CK1α promotes ubiquitin-dependent degradation of WAVE. Consistently, loss of Ck1α but not ck2 function phenocopies the depletion of WAVE. Phosphorylation-deficient mutations in the CK1α consensus sequences within the VCA domain of WAVE can neither rescue mutant lethality nor lamellipodium defects. By contrast, phosphomimetic mutations rescue all cellular and developmental defects. Finally, RNAi-mediated suppression of 26S proteasome or E3 ligase complexes substantially rescues lamellipodia defects in CK1α-depleted macrophages. Therefore, we conclude that basal phosphorylation of WAVE by CK1α protects it from premature ubiquitin-dependent degradation, thus promoting WAVE function in vivo. This article has an associated First Person interview with the first author of the paper. Summary: We identified CK1α as a novel regulator of WAVE controlling cell shape and motility in immune response. Basal phosphorylation of WAVE by CK1α protects it from premature proteasomal degradation.
Collapse
Affiliation(s)
- Alexander Hirschhäuser
- Institute of Physiology and Pathophysiology, Dept. of Molecular Cell Physiology, Philipps-University Marburg, Germany
| | | | - Sven Bogdan
- Institute of Physiology and Pathophysiology, Dept. of Molecular Cell Physiology, Philipps-University Marburg, Germany.,Institute for Neurobiology, University of Münster, Germany
| |
Collapse
|
14
|
Cai YD, Chiu JC. Timeless in animal circadian clocks and beyond. FEBS J 2021; 289:6559-6575. [PMID: 34699674 PMCID: PMC9038958 DOI: 10.1111/febs.16253] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/09/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022]
Abstract
TIMELESS (TIM) was first identified as a molecular cog in the Drosophila circadian clock. Almost three decades of investigations have resulted in an insightful model describing the critical role of Drosophila TIM (dTIM) in circadian timekeeping in insects, including its function in mediating light entrainment and temperature compensation of the molecular clock. Furthermore, exciting discoveries on its sequence polymorphism and thermosensitive alternative RNA splicing have also established its role in regulating seasonal biology. Although mammalian TIM (mTIM), its mammalian paralog, was first identified as a potential circadian clock component in 1990s due to sequence similarity to dTIM, its role in clock regulation has been more controversial. Mammalian TIM has now been characterized as a DNA replication fork component and has been shown to promote fork progression and participate in cell cycle checkpoint signaling in response to DNA damage. Despite defective circadian rhythms displayed by mtim mutants, it remains controversial whether the regulation of circadian clocks by mTIM is direct, especially given the interconnection between the cell cycle and circadian clocks. In this review, we provide a historical perspective on the identification of animal tim genes, summarize the roles of TIM proteins in biological timing and genomic stability, and draw parallels between dTIM and mTIM despite apparent functional divergence.
Collapse
Affiliation(s)
- Yao D Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, CA, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, CA, USA
| |
Collapse
|
15
|
Mosier AE, Hurley JM. Circadian Interactomics: How Research Into Protein-Protein Interactions Beyond the Core Clock Has Influenced the Model of Circadian Timekeeping. J Biol Rhythms 2021; 36:315-328. [PMID: 34056936 DOI: 10.1177/07487304211014622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The circadian clock is the broadly conserved, protein-based, timekeeping mechanism that synchronizes biology to the Earth's 24-h light-dark cycle. Studies of the mechanisms of circadian timekeeping have placed great focus on the role that individual protein-protein interactions play in the creation of the timekeeping loop. However, research has shown that clock proteins most commonly act as part of large macromolecular protein complexes to facilitate circadian control over physiology. The formation of these complexes has led to the large-scale study of the proteins that comprise these complexes, termed here "circadian interactomics." Circadian interactomic studies of the macromolecular protein complexes that comprise the circadian clock have uncovered many basic principles of circadian timekeeping as well as mechanisms of circadian control over cellular physiology. In this review, we examine the wealth of knowledge accumulated using circadian interactomics approaches to investigate the macromolecular complexes of the core circadian clock, including insights into the core mechanisms that impart circadian timing and the clock's regulation of many physiological processes. We examine data acquired from the investigation of the macromolecular complexes centered on both the activating and repressing arm of the circadian clock and from many circadian model organisms.
Collapse
Affiliation(s)
- Alexander E Mosier
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY
| | - Jennifer M Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY.,Center for Biotechnology & Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY
| |
Collapse
|
16
|
Cai YD, Xue Y, Truong CC, Del Carmen-Li J, Ochoa C, Vanselow JT, Murphy KA, Li YH, Liu X, Kunimoto BL, Zheng H, Zhao C, Zhang Y, Schlosser A, Chiu JC. CK2 Inhibits TIMELESS Nuclear Export and Modulates CLOCK Transcriptional Activity to Regulate Circadian Rhythms. Curr Biol 2021; 31:502-514.e7. [PMID: 33217322 PMCID: PMC7878342 DOI: 10.1016/j.cub.2020.10.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 09/25/2020] [Accepted: 10/20/2020] [Indexed: 11/06/2022]
Abstract
Circadian clocks orchestrate daily rhythms in organismal physiology and behavior to promote optimal performance and fitness. In Drosophila, key pacemaker proteins PERIOD (PER) and TIMELESS (TIM) are progressively phosphorylated to perform phase-specific functions. Whereas PER phosphorylation has been extensively studied, systematic analysis of site-specific TIM phosphorylation is lacking. Here, we identified phosphorylation sites of PER-bound TIM by mass spectrometry, given the importance of TIM as a modulator of PER function in the pacemaker. Among the 12 TIM phosphorylation sites we identified, at least two of them are critical for circadian timekeeping as mutants expressing non-phosphorylatable mutations exhibit altered behavioral rhythms. In particular, we observed that CK2-dependent phosphorylation of TIM(S1404) promotes nuclear accumulation of PER-TIM heterodimers by inhibiting the interaction of TIM and nuclear export component, Exportin 1 (XPO1). We propose that proper level of nuclear PER-TIM accumulation is necessary to facilitate kinase recruitment for the regulation of daily phosphorylation rhythm and phase-specific transcriptional activity of CLOCK (CLK). Our results highlight the contribution of phosphorylation-dependent nuclear export of PER-TIM heterodimers to the maintenance of circadian periodicity and identify a new mechanism by which the negative elements of the circadian clock (PER-TIM) regulate the positive elements (CLK-CYC). Finally, because the molecular phenotype of tim(S1404A) non-phosphorylatable mutant exhibits remarkable similarity to that of a mutation in human timeless that underlies familial advanced sleep phase syndrome (FASPS), our results revealed an unexpected parallel between the functions of Drosophila and human TIM and may provide new insights into the molecular mechanisms underlying human FASPS. Organisms in all domains of life exhibit circadian rhythms. Cai et al. reveal that phosphorylation of TIMELESS modulates kinase accessibility to CLOCK in the nucleus. This mechanism is important in controlling daily phosphorylation rhythm of CLOCK, which is critical for its function as a key regulator of circadian rhythms.
Collapse
Affiliation(s)
- Yao D Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Yongbo Xue
- Department of Biology, University of Nevada, Reno, NV 89557, USA
| | - Cindy C Truong
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Jose Del Carmen-Li
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Christopher Ochoa
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Jens T Vanselow
- Rudolf Virchow Center for Experimental Biomedicine, University of Wurzburg, Wurzburg, Germany
| | - Katherine A Murphy
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Ying H Li
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Xianhui Liu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Ben L Kunimoto
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Haiyan Zheng
- Biological Mass Spectrometry Facility, Robert Wood Johnson Medical School and Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Caifeng Zhao
- Biological Mass Spectrometry Facility, Robert Wood Johnson Medical School and Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yong Zhang
- Department of Biology, University of Nevada, Reno, NV 89557, USA
| | - Andreas Schlosser
- Rudolf Virchow Center for Experimental Biomedicine, University of Wurzburg, Wurzburg, Germany
| | - Joanna C Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.
| |
Collapse
|
17
|
Wang X, Xu Z, Cai Y, Zeng S, Peng B, Ren X, Yan Y, Gong Z. Rheostatic Balance of Circadian Rhythm and Autophagy in Metabolism and Disease. Front Cell Dev Biol 2020; 8:616434. [PMID: 33330516 PMCID: PMC7732583 DOI: 10.3389/fcell.2020.616434] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/04/2020] [Indexed: 02/05/2023] Open
Abstract
Circadian rhythms are physical, behavioral and environmental cycles that respond primarily to light and dark, with a period of time of approximately 24 h. The most essential physiological functions of mammals are manifested in circadian rhythm patterns, including the sleep-wake cycle and nutrient and energy metabolism. Autophagy is a conserved biological process contributing to nutrient and cellular homeostasis. The factors affecting autophagy are numerous, such as diet, drugs, and aging. Recent studies have indicated that autophagy is activated rhythmically in a clock-dependent manner whether the organism is healthy or has certain diseases. In addition, autophagy can affect circadian rhythm by degrading circadian proteins. This review discusses the interaction and mechanisms between autophagy and circadian rhythm. Moreover, we introduce the molecules influencing both autophagy and circadian rhythm. We then discuss the drugs affecting the circadian rhythm of autophagy. Finally, we present the role of rhythmic autophagy in nutrient and energy metabolism and its significance in physiology and metabolic disease.
Collapse
Affiliation(s)
- Xiang Wang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuan Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Shuangshuang Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Bi Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Xinxin Ren
- Key Laboratory of Molecular Radiation Oncology of Hunan Province, Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| |
Collapse
|
18
|
Wang C, Shui K, Ma S, Lin S, Zhang Y, Wen B, Deng W, Xu H, Hu H, Guo A, Xue Y, Zhang L. Integrated omics in Drosophila uncover a circadian kinome. Nat Commun 2020; 11:2710. [PMID: 32483184 PMCID: PMC7264355 DOI: 10.1038/s41467-020-16514-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/06/2020] [Indexed: 02/06/2023] Open
Abstract
Most organisms on the earth exhibit circadian rhythms in behavior and physiology, which are driven by endogenous clocks. Phosphorylation plays a central role in timing the clock, but how this contributes to overt rhythms is unclear. Here we conduct phosphoproteomics in conjunction with transcriptomic and proteomic profiling using fly heads. By developing a pipeline for integrating multi-omics data, we identify 789 (~17%) phosphorylation sites with circadian oscillations. We predict 27 potential circadian kinases to participate in phosphorylating these sites, including 7 previously known to function in the clock. We screen the remaining 20 kinases for effects on circadian rhythms and find an additional 3 to be involved in regulating locomotor rhythm. We re-construct a signal web that includes the 10 circadian kinases and identify GASKET as a potentially important regulator. Taken together, we uncover a circadian kinome that potentially shapes the temporal pattern of the entire circadian molecular landscapes. Phosphorylation plays an important role in the regulation of molecular circadian clocks. Here the authors utilize multi-omics data from flies to describe the circadian kinome and identify GASKET as a potentially important regulator within the circadian kinase network.
Collapse
Affiliation(s)
- Chenwei Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Ke Shui
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Shanshan Ma
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Shaofeng Lin
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Ying Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Bo Wen
- Department of Molecular and Human Genetics, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wankun Deng
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Haodong Xu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Hui Hu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Anyuan Guo
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China. .,Institute of Brain Research, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
| | - Luoying Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China. .,Institute of Brain Research, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
| |
Collapse
|
19
|
Abstract
The speed of the circadian clock is regulated by phosphorylation-regulated degradation of the PER protein. However, this model has recently been challenged by genetic studies in mice and fungi. Here, we provide definitive genetic and biochemical evidence that strongly supports the importance of the phosphoswitch-regulated proteolysis of PER2 in regulating the clock. We generated two independent mouse lines with a point mutation in a casein kinase 1-dependent phosphodegron in PER2. These mice have longer circadian rhythms, increased accumulation of circadian proteins, and perturbed temperature compensation. The findings strongly support the phosphoswitch model of regulated PER2 degradation as a central mechanism controlling the speed of the circadian clock. Casein kinase 1 (CK1) plays a central role in regulating the period of the circadian clock. In mammals, PER2 protein abundance is regulated by CK1-mediated phosphorylation and proteasomal degradation. On the other hand, recent studies have questioned whether the degradation of the core circadian machinery is a critical step in clock regulation. Prior cell-based studies found that CK1 phosphorylation of PER2 at Ser478 recruits the ubiquitin E3 ligase β-TrCP, leading to PER2 degradation. Creation of this phosphodegron is regulated by a phosphoswitch that is also implicated in temperature compensation. However, in vivo evidence that this phosphodegron influences circadian period is lacking. Here, we generated and analyzed PER2-Ser478Ala knock-in mice. The mice showed longer circadian period in behavioral analysis. Molecularly, mutant PER2 protein accumulated in both the nucleus and cytoplasm of the mouse liver, while Per2 messenger RNA (mRNA) levels were minimally affected. Nuclear PER1, CRY1, and CRY2 proteins also increased, probably due to stabilization of PER2-containing complexes. In mouse embryonic fibroblasts derived from PER2-Ser478Ala::LUC mice, three-phase decay and temperature compensation of the circadian period was perturbed. These data provide direct in vivo evidence for the importance of phosphorylation-regulated PER2 stability in the circadian clock and validate the phosphoswitch in a mouse model.
Collapse
|
20
|
White JM, Piron MJ, Rangaraj VR, Hanlon EC, Cohen RN, Brady MJ. Reference Gene Optimization for Circadian Gene Expression Analysis in Human Adipose Tissue. J Biol Rhythms 2020; 35:84-97. [PMID: 31668115 PMCID: PMC7409766 DOI: 10.1177/0748730419883043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A hallmark of biology is the cyclical nature of organismal physiology driven by networks of biological, including circadian, rhythms. Unsurprisingly, disruptions of the circadian rhythms through sleep curtailment or shift work have been connected through numerous studies to positive associations with obesity, insulin resistance, and diabetes. Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) measures oscillation in messenger RNA expression, an essential foundation for the study of the physiological circadian regulatory network. Primarily, measured oscillations have involved the use of reference gene normalization. However, the validation and identification of suitable reference genes is a significant challenge across different biological systems. This study focuses on adipose tissue of premenopausal, otherwise healthy, morbidly obese women voluntarily enrolled after being scheduled for laparoscopic sleeve gastrectomy surgery. Acquisition of tissue was accomplished by aspiratory needle biopsies of subcutaneous adipose tissue 1 to 2 weeks prior to surgery and 12 to 13 weeks following surgery and an in-surgery scalpel-assisted excision of mesenteric adipose tissue. Each biopsy was sterile cultured ex vivo and serially collected every 4 h over approximately 36 h. The candidate reference genes that were tested were 18S rRNA, GAPDH, HPRT1, RPII, RPL13α, and YWHAZ. Three analytic tools were used to test suitability, and the candidate reference genes were used to measure oscillation in expression of a known circadian clock element (Dbp). No gene was deemed suitable as an individual reference gene control, which indicated that the optimal reference gene set was the geometrically averaged 3-gene panel composed of YWHAZ, RPL13α, and GAPDH. These methods can be employed to identify optimal reference genes in other systems.
Collapse
Affiliation(s)
- Jeremy M. White
- Committee on Molecular Metabolism and Nutrition, University of Chicago, Chicago IL, 60637
| | - Matthew J. Piron
- Department of Medicine, Section of Endocrinology, Diabetes and Metabolism, University of Chicago, Chicago IL, 60637
| | - Vittobai R. Rangaraj
- Committee on Molecular Metabolism and Nutrition, University of Chicago, Chicago IL, 60637
| | - Erin C. Hanlon
- Department of Medicine, Section of Endocrinology, Diabetes and Metabolism, University of Chicago, Chicago IL, 60637
| | - Ronald N. Cohen
- Committee on Molecular Metabolism and Nutrition, University of Chicago, Chicago IL, 60637
- Department of Medicine, Section of Endocrinology, Diabetes and Metabolism, University of Chicago, Chicago IL, 60637
| | - Matthew J. Brady
- Committee on Molecular Metabolism and Nutrition, University of Chicago, Chicago IL, 60637
- Department of Medicine, Section of Endocrinology, Diabetes and Metabolism, University of Chicago, Chicago IL, 60637
| |
Collapse
|
21
|
Beale AD, Kruchek E, Kitcatt SJ, Henslee EA, Parry JS, Braun G, Jabr R, von Schantz M, O’Neill JS, Labeed FH. Casein Kinase 1 Underlies Temperature Compensation of Circadian Rhythms in Human Red Blood Cells. J Biol Rhythms 2019; 34:144-153. [PMID: 30898060 PMCID: PMC6458989 DOI: 10.1177/0748730419836370] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Temperature compensation and period determination by casein kinase 1 (CK1) are conserved features of eukaryotic circadian rhythms, whereas the clock gene transcription factors that facilitate daily gene expression rhythms differ between phylogenetic kingdoms. Human red blood cells (RBCs) exhibit temperature-compensated circadian rhythms, which, because RBCs lack nuclei, must occur in the absence of a circadian transcription-translation feedback loop. We tested whether period determination and temperature compensation are dependent on CKs in RBCs. As with nucleated cell types, broad-spectrum kinase inhibition with staurosporine lengthened the period of the RBC clock at 37°C, with more specific inhibition of CK1 and CK2 also eliciting robust changes in circadian period. Strikingly, inhibition of CK1 abolished temperature compensation and increased the Q10 for the period of oscillation in RBCs, similar to observations in nucleated cells. This indicates that CK1 activity is essential for circadian rhythms irrespective of the presence or absence of clock gene expression cycles.
Collapse
Affiliation(s)
- Andrew D. Beale
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, UK
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Emily Kruchek
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Stephen J. Kitcatt
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Erin A. Henslee
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Jack S.W. Parry
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Gabriella Braun
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Rita Jabr
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Malcolm von Schantz
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK
| | - John S. O’Neill
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Fatima H. Labeed
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, UK
| |
Collapse
|