1
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Barone I, Gilette NM, Hawks-Mayer H, Handy J, Zhang KJ, Chifamba FF, Mostafa E, Johnson-Venkatesh EM, Sun Y, Gibson JM, Rotenberg A, Umemori H, Tsai PT, Lipton JO. Synaptic BMAL1 phosphorylation controls circadian hippocampal plasticity. SCIENCE ADVANCES 2023; 9:eadj1010. [PMID: 37878694 PMCID: PMC10599629 DOI: 10.1126/sciadv.adj1010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023]
Abstract
The time of day strongly influences adaptive behaviors like long-term memory, but the correlating synaptic and molecular mechanisms remain unclear. The circadian clock comprises a canonical transcription-translation feedback loop (TTFL) strictly dependent on the BMAL1 transcription factor. We report that BMAL1 rhythmically localizes to hippocampal synapses in a manner dependent on its phosphorylation at Ser42 [pBMAL1(S42)]. pBMAL1(S42) regulates the autophosphorylation of synaptic CaMKIIα and circadian rhythms of CaMKIIα-dependent molecular interactions and LTP but not global rest/activity behavior. Therefore, our results suggest a model in which repurposing of the clock protein BMAL1 to synapses locally gates the circadian timing of plasticity.
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Affiliation(s)
- Ilaria Barone
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Nicole M. Gilette
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Hannah Hawks-Mayer
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Jonathan Handy
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Kevin J. Zhang
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Fortunate F. Chifamba
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Engie Mostafa
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Erin M. Johnson-Venkatesh
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Yan Sun
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Jennifer M. Gibson
- Departments of Neurology, Neuroscience, Pediatrics, and Psychiatry, University of Texas at Southwestern, Dallas, TX 75390, USA
| | - Alexander Rotenberg
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Hisashi Umemori
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Peter T. Tsai
- Departments of Neurology, Neuroscience, Pediatrics, and Psychiatry, University of Texas at Southwestern, Dallas, TX 75390, USA
| | - Jonathan O. Lipton
- Department of Neurology and F.M. Kirby Center for Neurobiology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Neurology and Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
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2
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Klonisch T, Logue SE, Hombach-Klonisch S, Vriend J. DUBing Primary Tumors of the Central Nervous System: Regulatory Roles of Deubiquitinases. Biomolecules 2023; 13:1503. [PMID: 37892185 PMCID: PMC10605193 DOI: 10.3390/biom13101503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
The ubiquitin proteasome system (UPS) utilizes an orchestrated enzymatic cascade of E1, E2, and E3 ligases to add single or multiple ubiquitin-like molecules as post-translational modification (PTM) to proteins. Ubiquitination can alter protein functions and/or mark ubiquitinated proteins for proteasomal degradation but deubiquitinases (DUBs) can reverse protein ubiquitination. While the importance of DUBs as regulatory factors in the UPS is undisputed, many questions remain on DUB selectivity for protein targeting, their mechanism of action, and the impact of DUBs on the regulation of diverse biological processes. Furthermore, little is known about the expression and role of DUBs in tumors of the human central nervous system (CNS). In this comprehensive review, we have used publicly available transcriptional datasets to determine the gene expression profiles of 99 deubiquitinases (DUBs) from five major DUB families in seven primary pediatric and adult CNS tumor entities. Our analysis identified selected DUBs as potential new functional players and biomarkers with prognostic value in specific subtypes of primary CNS tumors. Collectively, our analysis highlights an emerging role for DUBs in regulating CNS tumor cell biology and offers a rationale for future therapeutic targeting of DUBs in CNS tumors.
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Affiliation(s)
- Thomas Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Department of Pathology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Department of Medical Microbiology & Infectious Diseases, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- CancerCare Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Susan E. Logue
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- CancerCare Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Sabine Hombach-Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Department of Pathology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Jerry Vriend
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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3
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Obodo D, Outland EH, Hughey JJ. LimoRhyde2: genomic analysis of biological rhythms based on effect sizes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526897. [PMID: 36778295 PMCID: PMC9915588 DOI: 10.1101/2023.02.02.526897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genome-scale data have revealed daily rhythms in various species and tissues. However, current methods to assess rhythmicity largely restrict their focus to quantifying statistical significance, which may not reflect biological relevance. To address this limitation, we developed a method called LimoRhyde2 (the successor to our method LimoRhyde), which focuses instead on rhythm-related effect sizes and their uncertainty. For each genomic feature, LimoRhyde2 fits a curve using a series of linear models based on periodic splines, moderates the fits using an Empirical Bayes approach called multivariate adaptive shrinkage (Mash), then uses the moderated fits to calculate rhythm statistics such as peak-to-trough amplitude. The periodic splines capture non-sinusoidal rhythmicity, while Mash uses patterns in the data to account for different fits having different levels of noise. To demonstrate LimoRhyde2's utility, we applied it to multiple circadian transcriptome datasets. Overall, LimoRhyde2 prioritized genes having high-amplitude rhythms in expression, whereas a prior method (BooteJTK) prioritized "statistically significant" genes whose amplitudes could be relatively small. Thus, quantifying effect sizes using approaches such as LimoRhyde2 has the potential to transform interpretation of genomic data related to biological rhythms.
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Affiliation(s)
- Dora Obodo
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Elliot H. Outland
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jacob J. Hughey
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
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4
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Gao J, Sun X, Zhou Q, Jiang S, Zhang Y, Ge H, Qin X. Circadian clock disruption aggravates alcohol liver disease in an acute mouse model. Chronobiol Int 2022; 39:1554-1566. [PMID: 36354126 DOI: 10.1080/07420528.2022.2132865] [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: 11/11/2022]
Abstract
Circadian rhythms are important for organisms to adapt to the environment and maintain homeostasis. Disruptions of circadian rhythms contribute to the occurrence, progression, and exacerbation of diseases, such as cancer, psychiatric disorders, and metabolic disorders. Alcohol-induced liver disease (ALD) is one of the most prevalent liver diseases. Disruptions of the circadian clock enhance the ALD symptoms using chronic mice models or genetic manipulated mice. However, chronic models are time consuming and clock gene deletions interfere with metabolisms. Here, we report that constant light (LL) condition significantly disrupted the circadian clock in an acute ALD model, resulting in aggravated ALD phenotypes in wild type mice. Comparative transcriptome analysis revealed that the alcohol feeding affected the circadian pathway, as well as metabolic pathways. The acute alcohol feeding plus the LL condition further interfered with metabolic pathways and dysregulated canonical circadian gene expressions. These findings support the idea that disrupting the circadian clock could provide an improved ALD mouse model for further applications, such as facilitating identification of potential therapeutic targets for the prevention and treatment of ALD.Abbreviations: ALD, alcohol-induced liver disease; LD, 12 h light _ 12 h dark; LL, constant light; HF, high-fat liquid control diet; ETH, ethanol-containing diet; NIAAA, National Institute on Alcohol Abuse and Alcoholism; TTFLs, transcription-translation feedback loops; FDA, US Foods and Drug Administration; NAFLD, non-alcoholic fatty liver disease; RER, respiratory exchange rate; DEGs, differentially expressed genes; H&E, haematoxylin and eosin; ALT, alanine transaminase; AST, aspartate transaminase; TG, triglycerides.
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Affiliation(s)
- Jiajia Gao
- Institute of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Xianpu Sun
- Institute of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Qin Zhou
- Institute of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Shuo Jiang
- Institute of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Yunfei Zhang
- Modern Experiment Technology Center, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Honghua Ge
- Institute of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Ximing Qin
- Institute of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
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5
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Kim H, Kim D, Choi H, Shin G, Lee JK. Deubiquitinase USP2 stabilizes the MRE11-RAD50-NBS1 complex at DNA double-strand break sites by counteracting the ubiquitination of NBS1. J Biol Chem 2022; 299:102752. [PMID: 36436562 PMCID: PMC9758435 DOI: 10.1016/j.jbc.2022.102752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/26/2022] Open
Abstract
The MRE11-RAD50-NBS1 (MRN) complex plays essential roles in the cellular response to DNA double-strand breaks (DSBs), which are the most cytotoxic DNA lesions, and is a target of various modifications and controls. Recently, lysine 48-linked ubiquitination of NBS1, resulting in premature disassembly of the MRN complex from DSB sites, was observed in cells lacking RECQL4 helicase activity. However, the role and control of this ubiquitination during the DSB response in cells with intact RECQL4 remain unknown. Here, we showed that USP2 counteracts this ubiquitination and stabilizes the MRN complex during the DSB response. By screening deubiquitinases that increase the stability of the MRN complex in RECQL4-deficient cells, USP2 was identified as a new deubiquitinase that acts at DSB sites to counteract NBS1 ubiquitination. We determined that USP2 is recruited to DSB sites in a manner dependent on ATM, a major checkpoint kinase against DSBs, and stably interacts with NBS1 and RECQL4 in immunoprecipitation experiments. Phosphorylation of two critical residues in the N terminus of USP2 by ATM is required for its recruitment to DSBs and its interaction with RECQL4. While inactivation of USP2 alone does not substantially influence the DSB response, we found that inactivation of USP2 and USP28, another deubiquitinase influencing NBS1 ubiquitination, results in premature disassembly of the MRN complex from DSB sites as well as defects in ATM activation and homologous recombination repair abilities. These results suggest that deubiquitinases counteracting NBS1 ubiquitination are essential for the stable maintenance of the MRN complex and proper cellular response to DSBs.
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Affiliation(s)
- Hyunsup Kim
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, Korea
| | - Dongmin Kim
- Department of Biology Education, Seoul National University, Seoul, Korea
| | - Hyemin Choi
- Department of Biology Education, Seoul National University, Seoul, Korea
| | - Gwangsu Shin
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, Korea
| | - Joon-Kyu Lee
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, Korea; Department of Biology Education, Seoul National University, Seoul, Korea.
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6
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Van den Eynde J, Jacquemyn X, Cloet N, Noé D, Gillijns H, Lox M, Gsell W, Himmelreich U, Luttun A, McCutcheon K, Janssens S, Oosterlinck W. Arteriovenous Fistulae in Chronic Kidney Disease and the Heart: Physiological, Histological, and Transcriptomic Characterization of a Novel Rat Model. J Am Heart Assoc 2022; 11:e027593. [PMID: 36205249 DOI: 10.1161/jaha.122.027593] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background Arteriovenous fistulae (AVFs) are the gold standard for vascular access in those requiring hemodialysis but may put an extra hemodynamic stress on the cardiovascular system. The complex interactions between the heart, kidney, and AVFs remain incompletely understood. Methods and Results We characterized a novel rat model of five-sixths partial nephrectomy (NX) and AVFs. NX induced increases in urea, creatinine, and hippuric acid. The addition of an AVF (AVF+NX) further increased urea and a number of uremic toxins such as trimethylamine N-oxide and led to increases in cardiac index, left and right ventricular volumes, and right ventricular mass. Plasma levels of uremic toxins correlated well with ventricular morphology and function. Heart transcriptomes identified altered expression of 8 genes following NX and 894 genes following AVF+NX, whereas 290 and 1431 genes were altered in the kidney transcriptomes, respectively. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis revealed gene expression changes related to cell division and immune activation in both organs, suppression of ribosomes and transcriptional activity in the heart, and altered renin-angiotensin signaling as well as chronodisruption in the kidney. All except the latter were worsened in AVF+NX compared with NX. Conclusions Inflammation and organ dysfunction in chronic kidney disease are exacerbated following AVF creation. Furthermore, our study provides important information for the discovery of novel biomarkers and therapeutic targets in the management of cardiorenal syndrome.
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Affiliation(s)
| | | | - Nicolas Cloet
- Department of Cardiovascular Sciences KU Leuven Leuven Belgium
| | - Dries Noé
- Department of Cardiovascular Sciences KU Leuven Leuven Belgium
| | - Hilde Gillijns
- Department of Cardiovascular Sciences KU Leuven Leuven Belgium
| | - Marleen Lox
- Department of Cardiovascular Sciences KU Leuven Leuven Belgium
| | - Willy Gsell
- MoSAIC, Biomedical MRI, Department of Imaging and Pathology KU Leuven Leuven Belgium
| | - Uwe Himmelreich
- MoSAIC, Biomedical MRI, Department of Imaging and Pathology KU Leuven Leuven Belgium
| | - Aernout Luttun
- Department of Cardiovascular Sciences KU Leuven Leuven Belgium.,Endothelial Cell Biology Unit, Center for Molecular and Vascular Biology KU Leuven Leuven Belgium
| | - Keir McCutcheon
- Department of Cardiology Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle University Newcastle United Kingdom
| | - Stefan Janssens
- Department of Cardiovascular Sciences KU Leuven Leuven Belgium.,Department of Cardiovascular Diseases University Hospitals Leuven Leuven Belgium
| | - Wouter Oosterlinck
- Department of Cardiovascular Sciences KU Leuven Leuven Belgium.,Department of Cardiovascular Diseases University Hospitals Leuven Leuven Belgium
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7
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Abdalla OHMH, Mascarenhas B, Cheng HYM. Death of a Protein: The Role of E3 Ubiquitin Ligases in Circadian Rhythms of Mice and Flies. Int J Mol Sci 2022; 23:ijms231810569. [PMID: 36142478 PMCID: PMC9502492 DOI: 10.3390/ijms231810569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 12/04/2022] Open
Abstract
Circadian clocks evolved to enable organisms to anticipate and prepare for periodic environmental changes driven by the day–night cycle. This internal timekeeping mechanism is built on autoregulatory transcription–translation feedback loops that control the rhythmic expression of core clock genes and their protein products. The levels of clock proteins rise and ebb throughout a 24-h period through their rhythmic synthesis and destruction. In the ubiquitin–proteasome system, the process of polyubiquitination, or the covalent attachment of a ubiquitin chain, marks a protein for degradation by the 26S proteasome. The process is regulated by E3 ubiquitin ligases, which recognize specific substrates for ubiquitination. In this review, we summarize the roles that known E3 ubiquitin ligases play in the circadian clocks of two popular model organisms: mice and fruit flies. We also discuss emerging evidence that implicates the N-degron pathway, an alternative proteolytic system, in the regulation of circadian rhythms. We conclude the review with our perspectives on the potential for the proteolytic and non-proteolytic functions of E3 ubiquitin ligases within the circadian clock system.
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Affiliation(s)
- Osama Hasan Mustafa Hasan Abdalla
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Brittany Mascarenhas
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Hai-Ying Mary Cheng
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
- Correspondence:
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8
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Protein interaction networks of the mammalian core clock proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 131:207-233. [PMID: 35871891 DOI: 10.1016/bs.apcsb.2022.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Circadian rhythm is a 24-h cycle that regulates the biochemical and behavioral changes of organisms. It controls a wide range of functions, from gene expression to behavior, allowing organisms to anticipate daily changes in their environment. In mammals, circadian rhythm is generated by a complex transcriptional and translational feedback loop mechanism. The binding of CLOCK/BMAL1 heterodimer to the E-box of DNA located within the promoter region initiates transcription of clock control genes including the transcription of the other two core clock genes of Periods (Pers) and Cryptochromes (Crys). Then PERs and CRYs along with casein kinase 1ɛ/Δ translocate into the nucleus where they suppress CLOCK/BMAL1 transactivation and, in turn, clock-regulated gene expression. Various clock components must be operational to aid in their stabilization and period extension in circadian rhythm. In this review, we have highlighted the recent progress for the core clock interacting proteins to maintain and to stabilize circadian rhythm in mammals.
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9
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Behavioral phenotyping of mice lacking the deubiquitinase USP2. PLoS One 2021; 16:e0241403. [PMID: 33621249 PMCID: PMC7901773 DOI: 10.1371/journal.pone.0241403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/08/2021] [Indexed: 11/19/2022] Open
Abstract
Ubiquitin specific peptidase 2 (USP2) is a deubiquitinating enzyme expressed almost ubiquitously in the body, including in multiple brain regions. We previously showed that mice lacking USP2 present altered locomotor activity rhythms and response of the clock to light. However, the possible implication of USP2 in regulating other behaviors has yet to be tested. To address this, we ran a battery of behavioral tests on Usp2 KO mice. Firstly, we confirmed our prior findings of increased daily activity and reduced activity fragmentation in Usp2 KO mice. Further, mice lacking USP2 showed impaired motor coordination and equilibrium, a decrease in anxiety-like behavior, a deficit in working memory and in sensorimotor gating. On the other hand, no effects of Usp2 gene deletion were found on spatial memory. Hence, our data uncover the implication of USP2 in different behaviors and expands the range of the known functions of this deubiquitinase.
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10
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Kitamura H, Hashimoto M. USP2-Related Cellular Signaling and Consequent Pathophysiological Outcomes. Int J Mol Sci 2021; 22:1209. [PMID: 33530560 PMCID: PMC7865608 DOI: 10.3390/ijms22031209] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 12/13/2022] Open
Abstract
Ubiquitin specific protease (USP) 2 is a multifunctional deubiquitinating enzyme. USP2 modulates cell cycle progression, and therefore carcinogenesis, via the deubiquitination of cyclins and Aurora-A. Other tumorigenic molecules, including epidermal growth factor and fatty acid synthase, are also targets for USP2. USP2 additionally prevents p53 signaling. On the other hand, USP2 functions as a key component of the CLOCK/BMAL1 complex and participates in rhythmic gene expression in the suprachiasmatic nucleus and liver. USP2 variants influence energy metabolism by controlling hepatic gluconeogenesis, hepatic cholesterol uptake, adipose tissue inflammation, and subsequent systemic insulin sensitivity. USP2 also has the potential to promote surface expression of ion channels in renal and intestinal epithelial cells. In addition to modifying the production of cytokines in immune cells, USP2 also modulates the signaling molecules that are involved in cytokine signaling in the target cells. Usp2 knockout mice exhibit changes in locomotion and male fertility, which suggest roles for USP2 in the central nervous system and male genital tract, respectively. In this review, we summarize the cellular events with USP2 contributions and list the signaling molecules that are upstream or downstream of USP2. Additionally, we describe phenotypic differences found in the in vitro and in vivo experimental models.
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Affiliation(s)
- Hiroshi Kitamura
- Laboratory of Veterinary Physiology, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido 069-8501, Japan;
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11
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Srikanta SB, Cermakian N. To Ub or not to Ub: Regulation of circadian clocks by ubiquitination and deubiquitination. J Neurochem 2020; 157:11-30. [PMID: 32717140 DOI: 10.1111/jnc.15132] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/10/2020] [Accepted: 07/14/2020] [Indexed: 12/28/2022]
Abstract
Circadian clocks are internal timing systems that enable organisms to adjust their behavioral and physiological rhythms to the daily changes of their environment. These clocks generate self-sustained oscillations at the cellular, tissue, and behavioral level. The rhythm-generating mechanism is based on a gene expression network with a delayed negative feedback loop that causes the transcripts to oscillate with a period of approximately 24 hr. This oscillatory nature of the proteins involved in this network necessitates that they are intrinsically unstable, with a short half-life. Hence, post-translational modifications (PTMs) are important to precisely time the presence, absence, and interactions of these proteins at appropriate times of the day. Ubiquitination and deubiquitination are counter-balancing PTMs which play a key role in this regulatory process. In this review, we take a comprehensive look at the roles played by the processes of ubiquitination and deubiquitination in the clock machinery of the most commonly studied eukaryotic models of the circadian clock: plants, fungi, fruit flies, and mammals. We present the effects exerted by ubiquitinating and deubiquitinating enzymes on the stability, but also the activity, localization, and interactions of clock proteins. Overall, these PTMs have key roles in regulating not only the pace of the circadian clocks but also their response to external cues and their control of cellular functions.
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Affiliation(s)
- Shashank Bangalore Srikanta
- Integrated Program in Neuroscience, McGill University, Montréal, QC, Canada.,Laboratory of Molecular Chronobiology, Douglas Research Centre, Montréal, QC, Canada
| | - Nicolas Cermakian
- Laboratory of Molecular Chronobiology, Douglas Research Centre, Montréal, QC, Canada.,Department of Psychiatry, McGill University, Montréal, QC, Canada
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12
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Effects of aging and tumorigenesis on coupling between the circadian clock and cell cycle in colonic mucosa. Mech Ageing Dev 2020; 190:111317. [PMID: 32745473 DOI: 10.1016/j.mad.2020.111317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 06/21/2020] [Accepted: 07/14/2020] [Indexed: 01/20/2023]
Abstract
Aging and tumorigenesis are associated with decline and disruption of circadian rhythms in many tissues and accumulating evidence indicates molecular link between circadian clock and cell cycle. The aim of this study was to investigate the effect of aging and tumorigenesis on coupling between cell cycle and circadian clock oscillators in colon, which undergoes regular rhythmicity of cell cycle and expresses peripheral circadian clock. Using healthy 14-week-old mice and 33-week-old mice with and without colorectal tumors, we showed that the 24-h expression profiles of clock genes and clock-controlled genes were mostly unaffected by aging, whereas the genes of cell cycle and cell proliferation were rhythmic in the young colons but were silenced during aging. On the other hand, tumorigenesis completely silenced or dampened the circadian rhythmicity of the clock genes but only a few genes associated with cell cycle progression and cell proliferation. These results suggest that aging impacts the colonic circadian clock moderately but markedly suppresses the rhythms of cell cycle genes and appears to uncouple the cell cycle machinery from circadian clock control. Conversely, tumorigenesis predominantly affects the rhythms of colonic circadian clocks but is not associated with uncoupling of circadian clock and cell cycle.
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13
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Meng X, Xiong Z, Xiao W, Yuan C, Wang C, Huang Y, Tong J, Shi J, Chen Z, Liu C, Xie K, Xiong H, Chen K, Yang H, Zhang X. Downregulation of ubiquitin-specific protease 2 possesses prognostic and diagnostic value and promotes the clear cell renal cell carcinoma progression. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:319. [PMID: 32355763 PMCID: PMC7186618 DOI: 10.21037/atm.2020.02.141] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background Clear cell renal cell carcinoma (ccRCC), characterized by high mortality, invasion, metastasis, recurrence and drug resistance, is the most common malignant tumor of the urinary system. A clear understanding of the underlying molecular mechanisms and its role during tumorigenesis of RCC can contribute to development of prognostic and targeted therapies. Methods We analyzed datasets from the public database, TCGA, Oncomine, for differential expression of ubiquitin-specific protease 2 (USP2), and further investigated its relationship with the clinical stage, pathological grade and prognosis of renal cancer. We used real-time quantitative PCR and western blot analysis to validate USP2 expression in clinical samples and renal cancer cell lines. Finally, we used CCK-8 and transwell assays to determine its effects on biological functions in cells. Results We observed significantly lower levels of USP2 mRNA in renal cancer, relative to normal, tissues across the four datasets from the Oncomine database (P<0.001), 533 cases from TCGA database (P<0.0001) and 30 pairs of clinical samples (P<0.0001). Similarly, a decreased USP2 protein expression in ccRCC was detected following immunohistochemical (IHC) and western blot analyses. Furthermore, the aberrant expression of USP2 resulted in significant relationship with clinical stage, pathological grade and lower USP2 mRNA expression was interrelated to poor prognosis of renal cell carcinoma. USP2 acted as an independent factor for ccRCC diagnosis, with an AUC of 0.8888 (95% CI: 0.8529 to 0.9246; P<0.0001). Exogenous restoration of USP2 in ccRCC cells resulted in repression of cell proliferation, migration, and invasion. Conclusions Overall, these results show that USP2 acts as an anti-oncogene and an independent factor for ccRCC prognosis. Positive modulation of USP2 might lead to development of a novel strategy for ccRCC treatment.
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Affiliation(s)
- Xiangui Meng
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Zhiyong Xiong
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Wen Xiao
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Changfei Yuan
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Cheng Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yu Huang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Junwei Tong
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jian Shi
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Zhixian Chen
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Chenchen Liu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Kairu Xie
- Department of Pathogenic Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hailong Xiong
- Department of Pathogenic Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ke Chen
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Hongmei Yang
- Department of Pathogenic Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaoping Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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14
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Pan X, Mota S, Zhang B. Circadian Clock Regulation on Lipid Metabolism and Metabolic Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1276:53-66. [PMID: 32705594 PMCID: PMC8593891 DOI: 10.1007/978-981-15-6082-8_5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The basic helix-loop-helix-PAS transcription factor (CLOCK, Circadian locomotor output cycles protein kaput) was discovered in 1994 as a circadian clock. Soon after its discovery, the circadian clock, Aryl hydrocarbon receptor nuclear translocator-like protein 1 (ARNTL, also call BMAL1), was shown to regulate adiposity and body weight by controlling on the brain hypothalamic suprachiasmatic nucleus (SCN). Farther, circadian clock genes were determined to exert several of lipid metabolic and diabetes effects, overall indicating that CLOCK and BMAL1 act as a central master circadian clock. A master circadian clock acts through the neurons and hormones, with expression in the intestine, liver, kidney, lung, heart, SCN of brain, and other various cell types of the organization. Among circadian clock genes, numerous metabolic syndromes are the most important in the regulation of food intake (via regulation of circadian clock genes or clock-controlled genes in peripheral tissue), which lead to a variation in plasma phospholipids and tissue phospholipids. Circadian clock genes affect the regulation of transporters and proteins included in the regulation of phospholipid metabolism. These genes have recently received increasing recognition because a pharmacological target of circadian clock genes may be of therapeutic worth to make better resistance against insulin, diabetes, obesity, metabolism syndrome, atherosclerosis, and brain diseases. In this book chapter, we focus on the regulation of circadian clock and summarize its phospholipid effect as well as discuss the chemical, physiology, and molecular value of circadian clock pathway regulation for the treatment of plasma lipids and atherosclerosis.
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Affiliation(s)
- Xiaoyue Pan
- Department of Foundations of Medicine, New York University Long Island School of Medicine, Mineola, NY, USA.
- Diabetes and Obesity Research Center, New York University Winthrop Hospital, Mineola, NY, USA.
| | - Samantha Mota
- Department of Foundations of Medicine, New York University Long Island School of Medicine, Mineola, NY, USA
- Diabetes and Obesity Research Center, New York University Winthrop Hospital, Mineola, NY, USA
| | - Boyang Zhang
- Department of Foundations of Medicine, New York University Long Island School of Medicine, Mineola, NY, USA
- Diabetes and Obesity Research Center, New York University Winthrop Hospital, Mineola, NY, USA
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15
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Farmahin R, Gannon AM, Gagné R, Rowan-Carroll A, Kuo B, Williams A, Curran I, Yauk CL. Hepatic transcriptional dose-response analysis of male and female Fischer rats exposed to hexabromocyclododecane. Food Chem Toxicol 2018; 133:110262. [PMID: 30594549 DOI: 10.1016/j.fct.2018.12.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/13/2018] [Accepted: 12/20/2018] [Indexed: 12/14/2022]
Abstract
Hexabromocyclododecane (HBCD) is a brominated flame retardant found in the environment and human tissues. The toxicological effects of HBCD exposure are not clearly understood. We employed whole-genome RNA-sequencing on liver samples from male and female Fischer rats exposed to 0, 250, 1250, and 5000 mg technical mixture of HBCD/kg diet for 28 days to gain further insight into HBCD toxicity. HBCD altered 428 and 250 gene transcripts in males and females, respectively, which were involved in metabolism of xenobiotics, oxidative stress, immune response, metabolism of glucose and lipids, circadian regulation, cell cycle, fibrotic activity, and hormonal balance. Signature analysis supported that HBCD operates through the constitutive androstane and pregnane X receptors. The median transcriptomic benchmark dose (BMD) for the lowest statistically significant pathway was within 1.5-fold of the BMD for increased liver weight, while the BMD for the lowest pathway with at least three modeled genes (minimum 5% of pathway) was similar to the lowest apical endpoint BMD. The results show how transcriptional analyses can inform mechanisms underlying chemical toxicity and the doses at which potentially adverse effects occur. This experiment is part of a larger study exploring the use of toxicogenomics and high-throughput screening for human health risk assessment.
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Affiliation(s)
- Reza Farmahin
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Anne Marie Gannon
- Regulatory Toxicology Research Division, Health Products and Food Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Rémi Gagné
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Andrea Rowan-Carroll
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Byron Kuo
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Ivan Curran
- Regulatory Toxicology Research Division, Health Products and Food Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada.
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Chen S, Yang J, Yang L, Zhang Y, Zhou L, Liu Q, Duan C, Mieres CA, Zhou G, Xu G. Ubiquitin ligase
TRAF
2 attenuates the transcriptional activity of the core clock protein
BMAL
1 and affects the maximal
Per1
mRNA
level of the circadian clock in cells. FEBS J 2018; 285:2987-3001. [DOI: 10.1111/febs.14595] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 05/30/2018] [Accepted: 06/21/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Suping Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases Soochow University Suzhou Jiangsu China
| | - Jing Yang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases Soochow University Suzhou Jiangsu China
| | - Lu Yang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases Soochow University Suzhou Jiangsu China
| | - Yang Zhang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases Soochow University Suzhou Jiangsu China
| | - Liang Zhou
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases Soochow University Suzhou Jiangsu China
| | - Qing Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases Soochow University Suzhou Jiangsu China
| | - Chunyan Duan
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases Soochow University Suzhou Jiangsu China
| | - Crystal A. Mieres
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases Soochow University Suzhou Jiangsu China
- Molecular and Cellular Therapeutics Royal College of Surgeons in Ireland Dublin Ireland
| | - Guanghai Zhou
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases Soochow University Suzhou Jiangsu China
- Institute of Cardiovascular Endocrinology Key Laboratory of Atherosclerosis in Universities of Shandong Taishan Medical University Tai'an Shandong China
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases Soochow University Suzhou Jiangsu China
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17
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Chen S, Yang J, Zhang Y, Duan C, Liu Q, Huang Z, Xu Y, Zhou L, Xu G. Ubiquitin-conjugating enzyme UBE2O regulates cellular clock function by promoting the degradation of the transcription factor BMAL1. J Biol Chem 2018; 293:11296-11309. [PMID: 29871923 DOI: 10.1074/jbc.ra117.001432] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 05/16/2018] [Indexed: 12/25/2022] Open
Abstract
Dysregulation of the circadian rhythm is associated with many diseases, including diabetes, obesity, and cancer. Aryl hydrocarbon receptor nuclear translocator-like protein 1 (Arntl or Bmal1) is the only clock gene whose loss disrupts circadian locomotor behavior in constant darkness. BMAL1 levels are affected by proteasomal inhibition and by several enzymes in the ubiquitin-proteasome system, but the exact molecular mechanism remains unclear. Here, using immunoprecipitation and MS analyses, we discovered an interaction between BMAL1 and ubiquitin-conjugating enzyme E2 O (UBE2O), an E3-independent E2 ubiquitin-conjugating enzyme (i.e. hybrid E2/E3 enzyme). Biochemical experiments with cell lines and animal tissues validated this specific interaction and uncovered that UBE2O expression reduces BMAL1 levels by promoting its ubiquitination and degradation. Moreover, UBE2O expression/knockdown diminished/increased, respectively, BMAL1-mediated transcriptional activity but did not affect BMAL1 gene expression. Bioluminescence experiments disclosed that UBE2O knockdown elevates the amplitude of the circadian clock in human osteosarcoma U2OS cells. Furthermore, mapping of the BMAL1-interacting domain in UBE2O and analyses of BMAL1 stability and ubiquitination revealed that the conserved region 2 (CR2) in UBE2O significantly enhances BMAL1 ubiquitination and decreases BMAL1 protein levels. A Cys-to-Ser substitution experiment identified the critical Cys residue in the CR2 domain responsible for BMAL1 ubiquitination. This work identifies UBE2O as a critical regulator in the ubiquitin-proteasome system, which modulates BMAL1 transcriptional activity and circadian function by promoting BMAL1 ubiquitination and degradation under normal physiological conditions.
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Affiliation(s)
- Suping Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Jing Yang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Yang Zhang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Chunyan Duan
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Qing Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Zhengyun Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Ying Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Liang Zhou
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China.
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China; Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China.
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18
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Zhang Y, Duan C, Yang J, Chen S, Liu Q, Zhou L, Huang Z, Xu Y, Xu G. Deubiquitinating enzyme USP9X regulates cellular clock function by modulating the ubiquitination and degradation of a core circadian protein BMAL1. Biochem J 2018; 475:1507-1522. [PMID: 29626158 DOI: 10.1042/bcj20180005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 04/03/2018] [Accepted: 04/04/2018] [Indexed: 01/12/2023]
Abstract
Living organisms on the earth maintain a roughly 24 h circadian rhythm, which is regulated by circadian clock genes and their protein products. Post-translational modifications of core clock proteins could affect the circadian behavior. Although ubiquitination of core clock proteins was studied extensively, the reverse process, deubiquitination, has only begun to unfold and the role of this regulation on circadian function is not completely understood. Here, we use affinity purification and mass spectrometry analysis to identify probable ubiquitin carboxyl-terminal hydrolase FAF-X (USP9X) as an interacting protein of the core clock protein aryl hydrocarbon receptor nuclear translocator-like protein 1 (ARNTL or BMAL1). Through biochemical experiments, we discover that USP9X reduces BMAL1 ubiquitination, enhances its stability, and increases its protein level, leading to the elevated transcriptional activity. Bioluminescence measurement reveals that USP9X knockdown decreases the amplitude of the cellular circadian rhythm but the period and phase are not affected. Our experiments find a new regulator for circadian clock at the post-translational level and demonstrate a different regulatory function for the circadian clock through the deubiquitination and the up-regulation of the core clock protein BMAL1 in the positive limb of the transcription-translation feedback loop.
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Affiliation(s)
- Yang Zhang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Chunyan Duan
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Jing Yang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Suping Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Qing Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Liang Zhou
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Zhengyun Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda (CAM-SU) Genomic Resource Center, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Ying Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda (CAM-SU) Genomic Resource Center, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
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19
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Park N, Song J, Jeong S, Thi Tran T, Ko HW, Kim EY. Vaccinia-related kinase 3 (VRK3) sets the circadian period and amplitude by affecting the subcellular localization of clock proteins in mammalian cells. Biochem Biophys Res Commun 2017; 487:320-326. [PMID: 28412365 DOI: 10.1016/j.bbrc.2017.04.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 04/09/2017] [Indexed: 11/26/2022]
Abstract
In the eukaryotic circadian clock machinery, negative feedback repression of CLOCK (CLK) and BMAL1 transcriptional activity by PERIOD (PER) and CRYPTOCHROME (CRY) underlies the basis for 24 h rhythmic gene expression. Thus, precise regulation of the time-dependent nuclear entry of circadian repressors is crucial to generating normal circadian rhythms. Here, we sought to identify novel kinase(s) that regulate nuclear entry of mammalian CRY1 (mCRY1) with an unbiased screening using red fluorescent protein (RFP)-tagged human kinome expression plasmids in mammalian cells. Transient expression of human vaccinia-related kinase 3 (hVRK3) reduced the nuclear presence of mCRY1. hVRK3 expression also induced alterations in the subcellular localization of other core clock proteins, including mCRY2, mPER2, and BMAL1. In contrast, the subcellular localization of mCLK was not changed. Given that singly expressed mCLK mostly resides in the cytoplasm and that nuclear localization sequence (NLS) mutation of hVRK3 attenuated the effect of hVRK3 co-expression on subcellular localization, ectopically expressed hVRK3 presumably reduces the retention of proteins in the nucleus. Finally, downregulation of hvrk3 using siRNA reduced the amplitude and lengthened the period of the cellular bioluminescence rhythm. Taken together, these data suggest that VRK3 plays a role in setting the amplitude and period length of circadian rhythms in mammalian cells.
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Affiliation(s)
- Nayoung Park
- Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, Kyunggi-do, 16499, Republic of Korea; Department of Brain Science, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, Kyunggi-do, 16499, Republic of Korea
| | - Jieun Song
- College of Pharmacy, Dongguk University-Seoul, 32 Donggukro, Ilsandonggu, Goyangsi, Gyeonggido, 410-820, Republic of Korea
| | - Seongsu Jeong
- Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, Kyunggi-do, 16499, Republic of Korea; Department of Brain Science, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, Kyunggi-do, 16499, Republic of Korea
| | - Thanh Thi Tran
- College of Pharmacy, Dongguk University-Seoul, 32 Donggukro, Ilsandonggu, Goyangsi, Gyeonggido, 410-820, Republic of Korea
| | - Hyuk Wan Ko
- College of Pharmacy, Dongguk University-Seoul, 32 Donggukro, Ilsandonggu, Goyangsi, Gyeonggido, 410-820, Republic of Korea
| | - Eun Young Kim
- Neuroscience Graduate Program, Department of Biomedical Sciences, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, Kyunggi-do, 16499, Republic of Korea; Department of Brain Science, Ajou University School of Medicine, 164 Worldcup-ro, Yeongtong-gu, Suwon, Kyunggi-do, 16499, Republic of Korea.
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20
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Vriend J, Liu W, Reiter RJ. The pineal gland: A model for adrenergic modulation of ubiquitin ligases. PLoS One 2017; 12:e0172441. [PMID: 28212404 PMCID: PMC5315301 DOI: 10.1371/journal.pone.0172441] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/04/2017] [Indexed: 12/26/2022] Open
Abstract
INTRODUCTION A recent study of the pineal gland of the rat found that the expression of more than 3000 genes showed significant day/night variations (The Hartley dataset). The investigators of this report made available a supplemental table in which they tabulated the expression of many genes that they did not discuss, including those coding for components of the ubiquitin proteasome system. Herein we identify the genes of the ubiquitin proteasome system whose expression were significantly influenced by environmental lighting in the Hartley dataset, those that were stimulated by DBcAMP in pineal glands in culture, and those that were stimulated by norepinephrine. PURPOSE Using the Ubiquitin and Ubiquitin-like Conjugation Database (UUCA) we identified ubiquitin ligases and conjugases, and deubiquitinases in the Hartley dataset for the purpose of determining whether expression of genes of the ubiquitin proteasome pathway were significantly influenced by day/night variations and if these variations were regulated by autonomic innervation of the pineal gland from the superior cervical ganglia. METHODS In the Hartley experiments pineal glands groups of rats sacrificed during the day and groups sacrificed during the night were examined for gene expression. Additional groups of rats had their superior cervical ganglia removed surgically or surgically decentralized and the pineal glands likewise examined for gene expression. RESULTS The genes with at least a 2-fold day/night significant difference in expression included genes for 5 ubiquitin conjugating enzymes, genes for 58 ubiquitin E3 ligases and genes for 6 deubiquitinases. A 35-fold day/night difference was noted in the expression of the gene Sik1, which codes for a protein containing both an ubiquitin binding domain (UBD) and an ubiquitin-associated (UBA) domain. Most of the significant differences in these genes were prevented by surgical removal, or disconnection, of the superior cervical ganglia, and most were responsive, in vitro, to treatment with a cyclic AMP analog, and norepinephrine. All previously described 24-hour rhythms in the pineal require an intact sympathetic input from the superior cervical ganglia. CONCLUSIONS The Hartley dataset thus provides evidence that the pineal gland is a highly useful model for studying adrenergically dependent mechanisms regulating variations in ubiquitin ligases, ubiquitin conjugases, and deubiquitinases, mechanisms that may be physiologically relevant not only in the pineal gland, but in all adrenergically innervated tissue.
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Affiliation(s)
- Jerry Vriend
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Wenjun Liu
- Department of Pathology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, Texas, United States of America
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21
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Ren Y, Zhao P, Liu J, Yuan Y, Cheng Q, Zuo Y, Qian L, Liu C, Guo T, Zhang L, Wang X, Qian G, Li L, Ge J, Dai J, Xiong S, Zheng H. Deubiquitinase USP2a Sustains Interferons Antiviral Activity by Restricting Ubiquitination of Activated STAT1 in the Nucleus. PLoS Pathog 2016; 12:e1005764. [PMID: 27434509 PMCID: PMC4951015 DOI: 10.1371/journal.ppat.1005764] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 06/22/2016] [Indexed: 11/29/2022] Open
Abstract
STAT1 is a critical transcription factor for regulating host antiviral defenses. STAT1 activation is largely dependent on phosphorylation at tyrosine 701 site of STAT1 (pY701-STAT1). Understanding how pY701-STAT1 is regulated by intracellular signaling remains a major challenge. Here we find that pY701-STAT1 is the major form of ubiquitinated-STAT1 induced by interferons (IFNs). While total STAT1 remains relatively stable during the early stages of IFNs signaling, pY701-STAT1 can be rapidly downregulated by the ubiquitin-proteasome system. Moreover, ubiquitinated pY701-STAT1 is located predominantly in the nucleus, and inhibiting nuclear import of pY701-STAT1 significantly blocks ubiquitination and downregulation of pY701-STAT1. Furthermore, we reveal that the deubiquitinase USP2a translocates into the nucleus and binds to pY701-STAT1, and inhibits K48-linked ubiquitination and degradation of pY701-STAT1. Importantly, USP2a sustains IFNs-induced pY701-STAT1 levels, and enhances all three classes of IFNs- mediated signaling and antiviral activity. To our knowledge, this is the first identified deubiquitinase that targets activated pY701-STAT1. These findings uncover a positive mechanism by which IFNs execute efficient antiviral signaling and function, and may provide potential targets for improving IFNs-based antiviral therapy. Phosphorylated STAT1 at tyrosine 701 site (pY701-STAT1) is critical for regulating many cellular functions including antiviral immunity. Maintaining sufficient pY701-STAT1 levels in the nucleus is essential to sustain efficient interferons (IFNs) signaling and antiviral functions. Therefore, it is important to clarify how pY701-STAT1 levels are positively regulated in the nucleus. Here, we demonstrated for the first time that IFNs-induced pY701-STAT1 largely raised STAT1 ubiquitination, and ubiquitinated-pY701-STAT1 is located predominantly in the nucleus and regulated by proteasome-dependent degradation. In IFNs signaling, the deubiquitinase USP2a translocates into the nucleus and binds to pY701-STAT1. USP2a positively regulates pY701-STAT1 levels through inhibiting its K48-linked ubiquitination and degradation. Importantly, USP2a sustains all three classes of IFNs-mediated signaling and antiviral function. Our studies uncover an important positive mechanism in the nucleus by which IFNs can execute efficient antiviral signaling and functions.
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Affiliation(s)
- Ying Ren
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Peng Zhao
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Jin Liu
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Yukang Yuan
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Qiao Cheng
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Yibo Zuo
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Liping Qian
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Chang Liu
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Tingting Guo
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Liting Zhang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Xiaofang Wang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Guanghui Qian
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Lemin Li
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Jun Ge
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Jianfeng Dai
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Sidong Xiong
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Jiangsu, China
- * E-mail: (SX); (HZ)
| | - Hui Zheng
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Jiangsu, China
- * E-mail: (SX); (HZ)
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22
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USP2-45 Is a Circadian Clock Output Effector Regulating Calcium Absorption at the Post-Translational Level. PLoS One 2016; 11:e0145155. [PMID: 26756164 PMCID: PMC4710524 DOI: 10.1371/journal.pone.0145155] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 12/01/2015] [Indexed: 01/06/2023] Open
Abstract
The mammalian circadian clock influences most aspects of physiology and behavior through the transcriptional control of a wide variety of genes, mostly in a tissue-specific manner. About 20 clock-controlled genes (CCGs) oscillate in virtually all mammalian tissues and are generally considered as core clock components. One of them is Ubiquitin-Specific Protease 2 (Usp2), whose status remains controversial, as it may be a cogwheel regulating the stability or activity of core cogwheels or an output effector. We report here that Usp2 is a clock output effector related to bodily Ca2+ homeostasis, a feature that is conserved across evolution. Drosophila with a whole-body knockdown of the orthologue of Usp2, CG14619 (dUsp2-kd), predominantly die during pupation but are rescued by dietary Ca2+ supplementation. Usp2-KO mice show hyperabsorption of dietary Ca2+ in small intestine, likely due to strong overexpression of the membrane scaffold protein NHERF4, a regulator of the Ca2+ channel TRPV6 mediating dietary Ca2+ uptake. In this tissue, USP2-45 is found in membrane fractions and negatively regulates NHERF4 protein abundance in a rhythmic manner at the protein level. In clock mutant animals (Cry1/Cry2-dKO), rhythmic USP2-45 expression is lost, as well as the one of NHERF4, confirming the inverse relationship between USP2-45 and NHERF4 protein levels. Finally, USP2-45 interacts in vitro with NHERF4 and endogenous Clathrin Heavy Chain. Taken together these data prompt us to define USP2-45 as the first clock output effector acting at the post-translational level at cell membranes and possibly regulating membrane permeability of Ca2+.
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23
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Udoh US, Valcin JA, Gamble KL, Bailey SM. The Molecular Circadian Clock and Alcohol-Induced Liver Injury. Biomolecules 2015; 5:2504-37. [PMID: 26473939 PMCID: PMC4693245 DOI: 10.3390/biom5042504] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/02/2015] [Accepted: 09/09/2015] [Indexed: 12/11/2022] Open
Abstract
Emerging evidence from both experimental animal studies and clinical human investigations demonstrates strong connections among circadian processes, alcohol use, and alcohol-induced tissue injury. Components of the circadian clock have been shown to influence the pathophysiological effects of alcohol. Conversely, alcohol may alter the expression of circadian clock genes and the rhythmic behavioral and metabolic processes they regulate. Therefore, we propose that alcohol-mediated disruption in circadian rhythms likely underpins many adverse health effects of alcohol that cut across multiple organ systems. In this review, we provide an overview of the circadian clock mechanism and showcase results from new studies in the alcohol field implicating the circadian clock as a key target of alcohol action and toxicity in the liver. We discuss various molecular events through which alcohol may work to negatively impact circadian clock-mediated processes in the liver, and contribute to tissue pathology. Illuminating the mechanistic connections between the circadian clock and alcohol will be critical to the development of new preventative and pharmacological treatments for alcohol use disorders and alcohol-mediated organ diseases.
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Affiliation(s)
- Uduak S Udoh
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA.
| | - Jennifer A Valcin
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA.
| | - Karen L Gamble
- Department of Psychiatry, Division of Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35233, USA.
| | - Shannon M Bailey
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL 35233, USA.
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24
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Antigen exposure in the late light period induces severe symptoms of food allergy in an OVA-allergic mouse model. Sci Rep 2015; 5:14424. [PMID: 26419283 PMCID: PMC4588575 DOI: 10.1038/srep14424] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 08/28/2015] [Indexed: 11/08/2022] Open
Abstract
The mammalian circadian clock controls many physiological processes that include immune responses and allergic reactions. Several studies have investigated the circadian regulation of intestinal permeability and tight junctions known to be affected by cytokines. However, the contribution of circadian clock to food allergy symptoms remains unclear. Therefore, we investigated the role of the circadian clock in determining the severity of food allergies. We prepared an ovalbumin food allergy mouse model, and orally administered ovalbumin either late in the light or late in the dark period under light-dark cycle. The light period group showed higher allergic diarrhea and weight loss than the dark period group. The production of type 2 cytokines, IL-13 and IL-5, from the mesenteric lymph nodes and ovalbumin absorption was higher in the light period group than in the dark period group. Compared to the dark period group, the mRNA expression levels of the tight junction proteins were lower in the light period group. We have demonstrated that increased production of type 2 cytokines and intestinal permeability in the light period induced severe food allergy symptoms. Our results suggest that the time of food antigen intake might affect the determination of the severity of food allergy symptoms.
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25
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Stojkovic K, Wing SS, Cermakian N. A central role for ubiquitination within a circadian clock protein modification code. Front Mol Neurosci 2014; 7:69. [PMID: 25147498 PMCID: PMC4124793 DOI: 10.3389/fnmol.2014.00069] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 07/08/2014] [Indexed: 11/19/2022] Open
Abstract
Circadian rhythms, endogenous cycles of about 24 h in physiology, are generated by a master clock located in the suprachiasmatic nucleus of the hypothalamus and other clocks located in the brain and peripheral tissues. Circadian disruption is known to increase the incidence of various illnesses, such as mental disorders, metabolic syndrome, and cancer. At the molecular level, periodicity is established by a set of clock genes via autoregulatory translation–transcription feedback loops. This clock mechanism is regulated by post-translational modifications such as phosphorylation and ubiquitination, which set the pace of the clock. Ubiquitination in particular has been found to regulate the stability of core clock components but also other clock protein functions. Mutation of genes encoding ubiquitin ligases can cause either elongation or shortening of the endogenous circadian period. Recent research has also started to uncover roles for deubiquitination in the molecular clockwork. Here, we review the role of the ubiquitin pathway in regulating the circadian clock and we propose that ubiquitination is a key element in a clock protein modification code that orchestrates clock mechanisms and circadian behavior over the daily cycle.
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Affiliation(s)
- Katarina Stojkovic
- Douglas Mental Health University Institute, McGill University, Montréal, QC Canada
| | - Simon S Wing
- Polypeptide Laboratory, Department of Medicine-McGill University Health Centre Research Institute, McGill University, Montréal, QC Canada
| | - Nicolas Cermakian
- Douglas Mental Health University Institute, McGill University, Montréal, QC Canada
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