1
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Lamberti ML, Spangler RK, Cerdeira V, Ares M, Rivollet L, Ashley GE, Coronado AR, Tripathi S, Spiousas I, Ward JD, Partch CL, Bénard CY, Goya ME, Golombek DA. Clock gene homologs lin-42 and kin-20 regulate circadian rhythms in C. elegans. Sci Rep 2024; 14:12936. [PMID: 38839826 PMCID: PMC11153552 DOI: 10.1038/s41598-024-62303-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024] Open
Abstract
Circadian rhythms are endogenous oscillations in nearly all organisms, from prokaryotes to humans, allowing them to adapt to cyclical environments for close to 24 h. Circadian rhythms are regulated by a central clock, based on a transcription-translation feedback loop. One important protein in the central loop in metazoan clocks is PERIOD, which is regulated in part by Casein kinase 1ε/δ (CK1ε/δ) phosphorylation. In the nematode Caenorhabditis elegans, period and casein kinase 1ε/δ are conserved as lin-42 and kin-20, respectively. Here, we studied the involvement of lin-42 and kin-20 in the circadian rhythms of the adult nematode using a bioluminescence-based circadian transcriptional reporter. We show that mutations of lin-42 and kin-20 generate a significantly longer endogenous period, suggesting a role for both genes in the nematode circadian clock, as in other organisms. These phenotypes can be partially rescued by overexpression of either gene under their native promoter. Both proteins are expressed in neurons and epidermal seam cells, as well as in other cells. Depletion of LIN-42 and KIN-20, specifically in neuronal cells after development, was sufficient to lengthen the period of oscillating sur-5 expression. Therefore, we conclude that LIN-42 and KIN-20 are critical regulators of the adult nematode circadian clock through neuronal cells.
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Affiliation(s)
- Melisa L Lamberti
- Laboratorio de Cronobiología, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - Rebecca K Spangler
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, USA
| | - Victoria Cerdeira
- Department of Biological Sciences, Université du Québec à Montréal, CERMO-FC Research Center, Montréal, QC, Canada
| | - Myriam Ares
- Department of Biological Sciences, Université du Québec à Montréal, CERMO-FC Research Center, Montréal, QC, Canada
| | - Lise Rivollet
- Department of Biological Sciences, Université du Québec à Montréal, CERMO-FC Research Center, Montréal, QC, Canada
| | - Guinevere E Ashley
- Department of Molecular, Cell & Developmental Biology, University of California Santa Cruz, Santa Cruz, USA
| | - Andrea Ramos Coronado
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, USA
| | - Ignacio Spiousas
- Laboratorio Interdisciplinario del Tiempo (LITERA), Universidad de San Andrés/CONICET, Buenos Aires, Argentina
| | - Jordan D Ward
- Department of Molecular, Cell & Developmental Biology, University of California Santa Cruz, Santa Cruz, USA
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, USA
- Center for Circadian Biology, UC San Diego, La Jolla, CA, USA
| | - Claire Y Bénard
- Department of Biological Sciences, Université du Québec à Montréal, CERMO-FC Research Center, Montréal, QC, Canada
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - M Eugenia Goya
- European Institute for the Biology of Aging, University Medical Center Groningen, Groningen, The Netherlands.
| | - Diego A Golombek
- Laboratorio de Cronobiología, Universidad Nacional de Quilmes, Buenos Aires, Argentina.
- Laboratorio Interdisciplinario del Tiempo (LITERA), Universidad de San Andrés/CONICET, Buenos Aires, Argentina.
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2
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Francisco JC, Virshup DM. Hierarchical and scaffolded phosphorylation of two degrons controls PER2 stability. J Biol Chem 2024; 300:107391. [PMID: 38777144 PMCID: PMC11223080 DOI: 10.1016/j.jbc.2024.107391] [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: 11/02/2023] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
The duration of the transcription-repression cycles that give rise to mammalian circadian rhythms is largely determined by the stability of the PERIOD (PER) protein, the rate-limiting components of the molecular clock. The degradation of PERs is tightly regulated by multisite phosphorylation by casein kinase 1 (CK1δ/ε). In this phosphoswitch, phosphorylation of a PER2 degron [degron 2 (D2)] causes degradation, while phosphorylation of the PER2 familial advanced sleep phase (FASP) domain blocks CK1 activity on the degron, stabilizing PER2. However, this model and many other studies of PER2 degradation do not include the second degron of PER2 that is conserved in PER1, termed degron 1 (D1). We examined how these two degrons contribute to PER2 stability, affect the balance of the phosphoswitch, and how they are differentiated by CK1. Using PER2-luciferase fusions and real-time luminometry, we investigated the contribution of both D2 and of CK1-PER2 binding. We find that D1, like D2, is a substrate of CK1 but that D1 plays only a 'backup' role in PER2 degradation. Notably, CK1 bound to a PER1:PER2 dimer protein can phosphorylate PER1 D1 in trans. This scaffolded phosphorylation provides additional levels of control to PER stability and circadian rhythms.
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Affiliation(s)
- Joel Celio Francisco
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - David M Virshup
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore; Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA.
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3
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Rojas BL, Vazquez-Rivera E, Partch CL, Bradfield CA. Dimerization Rules of Mammalian PAS Proteins. J Mol Biol 2024; 436:168406. [PMID: 38109992 PMCID: PMC10922841 DOI: 10.1016/j.jmb.2023.168406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/20/2023]
Abstract
The PAS (PER, ARNT, SIM) protein family plays a vital role in mammalian biology and human disease. This analysis arose from an interest in the signaling mechanics by the Ah receptor (AHR) and the Ah receptor nuclear translocator (ARNT). After more than fifty years by studying this and related mammalian sensor systems, describing the role of PAS domains in signal transduction is still challenging. In this perspective, we attempt to interpret recent studies of mammalian PAS protein structure and consider how this new insight might explain how these domains are employed in human signal transduction with an eye towards developing strategies to target and engineer these molecules for a new generation of therapeutics. Our approach is to integrate our understanding of PAS protein history, cell biology, and molecular biology with recent structural discoveries to help explain the mechanics of mammalian PAS protein signaling. As a learning set, we focus on sequences and crystal structures of mammalian PAS protein dimers that can be visualized using readily available software.
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Affiliation(s)
- Brenda L Rojas
- Molecular and Environmental Toxicology Center, University of Wisconsin at Madison, USA
| | | | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, USA
| | - Christopher A Bradfield
- Molecular and Environmental Toxicology Center, University of Wisconsin at Madison, USA; McArdle Laboratory for Cancer Research. University of Wisconsin, School of Medicine and Public Health, Madison, WI, USA.
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4
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Sharma D, Partch CL. PAS Dimerization at the Nexus of the Mammalian Circadian Clock. J Mol Biol 2024; 436:168341. [PMID: 37924861 DOI: 10.1016/j.jmb.2023.168341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/23/2023] [Accepted: 10/29/2023] [Indexed: 11/06/2023]
Abstract
Circadian rhythms are genetically encoded molecular clocks for internal biological timekeeping. Organisms from single-cell bacteria to humans use these clocks to adapt to the external environment and synchronize their physiology and behavior to solar light/dark cycles. Although the proteins that constitute the molecular 'cogs' and give rise to circadian rhythms are now known, we still lack a detailed understanding of how these proteins interact to generate and sustain the ∼24-hour circadian clock. Structural studies have helped to expand the architecture of clock proteins and have revealed the abundance of the only well-defined structured regions in the mammalian clock called Per-ARNT-Sim (PAS) domains. PAS domains are modular, evolutionarily conserved sensory and signaling domains that typically mediate protein-protein interactions. In the mammalian circadian clock, PAS domains modulate homo and heterodimerization of several core clock proteins that assemble into transcription factors or repressors. This review will focus on the functional importance of the PAS domains in the circadian clock from a biophysical and biochemical standpoint and describe their roles in clock protein interactions and circadian timekeeping.
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Affiliation(s)
- Diksha Sharma
- Department of Chemistry and Biochemistry, University of California Santa Cruz, CA, United States
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California Santa Cruz, CA, United States; Center for Circadian Biology, University of California San Diego, CA, United States.
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5
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Lamberti ML, Spangler RK, Cerdeira V, Ares M, Rivollet L, Ashley GE, Coronado AR, Tripathi S, Spiousas I, Ward JD, Partch CL, Bénard CY, Goya ME, Golombek DA. Regulation of the circadian clock in C. elegans by clock gene homologs kin-20 and lin-42. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.13.536481. [PMID: 38105938 PMCID: PMC10723253 DOI: 10.1101/2023.04.13.536481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Circadian rhythms are endogenous oscillations present in nearly all organisms from prokaryotes to humans, allowing them to adapt to cyclical environments close to 24 hours. Circadian rhythms are regulated by a central clock, which is based on a transcription-translation feedback loop. One important protein in the central loop in metazoan clocks is PERIOD, which is regulated in part by Casein kinase 1 ε/δ (CK1 ε/δ ) phosphorylation. In the nematode Caenorhabditis elegans , period and casein kinase 1ε/δ are conserved as lin-42 and kin-20 , respectively. Here we studied the involvement of lin-42 and kin-20 in circadian rhythms of the adult nematode using a bioluminescence-based circadian transcriptional reporter. We show that mutations of lin-42 and kin-20 generate a significantly longer endogenous period, suggesting a role for both genes in the nematode circadian clock, as in other organisms. These phenotypes can be partially rescued by overexpression of either gene under their native promoter. Both proteins are expressed in neurons and seam cells, a population of epidermal stem cells in C. elegans that undergo multiple divisions during development. Depletion of LIN-42 and KIN-20 specifically in neuronal cells after development was sufficient to lengthen the period of oscillating sur-5 expression. Therefore, we conclude that LIN-42 and KIN-20 are critical regulators of the adult nematode circadian clock through neuronal cells.
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6
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Laothamatas I, Rasmussen ES, Green CB, Takahashi JS. Metabolic and chemical architecture of the mammalian circadian clock. Cell Chem Biol 2023; 30:1033-1052. [PMID: 37708890 PMCID: PMC10631358 DOI: 10.1016/j.chembiol.2023.08.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/20/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023]
Abstract
Circadian rhythms are endogenous periodic biological processes that occur on a daily timescale. These rhythms are generated by a transcriptional/translational feedback loop that consists of the CLOCK-BMAL1 heterodimeric transcriptional activator complex and the PER1/2-CRY1/2-CK1δ/ε repressive complex. The output pathways of this molecular feedback loop generate circadian rhythmicity in various biological processes. Among these, metabolism is a primary regulatory target of the circadian clock which can also feedback to modulate clock function. This intertwined relationship between circadian rhythms and metabolism makes circadian clock components promising therapeutic targets. Despite this, pharmacological therapeutics that target the circadian clock are relatively rare. In this review, we hope to stimulate interest in chemical chronobiology by providing a comprehensive background on the molecular mechanism of mammalian circadian rhythms and their connection to metabolism, highlighting important studies in the chemical approach to circadian research, and offering our perspectives on future developments in the field.
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Affiliation(s)
- Isara Laothamatas
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Emil Sjulstok Rasmussen
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Carla B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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7
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Lee K, Lee C. Generation of CRISPR-Cas9-mediated knockin mutant models in mice and MEFs for studies of polymorphism in clock genes. Sci Rep 2023; 13:8109. [PMID: 37208532 DOI: 10.1038/s41598-023-35203-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 05/14/2023] [Indexed: 05/21/2023] Open
Abstract
The creation of mutant mice has been invaluable for advancing biomedical science, but is too time- and resource-intensive for investigating the full range of mutations and polymorphisms. Cell culture models are therefore an invaluable complement to mouse models, especially for cell-autonomous pathways like the circadian clock. In this study, we quantitatively assessed the use of CRISPR to create cell models in mouse embryonic fibroblasts (MEFs) as compared to mouse models. We generated two point mutations in the clock genes Per1 and Per2 in mice and in MEFs using the same sgRNAs and repair templates for HDR and quantified the frequency of the mutations by digital PCR. The frequency was about an order of magnitude higher in mouse zygotes compared to that in MEFs. However, the mutation frequency in MEFs was still high enough for clonal isolation by simple screening of a few dozen individual cells. The Per mutant cells that we generated provide important new insights into the role of the PAS domain in regulating PER phosphorylation, a key aspect of the circadian clock mechanism. Quantification of the mutation frequency in bulk MEF populations provides a valuable basis for optimizing CRISPR protocols and time/resource planning for generating cell models for further studies.
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Affiliation(s)
- Kwangjun Lee
- Program in Neuroscience, Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Choogon Lee
- Program in Neuroscience, Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA.
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8
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Giesecke A, Johnstone PS, Lamaze A, Landskron J, Atay E, Chen KF, Wolf E, Top D, Stanewsky R. A novel period mutation implicating nuclear export in temperature compensation of the Drosophila circadian clock. Curr Biol 2023; 33:336-350.e5. [PMID: 36584676 DOI: 10.1016/j.cub.2022.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/14/2022] [Accepted: 12/06/2022] [Indexed: 12/30/2022]
Abstract
Circadian clocks are self-sustained molecular oscillators controlling daily changes of behavioral activity and physiology. For functional reliability and precision, the frequency of these molecular oscillations must be stable at different environmental temperatures, known as "temperature compensation." Despite being an intrinsic property of all circadian clocks, this phenomenon is not well understood at the molecular level. Here, we use behavioral and molecular approaches to characterize a novel mutation in the period (per) clock gene of Drosophila melanogaster, which alters a predicted nuclear export signal (NES) of the PER protein and affects temperature compensation. We show that this new perI530A allele leads to progressively longer behavioral periods and clock oscillations with increasing temperature in both clock neurons and peripheral clock cells. While the mutant PERI530A protein shows normal circadian fluctuations and post-translational modifications at cool temperatures, increasing temperatures lead to both severe amplitude dampening and hypophosphorylation of PERI530A. We further show that PERI530A displays reduced repressor activity at warmer temperatures, presumably because it cannot inactivate the transcription factor CLOCK (CLK), indicated by temperature-dependent altered CLK post-translational modification in perI530A flies. With increasing temperatures, nuclear accumulation of PERI530A within clock neurons is increased, suggesting that wild-type PER is exported out of the nucleus at warm temperatures. Downregulating the nuclear export factor CRM1 also leads to temperature-dependent changes of behavioral rhythms, suggesting that the PER NES and the nuclear export of clock proteins play an important role in temperature compensation of the Drosophila circadian clock.
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Affiliation(s)
- Astrid Giesecke
- Institute of Neuro- and Behavioural Biology, Westfälische Wilhelms University, 48149 Münster, Germany
| | - Peter S Johnstone
- Department of Biochemistry and Molecular Biology and Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Angelique Lamaze
- Institute of Neuro- and Behavioural Biology, Westfälische Wilhelms University, 48149 Münster, Germany
| | - Johannes Landskron
- Centre for Molecular Medicine Norway, University of Oslo, 0318 Oslo, Norway
| | - Ezgi Atay
- Institute of Neuro- and Behavioural Biology, Westfälische Wilhelms University, 48149 Münster, Germany
| | - Ko-Fan Chen
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Eva Wolf
- Johannes Gutenberg University (JGU) and Institute of Molecular Biology (IMB) Mainz, 55128 Mainz, Germany
| | - Deniz Top
- Department of Biochemistry and Molecular Biology and Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Ralf Stanewsky
- Institute of Neuro- and Behavioural Biology, Westfälische Wilhelms University, 48149 Münster, Germany.
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9
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Rasmussen ES, Takahashi JS, Green CB. Time to target the circadian clock for drug discovery. Trends Biochem Sci 2022; 47:745-758. [PMID: 35577675 PMCID: PMC9378619 DOI: 10.1016/j.tibs.2022.04.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/01/2022] [Accepted: 04/18/2022] [Indexed: 11/30/2022]
Abstract
The circadian clock is an intracellular timekeeping device that drives daily rhythms in diverse and extensive processes throughout the body. The clock mechanism comprises a core transcription/translation negative feedback loop that is modulated by a complex set of additional interlocking feedback loops. Pharmacological manipulation of the clock may be valuable for treating many maladies including jet lag, shift work and related sleep disorders, various metabolic diseases, and cancer. We review recent identification of small-molecule clock modulators and discuss the biochemical features of the core clock that may be amenable to future drug discovery.
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Affiliation(s)
- Emil Sjulstok Rasmussen
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Joseph S Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Carla B Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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10
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Piersimoni L, Abd El Malek M, Bhatia T, Bender J, Brankatschk C, Calvo Sánchez J, Dayhoff GW, Di Ianni A, Figueroa Parra JO, Garcia-Martinez D, Hesselbarth J, Köppen J, Lauth LM, Lippik L, Machner L, Sachan S, Schmidt L, Selle R, Skalidis I, Sorokin O, Ubbiali D, Voigt B, Wedler A, Wei AAJ, Zorn P, Dunker AK, Köhn M, Sinz A, Uversky VN. Lighting up Nobel Prize-winning studies with protein intrinsic disorder. Cell Mol Life Sci 2022; 79:449. [PMID: 35882686 PMCID: PMC11072364 DOI: 10.1007/s00018-022-04468-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/18/2022] [Accepted: 07/04/2022] [Indexed: 11/03/2022]
Abstract
Intrinsically disordered proteins and regions (IDPs and IDRs) and their importance in biology are becoming increasingly recognized in biology, biochemistry, molecular biology and chemistry textbooks, as well as in current protein science and structural biology curricula. We argue that the sequence → dynamic conformational ensemble → function principle is of equal importance as the classical sequence → structure → function paradigm. To highlight this point, we describe the IDPs and/or IDRs behind the discoveries associated with 17 Nobel Prizes, 11 in Physiology or Medicine and 6 in Chemistry. The Nobel Laureates themselves did not always mention that the proteins underlying the phenomena investigated in their award-winning studies are in fact IDPs or contain IDRs. In several cases, IDP- or IDR-based molecular functions have been elucidated, while in other instances, it is recognized that the respective protein(s) contain IDRs, but the specific IDR-based molecular functions have yet to be determined. To highlight the importance of IDPs and IDRs as general principle in biology, we present here illustrative examples of IDPs/IDRs in Nobel Prize-winning mechanisms and processes.
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Affiliation(s)
- Lolita Piersimoni
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Marina Abd El Malek
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Twinkle Bhatia
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Julian Bender
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Christin Brankatschk
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Jaime Calvo Sánchez
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Guy W Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL, 33620, USA
| | - Alessio Di Ianni
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | | | - Dailen Garcia-Martinez
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Julia Hesselbarth
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Janett Köppen
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Luca M Lauth
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Laurin Lippik
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Lisa Machner
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Shubhra Sachan
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Lisa Schmidt
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Robin Selle
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Ioannis Skalidis
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Oleksandr Sorokin
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Daniele Ubbiali
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Bruno Voigt
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alice Wedler
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alan An Jung Wei
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Peter Zorn
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Alan Keith Dunker
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Marcel Köhn
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany.
| | - Andrea Sinz
- Research Training Group RTG2467, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany.
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
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11
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Cysteine Oxidation Promotes Dimerization/Oligomerization of Circadian Protein Period 2. Biomolecules 2022; 12:biom12070892. [PMID: 35883448 PMCID: PMC9313148 DOI: 10.3390/biom12070892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 11/17/2022] Open
Abstract
The molecular circadian clock is based on a transcriptional/translational feedback loop in which the stability and half-life of circadian proteins is of importance. Cysteine residues of proteins are subject to several redox reactions leading to S-thiolation and disulfide bond formation, altering protein stability and function. In this work, the ability of the circadian protein period 2 (PER2) to undergo oxidation of cysteine thiols was investigated in HEK-293T cells. PER2 includes accessible cysteines susceptible to oxidation by nitroso cysteine (CysNO), altering its stability by decreasing its monomer form and subsequently increasing PER2 homodimers and multimers. These changes were reversed by treatment with 2-mercaptoethanol and partially mimicked by hydrogen peroxide. These results suggest that cysteine oxidation can prompt PER2 homodimer and multimer formation in vitro, likely by S-nitrosation and disulphide bond formation. These kinds of post-translational modifications of PER2 could be part of the redox regulation of the molecular circadian clock.
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12
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Physical Interaction between Cyclin-Dependent Kinase 5 (CDK5) and Clock Factors Affects the Circadian Rhythmicity in Peripheral Oscillators. Clocks Sleep 2022; 4:185-201. [PMID: 35323171 PMCID: PMC8946863 DOI: 10.3390/clockssleep4010017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/22/2022] [Accepted: 03/01/2022] [Indexed: 11/17/2022] Open
Abstract
Circadian rhythms are self-sustained oscillators with a period of 24 h that is based on the output of transcriptional and post-translational feedback loops. Phosphorylation is considered one of the most important post-translational modifications affecting rhythmicity from cyanobacteria to mammals. For example, the lack of cyclin-dependent kinase 5 (CDK5) shortened the period length of the circadian oscillator in the Suprachiasmatic Nuclei (SCN) of mice via the destabilization of the PERIOD 2 (PER2) protein. Here, we show that CDK5 kinase activity and its interaction with clock components, including PER2 and CLOCK, varied over time in mouse embryonic fibroblast cells. Furthermore, the deletion of Cdk5 from cells resulted in a prolonged period and shifted the transcription of clock-controlled genes by about 2 to 4 h with a simple delay of chromatin binding of ARNTL (BMAL1) CLOCK. Taken together, our data indicate that CDK5 is critically involved in regulating the circadian clock in vitro at the molecular level.
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13
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PER2: a potential molecular marker for hematological malignancies. Mol Biol Rep 2021; 48:7587-7595. [PMID: 34642831 DOI: 10.1007/s11033-021-06751-w] [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: 08/12/2021] [Accepted: 09/16/2021] [Indexed: 11/27/2022]
Abstract
Circadian rhythm is a periodic change of organism according to the law of external environment, which is manifested in metabolism, cell proliferation, physiology and behavior. In recent years, the role of circadian genes in the occurrence and progression of hematological malignancies have been continuously demonstrated. PER2 is the core component of the circadian rhythm playing an important role in regulating the circadian rhythm of the biological clock. This review summarizes the research progress of PER2 in hematological malignancies, especially leukemia, in order to better understand its role in hematological malignancies, and provide new ideas for clinical diagnosis and treatment.
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14
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Philpott JM, Torgrimson MR, Harold RL, Partch CL. Biochemical mechanisms of period control within the mammalian circadian clock. Semin Cell Dev Biol 2021; 126:71-78. [PMID: 33933351 DOI: 10.1016/j.semcdb.2021.04.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/11/2021] [Accepted: 04/13/2021] [Indexed: 12/27/2022]
Abstract
Genetically encoded biological clocks are found broadly throughout life on Earth, where they generate circadian (about a day) rhythms that synchronize physiology and behavior with the daily light/dark cycle. Although the genetic networks that give rise to circadian timing are now fairly well established, our understanding of how the proteins that constitute the molecular 'cogs' of this biological clock regulate the intrinsic timing, or period, of circadian rhythms has lagged behind. New studies probing the biochemical and structural basis of clock protein function are beginning to reveal how assemblies of dedicated clock proteins form and evolve through post-translational regulation to generate circadian rhythms. This review will highlight some recent advances providing important insight into the molecular mechanisms of period control in mammalian clocks with an emphasis on structural analyses related to CK1-dependent control of PER stability.
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Affiliation(s)
- Jonathan M Philpott
- Department of Chemistry and Biochemistry, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
| | - Megan R Torgrimson
- Department of Chemistry and Biochemistry, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
| | - Rachel L Harold
- Department of Chemistry and Biochemistry, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA; Center for Circadian Biology, UC San Diego, 9500 Gilman Drive, MC 0116, La Jolla, CA 92093, USA.
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15
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Gong X, Tang H, Yang K. PER1 suppresses glycolysis and cell proliferation in oral squamous cell carcinoma via the PER1/RACK1/PI3K signaling complex. Cell Death Dis 2021; 12:276. [PMID: 33723221 PMCID: PMC7960720 DOI: 10.1038/s41419-021-03563-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/14/2021] [Accepted: 02/22/2021] [Indexed: 12/16/2022]
Abstract
There is increasing evidence that the core clock gene Period 1 (PER1) plays important roles in the formation of various tumors. However, the biological functions and mechanism of PER1 in promoting tumor progression remain largely unknown. Here, we discovered that PER1 was markedly downregulated in oral squamous cell carcinoma (OSCC). Then, OSCC cell lines with stable overexpression, knockdown, and mutation of PER1 were established. We found that PER1 overexpression significantly inhibited glycolysis, glucose uptake, proliferation, and the PI3K/AKT pathway in OSCC cells. The opposite effects were observed in PER1-knockdown OSCC cells. After treatment of PER1-overexpressing OSCC cells with an AKT activator or treatment of PER1-knockdown OSCC cells with an AKT inhibitor, glycolysis, glucose uptake, and proliferation were markedly rescued. In addition, after treatment of PER1-knockdown OSCC cells with a glycolysis inhibitor, the increase in cell proliferation was significantly reversed. Further, coimmunoprecipitation (Co-IP) and cycloheximide (CHX) chase experiment demonstrated that PER1 can bind with RACK1 and PI3K to form the PER1/RACK1/PI3K complex in OSCC cells. In PER1-overexpressing OSCC cells, the abundance of the PER1/RACK1/PI3K complex was significantly increased, the half-life of PI3K was markedly decreased, and glycolysis, proliferation, and the PI3K/AKT pathway were significantly inhibited. However, these effects were markedly reversed in PER1-mutant OSCC cells. In vivo tumorigenicity assays confirmed that PER1 overexpression inhibited tumor growth while suppressing glycolysis, proliferation, and the PI3K/AKT pathway. Collectively, this study generated the novel findings that PER1 suppresses OSCC progression by inhibiting glycolysis-mediated cell proliferation via the formation of the PER1/RACK1/PI3K complex to regulate the stability of PI3K and the PI3K/AKT pathway-dependent manner and that PER1 could potentially be a valuable therapeutic target in OSCC.
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Affiliation(s)
- Xiaobao Gong
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuzhong District, 400016, Chongqing, China
| | - Hong Tang
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuzhong District, 400016, Chongqing, China
| | - Kai Yang
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Chongqing Medical University, No. 1, Youyi Road, Yuzhong District, 400016, Chongqing, China.
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16
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Period1 mediates rhythmic metabolism of toxins by interacting with CYP2E1. Cell Death Dis 2021; 12:76. [PMID: 33436540 PMCID: PMC7804260 DOI: 10.1038/s41419-020-03343-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 01/14/2023]
Abstract
The biological clock is an endogenous biological timing system, which controls metabolic functions in almost all organs. Nutrient metabolism, substrate processing, and detoxification are circadian controlled in livers. However, how the clock genes respond to toxins and influence toxicity keeps unclear. We identified the clock gene Per1 was specifically elevated in mice exposed to toxins such as carbon tetrachloride (CCl4). Mice lacking Per1 slowed down the metabolic rate of toxins including CCl4, capsaicin, and acetaminophen, exhibiting relatively more residues in the plasma. Liver injury and fibrosis induced by acute and chronic CCl4 exposure were markedly alleviated in Per1-deficient mice. These processes involved the binding of PER1 protein and hepatocyte nuclear factor-1alpha (HNF-1α), which enhances the recruitment of HNF-1α to cytochrome P450 2E1 (Cyp2e1) promoter and increases Cyp2e1 expression, thereby promoting metabolism for toxins in the livers. These results indicate that PER1 mediates the metabolism of toxins and appropriate suppression of Per1 response is a potential therapeutic target for toxin-induced hepatotoxicity.
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17
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Brenna A, Albrecht U. Phosphorylation and Circadian Molecular Timing. Front Physiol 2020; 11:612510. [PMID: 33324245 PMCID: PMC7726318 DOI: 10.3389/fphys.2020.612510] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/03/2020] [Indexed: 01/08/2023] Open
Abstract
Endogenous circadian rhythms are biological processes generated by an internal body clock. They are self-sustaining, and they govern biochemical and physiological processes. However, circadian rhythms are influenced by many external stimuli to reprogram the phase in response to environmental change. Through their adaptability to environmental changes, they synchronize physiological responses to environmental challenges that occur within a sidereal day. The precision of this circadian system is assured by many post-translational modifications (PTMs) that occur on the protein components of the circadian clock mechanism. The most ancient example of circadian rhythmicity driven by phosphorylation of clock proteins was observed in cyanobacteria. The influence of phosphorylation on the circadian system is observed through different kingdoms, from plants to humans. Here, we discuss how phosphorylation modulates the mammalian circadian clock, and we give a detailed overview of the most critical discoveries in the field.
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Affiliation(s)
- Andrea Brenna
- Department of Medicine, University of Fribourg, Fribourg, Switzerland.,Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Urs Albrecht
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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18
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Wake-sleep cycles are severely disrupted by diseases affecting cytoplasmic homeostasis. Proc Natl Acad Sci U S A 2020; 117:28402-28411. [PMID: 33106420 PMCID: PMC7668169 DOI: 10.1073/pnas.2003524117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Circadian rhythms including wake-sleep cycles are driven by molecular time cues generated by a self-sustaining transcriptional negative feedback loop. Among all clock proteins, PERIOD (PER) is considered the pacemaker protein because its rhythm of accumulation and nuclear entry generates the timing and duration of feedback inhibition. Here we provide a new understanding of how robust PER rhythms are generated: the collective action of interacting PER molecules, not a random mass action of individual molecules, allows compensation of spatial and temporal differences (or “noise”) of individual molecules. We also show that the collective PER rhythm requires healthy cytoplasmic trafficking, and that circadian sleep disorders can arise in such conditions as obesity, aging, and neurodegenerative disorders in which the cytoplasm becomes congested. The circadian clock is based on a transcriptional feedback loop with an essential time delay before feedback inhibition. Previous work has shown that PERIOD (PER) proteins generate circadian time cues through rhythmic nuclear accumulation of the inhibitor complex and subsequent interaction with the activator complex in the feedback loop. Although this temporal manifestation of the feedback inhibition is the direct consequence of PER’s cytoplasmic trafficking before nuclear entry, how this spatial regulation of the pacemaker affects circadian timing has been largely unexplored. Here we show that circadian rhythms, including wake-sleep cycles, are lengthened and severely unstable if the cytoplasmic trafficking of PER is disrupted by any disease condition that leads to increased congestion in the cytoplasm. Furthermore, we found that the time delay and robustness in the circadian clock are seamlessly generated by delayed and collective phosphorylation of PER molecules, followed by synchronous nuclear entry. These results provide clear mechanistic insight into why circadian and sleep disorders arise in such clinical conditions as metabolic and neurodegenerative diseases and aging, in which the cytoplasm is congested.
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19
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Sun H, Li C, Zhang Y, Jiang M, Dong Q, Wang Z. Light-resetting impact on behavior and the central circadian clock in two vole species (genus: Lasiopodomys). Comp Biochem Physiol B Biochem Mol Biol 2020; 248-249:110478. [PMID: 32687979 DOI: 10.1016/j.cbpb.2020.110478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/03/2020] [Accepted: 07/13/2020] [Indexed: 10/23/2022]
Abstract
The behavioral circadian rhythms of subterranean rodents show intra- and interspecies diversity in terms of adaptation to dark underground environments, but the endogenous molecular mechanism of rhythm regulation in the suprachiasmatic nuclei (SCN) is stable to many species. In this study, we sought to determine the rhythms of behavior and central molecular regulatory mechanisms in the SCN of the subterranean Mandarin voles (Lasiopodomys mandarinus) compared with a related aboveground species, Brandt's voles (Lasiopodomys brandtii). Both species were reared under a 12 L:12 D cycle or in continuous darkness for 4 weeks. The pattern of wheel-running activity was similar in both species and had a periodicity of almost 24 h regardless of rearing conditions. However, the intensity of daily activity in Brandt's voles decreased markedly in darkness, while there was no significant difference in activity intensity in mandarin voles under different light regimes. In both vole species, all tested genes in the SCN showed significant time-dependent expression regardless of rearing conditions, and the expression levels of most genes did not differ significantly between different species and conditions. However, the peak phase shift in gene expression differed between the two species. In conclusion, behavioral patterns in mandarin and Brandt's voles were regulated by a stable molecular endogenous biological clock. The observed differences in activity intensity and phase shift suggest that different mechanisms regulate circadian rhythms in different living environments.
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Affiliation(s)
- Hong Sun
- College of Physical Education (main Campus), Zhengzhou University, Zhengzhou, Henan Province, China; School of Life Sciences, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Chuyi Li
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yifeng Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Mengwan Jiang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Qianqian Dong
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan Province, China
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan Province, China.
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20
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Partch CL. Orchestration of Circadian Timing by Macromolecular Protein Assemblies. J Mol Biol 2020; 432:3426-3448. [DOI: 10.1016/j.jmb.2019.12.046] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/13/2019] [Accepted: 12/18/2019] [Indexed: 12/13/2022]
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21
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Abstract
Circadian oscillators are networks of biochemical feedback loops that generate 24-hour rhythms in organisms from bacteria to animals. These periodic rhythms result from a complex interplay among clock components that are specific to the organism, but share molecular mechanisms across kingdoms. A full understanding of these processes requires detailed knowledge, not only of the biochemical properties of clock proteins and their interactions, but also of the three-dimensional structure of clockwork components. Posttranslational modifications and protein–protein interactions have become a recent focus, in particular the complex interactions mediated by the phosphorylation of clock proteins and the formation of multimeric protein complexes that regulate clock genes at transcriptional and translational levels. This review covers the structural aspects of circadian oscillators, and serves as a primer for this exciting realm of structural biology.
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Affiliation(s)
- Reena Saini
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Max-Planck-Institut für Pflanzenzüchtungsforschung, Cologne, Germany
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Seth J Davis
- Max-Planck-Institut für Pflanzenzüchtungsforschung, Cologne, Germany. .,Department of Biology, University of York, York, UK.
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22
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Kim P, Oster H, Lehnert H, Schmid SM, Salamat N, Barclay JL, Maronde E, Inder W, Rawashdeh O. Coupling the Circadian Clock to Homeostasis: The Role of Period in Timing Physiology. Endocr Rev 2019; 40:66-95. [PMID: 30169559 DOI: 10.1210/er.2018-00049] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/06/2018] [Indexed: 01/01/2023]
Abstract
A plethora of physiological processes show stable and synchronized daily oscillations that are either driven or modulated by biological clocks. A circadian pacemaker located in the suprachiasmatic nucleus of the ventral hypothalamus coordinates 24-hour oscillations of central and peripheral physiology with the environment. The circadian clockwork involved in driving rhythmic physiology is composed of various clock genes that are interlocked via a complex feedback loop to generate precise yet plastic oscillations of ∼24 hours. This review focuses on the specific role of the core clockwork gene Period1 and its paralogs on intra-oscillator and extra-oscillator functions, including, but not limited to, hippocampus-dependent processes, cardiovascular function, appetite control, as well as glucose and lipid homeostasis. Alterations in Period gene function have been implicated in a wide range of physical and mental disorders. At the same time, a variety of conditions including metabolic disorders also impact clock gene expression, resulting in circadian disruptions, which in turn often exacerbates the disease state.
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Affiliation(s)
- Pureum Kim
- School of Biomedical Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Henrik Oster
- Institute of Neurobiology, University of Lübeck, Lübeck, Germany
| | - Hendrik Lehnert
- Department of Internal Medicine 1, University of Lübeck, Lübeck, Germany
- German Center for Diabetes Research, Neuherberg, Germany
| | - Sebastian M Schmid
- Department of Internal Medicine 1, University of Lübeck, Lübeck, Germany
- German Center for Diabetes Research, Neuherberg, Germany
| | - Nicole Salamat
- School of Biomedical Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Johanna L Barclay
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Erik Maronde
- Department of Anatomy, Goethe University Frankfurt, Frankfurt, Germany
| | - Warrick Inder
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Department of Diabetes and Endocrinology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Oliver Rawashdeh
- School of Biomedical Sciences, University of Queensland, Brisbane, Queensland, Australia
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23
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Rosensweig C, Green CB. Periodicity, repression, and the molecular architecture of the mammalian circadian clock. Eur J Neurosci 2018; 51:139-165. [PMID: 30402960 DOI: 10.1111/ejn.14254] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/03/2018] [Accepted: 10/22/2018] [Indexed: 12/12/2022]
Abstract
Large molecular machines regulate daily cycles of transcriptional activity and help generate rhythmic behavior. In recent years, structural and biochemical analyses have elucidated a number of principles guiding the interactions of proteins that form the basis of circadian timing. In its simplest form, the circadian clock is composed of a transcription/translation feedback loop. However, this description elides a complicated process of activator recruitment, chromatin decompaction, recruitment of coactivators, expression of repressors, formation of a repressive complex, repression of the activators, and ultimately degradation of the repressors and reinitiation of the cycle. Understanding the core principles underlying the clock requires careful examination of molecular and even atomic level details of these processes. Here, we review major structural and biochemical findings in circadian biology and make the argument that shared protein interfaces within the clockwork are critical for both the generation of rhythmicity and timing of the clock.
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Affiliation(s)
- Clark Rosensweig
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Carla B Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas
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24
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Liu J, Zou X, Gotoh T, Brown AM, Jiang L, Wisdom EL, Kim JK, Finkielstein CV. Distinct control of PERIOD2 degradation and circadian rhythms by the oncoprotein and ubiquitin ligase MDM2. Sci Signal 2018; 11:11/556/eaau0715. [PMID: 30425162 DOI: 10.1126/scisignal.aau0715] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The circadian clock relies on posttranslational modifications to set the timing for degradation of core regulatory components, which drives clock progression. Ubiquitin-modifying enzymes that target clock components for degradation mainly recognize phosphorylated substrates. Degradation of the circadian clock component PERIOD 2 (PER2) is mediated by its phospho-specific recognition by β-transducin repeat-containing proteins (β-TrCPs), which are F-box-containing proteins that function as substrate recognition subunits of the SCFβ-TRCP ubiquitin ligase complex. However, this mode of regulating PER2 stability falls short of explaining the persistent oscillatory phenotypes reported in biological systems lacking functional elements of the phospho-dependent PER2 degradation machinery. We identified PER2 as a previously uncharacterized substrate for the ubiquitin ligase mouse double minute 2 homolog (MDM2) and found that MDM2 targeted PER2 for degradation in a manner independent of PER2 phosphorylation. Deregulation of MDM2 plays a major role in oncogenesis by contributing to the accumulation of genomic and epigenomic alterations that favor tumor development. MDM2-mediated PER2 turnover was important for defining the circadian period length in mammalian cells, a finding that emphasizes the connection between the circadian clock and cancer. Our results not only broaden the range of specific substrates of MDM2 beyond the cell cycle to include circadian components but also identify a previously unknown regulator of the clock as a druggable node that is often found to be deregulated during tumorigenesis.
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Affiliation(s)
- JingJing Liu
- Integrated Cellular Responses Laboratory, Department of Biological Sciences, Biocomplexity Institute, Virginia Tech, Blacksburg, VA, USA
| | - Xianlin Zou
- Integrated Cellular Responses Laboratory, Department of Biological Sciences, Biocomplexity Institute, Virginia Tech, Blacksburg, VA, USA
| | - Tetsuya Gotoh
- Integrated Cellular Responses Laboratory, Department of Biological Sciences, Biocomplexity Institute, Virginia Tech, Blacksburg, VA, USA
| | - Anne M Brown
- Research and Informatics, University Libraries, Virginia Tech, Blacksburg, VA, USA
| | - Liang Jiang
- Integrated Cellular Responses Laboratory, Department of Biological Sciences, Biocomplexity Institute, Virginia Tech, Blacksburg, VA, USA
| | - Esther L Wisdom
- Integrated Cellular Responses Laboratory, Department of Biological Sciences, Biocomplexity Institute, Virginia Tech, Blacksburg, VA, USA
| | - Jae Kyoung Kim
- Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Carla V Finkielstein
- Integrated Cellular Responses Laboratory, Department of Biological Sciences, Biocomplexity Institute, Virginia Tech, Blacksburg, VA, USA.
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25
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Evolution of circadian genes PER and CRY in subterranean rodents. Int J Biol Macromol 2018; 118:1400-1405. [DOI: 10.1016/j.ijbiomac.2018.06.133] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/05/2018] [Accepted: 06/26/2018] [Indexed: 01/11/2023]
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26
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Ode KL, Ueda HR. Design Principles of Phosphorylation-Dependent Timekeeping in Eukaryotic Circadian Clocks. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a028357. [PMID: 29038116 DOI: 10.1101/cshperspect.a028357] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The circadian clock in cyanobacteria employs a posttranslational oscillator composed of a sequential phosphorylation-dephosphorylation cycle of KaiC protein, in which the dynamics of protein structural changes driven by temperature-compensated KaiC's ATPase activity are critical for determining the period. On the other hand, circadian clocks in eukaryotes employ transcriptional feedback loops as a core mechanism. In this system, the dynamics of protein accumulation and degradation affect the circadian period. However, recent studies of eukaryotic circadian clocks reveal that the mechanism controlling the circadian period can be independent of the regulation of protein abundance. Instead, the circadian substrate is often phosphorylated at multiple sites at flexible protein regions to induce structural changes. The phosphorylation is catalyzed by kinases that induce sequential multisite phosphorylation such as casein kinase 1 (CK1) with temperature-compensated activity. We propose that the design principles of phosphorylation-dependent circadian-period determination in eukaryotes may share characteristics with the posttranslational oscillator in cyanobacteria.
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Affiliation(s)
- Koji L Ode
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.,Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.,Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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27
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Korge S, Maier B, Brüning F, Ehrhardt L, Korte T, Mann M, Herrmann A, Robles MS, Kramer A. The non-classical nuclear import carrier Transportin 1 modulates circadian rhythms through its effect on PER1 nuclear localization. PLoS Genet 2018; 14:e1007189. [PMID: 29377895 PMCID: PMC5805371 DOI: 10.1371/journal.pgen.1007189] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 02/08/2018] [Accepted: 01/05/2018] [Indexed: 12/31/2022] Open
Abstract
Circadian clocks are molecular timekeeping mechanisms that allow organisms to anticipate daily changes in their environment. The fundamental cellular basis of these clocks is delayed negative feedback gene regulation with PERIOD and CRYPTOCHROME containing protein complexes as main inhibitory elements. For a correct circadian period, it is essential that such clock protein complexes accumulate in the nucleus in a precisely timed manner, a mechanism that is poorly understood. We performed a systematic RNAi-mediated screen in human cells and identified 15 genes associated with the nucleo-cytoplasmic translocation machinery, whose expression is important for circadian clock dynamics. Among them was Transportin 1 (TNPO1), a non-classical nuclear import carrier, whose knockdown and knockout led to short circadian periods. TNPO1 was found in endogenous clock protein complexes and particularly binds to PER1 regulating its (but not PER2's) nuclear localization. While PER1 is also transported to the nucleus by the classical, Importin β-mediated pathway, TNPO1 depletion slowed down PER1 nuclear import rate as revealed by fluorescence recovery after photobleaching (FRAP) experiments. In addition, we found that TNPO1-mediated nuclear import may constitute a novel input pathway of how cellular redox state signals to the clock, since redox stress increases binding of TNPO1 to PER1 and decreases its nuclear localization. Together, our RNAi screen knocking down import carriers (but also export carriers) results in short and long circadian periods indicating that the regulatory pathways that control the timing of clock protein subcellular localization are far more complex than previously assumed. TNPO1 is one of the novel players essential for normal circadian periods and potentially for redox regulation of the clock.
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Affiliation(s)
- Sandra Korge
- Laboratory of Chronobiology, Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Bert Maier
- Laboratory of Chronobiology, Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Franziska Brüning
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Institute of Medical Psychology, LMU Munich, Munich, Germany
| | - Lea Ehrhardt
- Laboratory of Chronobiology, Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Thomas Korte
- Molecular Biophysics, Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andreas Herrmann
- Molecular Biophysics, Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Maria S. Robles
- Institute of Medical Psychology, LMU Munich, Munich, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Charité—Universitätsmedizin Berlin, Berlin, Germany
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Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1. Proc Natl Acad Sci U S A 2017; 114:1560-1565. [PMID: 28143926 DOI: 10.1073/pnas.1615310114] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The basic helix-loop-helix PAS domain (bHLH-PAS) transcription factor CLOCK:BMAL1 (brain and muscle Arnt-like protein 1) sits at the core of the mammalian circadian transcription/translation feedback loop. Precise control of CLOCK:BMAL1 activity by coactivators and repressors establishes the ∼24-h periodicity of gene expression. Formation of a repressive complex, defined by the core clock proteins cryptochrome 1 (CRY1):CLOCK:BMAL1, plays an important role controlling the switch from repression to activation each day. Here we show that CRY1 binds directly to the PAS domain core of CLOCK:BMAL1, driven primarily by interaction with the CLOCK PAS-B domain. Integrative modeling and solution X-ray scattering studies unambiguously position a key loop of the CLOCK PAS-B domain in the secondary pocket of CRY1, analogous to the antenna chromophore-binding pocket of photolyase. CRY1 docks onto the transcription factor alongside the PAS domains, extending above the DNA-binding bHLH domain. Single point mutations at the interface on either CRY1 or CLOCK disrupt formation of the ternary complex, highlighting the importance of this interface for direct regulation of CLOCK:BMAL1 activity by CRY1.
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29
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Takahashi JS. Transcriptional architecture of the mammalian circadian clock. NATURE REVIEWS. GENETICS 2016. [PMID: 27990019 DOI: 10.1038/nrg.2016.150]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Circadian clocks are endogenous oscillators that control 24-hour physiological and behavioural processes in organisms. These cell-autonomous clocks are composed of a transcription-translation-based autoregulatory feedback loop. With the development of next-generation sequencing approaches, biochemical and genomic insights into circadian function have recently come into focus. Genome-wide analyses of the clock transcriptional feedback loop have revealed a global circadian regulation of processes such as transcription factor occupancy, RNA polymerase II recruitment and initiation, nascent transcription, and chromatin remodelling. The genomic targets of circadian clocks are pervasive and are intimately linked to the regulation of metabolism, cell growth and physiology.
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Affiliation(s)
- Joseph S Takahashi
- Howard Hughes Medical Institute, Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, NA4.118, Dallas, Texas 75390-9111, USA
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30
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Takahashi JS. Transcriptional architecture of the mammalian circadian clock. Nat Rev Genet 2016; 18:164-179. [PMID: 27990019 DOI: 10.1038/nrg.2016.150] [Citation(s) in RCA: 1469] [Impact Index Per Article: 183.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Circadian clocks are endogenous oscillators that control 24-hour physiological and behavioural processes in organisms. These cell-autonomous clocks are composed of a transcription-translation-based autoregulatory feedback loop. With the development of next-generation sequencing approaches, biochemical and genomic insights into circadian function have recently come into focus. Genome-wide analyses of the clock transcriptional feedback loop have revealed a global circadian regulation of processes such as transcription factor occupancy, RNA polymerase II recruitment and initiation, nascent transcription, and chromatin remodelling. The genomic targets of circadian clocks are pervasive and are intimately linked to the regulation of metabolism, cell growth and physiology.
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Affiliation(s)
- Joseph S Takahashi
- Howard Hughes Medical Institute, Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, NA4.118, Dallas, Texas 75390-9111, USA
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31
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Corrêa F, Key J, Kuhlman B, Gardner K. Computational Repacking of HIF-2α Cavity Replaces Water-Based Stabilized Core. Structure 2016; 24:1918-1927. [DOI: 10.1016/j.str.2016.08.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 08/18/2016] [Accepted: 08/19/2016] [Indexed: 12/25/2022]
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Hurley JM, Loros JJ, Dunlap JC. Circadian Oscillators: Around the Transcription-Translation Feedback Loop and on to Output. Trends Biochem Sci 2016; 41:834-846. [PMID: 27498225 DOI: 10.1016/j.tibs.2016.07.009] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/10/2016] [Accepted: 07/14/2016] [Indexed: 12/20/2022]
Abstract
From cyanobacteria to mammals, organisms have evolved timing mechanisms to adapt to environmental changes in order to optimize survival and improve fitness. To anticipate these regular daily cycles, many organisms manifest ∼24h cell-autonomous oscillations that are sustained by transcription-translation-based or post-transcriptional negative-feedback loops that control a wide range of biological processes. With an eye to identifying emerging common themes among cyanobacterial, fungal, and animal clocks, some major recent developments in the understanding of the mechanisms that regulate these oscillators and their output are discussed. These include roles for antisense transcription, intrinsically disordered proteins, codon bias in clock genes, and a more focused discussion of post-transcriptional and translational regulation as a part of both the oscillator and output.
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Affiliation(s)
- Jennifer M Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - Jennifer J Loros
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jay C Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.
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Corrada D, Soshilov AA, Denison MS, Bonati L. Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation. PLoS Comput Biol 2016; 12:e1004981. [PMID: 27295348 PMCID: PMC4905635 DOI: 10.1371/journal.pcbi.1004981] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 05/12/2016] [Indexed: 01/15/2023] Open
Abstract
The Aryl hydrocarbon Receptor (AhR) is a transcription factor that mediates the biochemical response to xenobiotics and the toxic effects of a number of environmental contaminants, including dioxins. Recently, endogenous regulatory roles for the AhR in normal physiology and development have also been reported, thus extending the interest in understanding its molecular mechanisms of activation. Since dimerization with the AhR Nuclear Translocator (ARNT) protein, occurring through the Helix-Loop-Helix (HLH) and PER-ARNT-SIM (PAS) domains, is needed to convert the AhR into its transcriptionally active form, deciphering the AhR:ARNT dimerization mode would provide insights into the mechanisms of AhR transformation. Here we present homology models of the murine AhR:ARNT PAS domain dimer developed using recently available X-ray structures of other bHLH-PAS protein dimers. Due to the different reciprocal orientation and interaction surfaces in the different template dimers, two alternative models were developed for both the PAS-A and PAS-B dimers and they were characterized by combining a number of computational evaluations. Both well-established hot spot prediction methods and new approaches to analyze individual residue and residue-pairwise contributions to the MM-GBSA binding free energies were adopted to predict residues critical for dimer stabilization. On this basis, a mutagenesis strategy for both the murine AhR and ARNT proteins was designed and ligand-dependent DNA binding ability of the AhR:ARNT heterodimer mutants was evaluated. While functional analysis disfavored the HIF2α:ARNT heterodimer-based PAS-B model, most mutants derived from the CLOCK:BMAL1-based AhR:ARNT dimer models of both the PAS-A and the PAS-B dramatically decreased the levels of DNA binding, suggesting this latter model as the most suitable for describing AhR:ARNT dimerization. These novel results open new research directions focused at elucidating basic molecular mechanisms underlying the functional activity of the AhR. Computational modeling combined with experimental validation may give insight into structural and functional properties of protein systems. The basic Helix-Loop-Helix PER-ARNT-SIM (bHLH-PAS) proteins show conserved functional domains despite the broad range of functions exerted by the different systems. Within this protein family, the Aryl hydrocarbon Receptor (AhR) is known to mediate the toxic effects of a number of environmental contaminants, including dioxins and dioxin-like chemicals, and it also exerts other biochemical and physiological effects. Despite the absence of experimentally determined structures, theoretical models of the AhR PAS domains developed on the basis of homologous systems have allowed understanding of some aspects of the molecular mechanisms underlying its function. In this work we present alternative structural models of the transcriptionally active complex of AhR with the AhR Nuclear Translocator (ARNT) protein. Computational characterization of the modeled protein-protein interaction interfaces guided the design of mutagenesis experiments, and evaluation of the DNA binding ability of the resulting AhR:ARNT dimer mutants allowed validation of the models and selection of the most reliable one. These findings open new research directions for understanding the molecular mechanisms underlying the functional activity of the AhR.
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Affiliation(s)
- Dario Corrada
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Anatoly A. Soshilov
- Department of Environmental Toxicology, University of California, Davis, Davis, California, United States of America
| | - Michael S. Denison
- Department of Environmental Toxicology, University of California, Davis, Davis, California, United States of America
| | - Laura Bonati
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
- * E-mail:
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Wang T, Wang Z, Yang P, Xia L, Zhou M, Wang S, Du J, Zhang J. PER1 prevents excessive innate immune response during endotoxin-induced liver injury through regulation of macrophage recruitment in mice. Cell Death Dis 2016; 7:e2176. [PMID: 27054331 PMCID: PMC4855679 DOI: 10.1038/cddis.2016.9] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 01/06/2016] [Accepted: 01/07/2016] [Indexed: 01/20/2023]
Abstract
The severity of acute liver failure (ALF) induced by bacterial lipopolysaccharide (LPS) is associated with the hepatic innate immune response. The core circadian molecular clock modulates the innate immune response by controlling rhythmic pathogen recognition by the innate immune system and daily variations in cytokine gene expression. However, the molecular link between circadian genes and the innate immune system has remained unclear. Here, we showed that mice lacking the clock gene Per1 (Period1) are more susceptible to LPS/d-galactosamine (LPS/GalN)-induced macrophage-dependent ALF compared with wild-type (WT) mice. Per1 deletion caused a remarkable increase in the number of Kupffer cells (KCs) in the liver, resulting in an elevation of the levels of pro-inflammatory cytokines after LPS treatment. Loss of Per1 had no effect on the proliferation or apoptosis of macrophages; however, it enhanced the recruitment of macrophages, which was associated with an increase in CC chemokine receptor 2 (Ccr2) expression levels in monocytes/macrophages. Deletion of Ccr2 rescued d-GalN/LPS-induced liver injury in Per1−/− mice. We demonstrated that the upregulation of Ccr2 expression by Per1 deletion could be reversed by the synthetic peroxisome proliferator-activated receptor gamma (PPAR-γ) antagonist GW9662. Further analysis indicated that PER1 binds to PPAR-γ on the Ccr2 promoter and enhanced the inhibitory effect of PPAR-γ on Ccr2 expression. These results reveal that Per1 reduces hepatic macrophage recruitment through interaction with PPAR-γ and prevents an excessive innate immune response in endotoxin-induced liver injury.
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Affiliation(s)
- T Wang
- Center for Molecular Metabolism, Nanjing University of Science and Technology, Nanjing, China.,Cambridge Suda Genome Resource Center, Soochow University, Suzhou, China
| | - Z Wang
- Department of Radiology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - P Yang
- Center for Molecular Metabolism, Nanjing University of Science and Technology, Nanjing, China
| | - L Xia
- Center for Molecular Metabolism, Nanjing University of Science and Technology, Nanjing, China
| | - M Zhou
- Center for Molecular Metabolism, Nanjing University of Science and Technology, Nanjing, China
| | - S Wang
- Center for Molecular Metabolism, Nanjing University of Science and Technology, Nanjing, China
| | - Jie Du
- Beijing An Zhen Hospital, Capital Medical University, Beijing, China
| | - J Zhang
- Center for Molecular Metabolism, Nanjing University of Science and Technology, Nanjing, China
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35
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Cryptochrome 1 functions as nuclear co-receptor independence of circadian clock. Genes Genomics 2016. [DOI: 10.1007/s13258-015-0377-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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36
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Li W, Liu L, Liu D, Jin S, Yang Y, Tang W, Gong L. Decreased circadian component Bmal1 predicts tumor progression and poor prognosis in human pancreatic ductal adenocarcinoma. Biochem Biophys Res Commun 2016; 472:156-62. [PMID: 26915801 DOI: 10.1016/j.bbrc.2016.02.087] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 02/21/2016] [Indexed: 02/07/2023]
Abstract
The circadian clock has been demonstrated playing important roles in human tumorigenic process; however, the detailed clinical implications of circadian disruption on tumors have not been well understood. In this study, we investigated the expression pattern of Bmal1, the core component of the circadian system, in human pancreatic ductal adenocarcinoma (PDA). Our immunohistochemistry analysis showed that the protein level of Bmal1 was significantly decreased in tumor tissues from 87 patients with PDA compared with adjacent non-cancerous tissues. Low Bmal1 expression was associated with the TNM/clinical stage, histological differentiation, and vascular invasion of PDA; but no significant relevance to patient age, gender, the tumor location, or the size. Furthermore, Kaplan-Meier survival analysis revealed that PDA patients with low Bmal1 expression had shorter overall survival (OS) times as well as disease-free times (DFS) compared to the patients with high Bmal1 expression. Lastly, univariate and multivariate analyses identified low Bmal1 expression as an independent prognostic factor for poor survival outcome for patients with PDA. Collectively, our present study demonstrated that the decreased expression of Bmal1 is correlated with the tumor progression and poor prognosis in human PDA, which implicated its potential to be used as a biomarker for diagnosis and prognosis of PDA.
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Affiliation(s)
- Wenhua Li
- Department of Gastroenterology, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, No 68, Zhong Shan Road, Wuxi, 214002, China.
| | - Ling Liu
- Department of Gastroenterology, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, No 68, Zhong Shan Road, Wuxi, 214002, China.
| | - Di Liu
- Department of Gastroenterology, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, No 68, Zhong Shan Road, Wuxi, 214002, China.
| | - Shimao Jin
- Department of Gastroenterology, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, No 68, Zhong Shan Road, Wuxi, 214002, China.
| | - Yisha Yang
- Department of Gastroenterology, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, No 68, Zhong Shan Road, Wuxi, 214002, China.
| | - Wei Tang
- Department of Pathology, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, No 68, Zhong Shan Road, Wuxi, 214002, China.
| | - Lei Gong
- Department of Gastroenterology, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, No 68, Zhong Shan Road, Wuxi, 214002, China.
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37
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Early doors (Edo) mutant mouse reveals the importance of period 2 (PER2) PAS domain structure for circadian pacemaking. Proc Natl Acad Sci U S A 2016; 113:2756-61. [PMID: 26903623 DOI: 10.1073/pnas.1517549113] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The suprachiasmatic nucleus (SCN) defines 24 h of time via a transcriptional/posttranslational feedback loop in which transactivation of Per (period) and Cry (cryptochrome) genes by BMAL1-CLOCK complexes is suppressed by PER-CRY complexes. The molecular/structural basis of how circadian protein complexes function is poorly understood. We describe a novel N-ethyl-N-nitrosourea (ENU)-induced mutation, early doors (Edo), in the PER-ARNT-SIM (PAS) domain dimerization region of period 2 (PER2) (I324N) that accelerates the circadian clock of Per2(Edo/Edo) mice by 1.5 h. Structural and biophysical analyses revealed that Edo alters the packing of the highly conserved interdomain linker of the PER2 PAS core such that, although PER2(Edo) complexes with clock proteins, its vulnerability to degradation mediated by casein kinase 1ε (CSNK1E) is increased. The functional relevance of this mutation is revealed by the ultrashort (<19 h) but robust circadian rhythms in Per2(Edo/Edo); Csnk1e(Tau/Tau) mice and the SCN. These periods are unprecedented in mice. Thus, Per2(Edo) reveals a direct causal link between the molecular structure of the PER2 PAS core and the pace of SCN circadian timekeeping.
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Putteeraj M, Soga T, Ubuka T, Parhar IS. A "Timed" Kiss Is Essential for Reproduction: Lessons from Mammalian Studies. Front Endocrinol (Lausanne) 2016; 7:121. [PMID: 27630616 PMCID: PMC5005330 DOI: 10.3389/fendo.2016.00121] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/19/2016] [Indexed: 11/26/2022] Open
Abstract
Reproduction is associated with the circadian system, primarily as a result of the connectivity between the biological clock in the suprachiasmatic nucleus (SCN) and reproduction-regulating brain regions, such as preoptic area (POA), anteroventral periventricular nucleus (AVPV), and arcuate nucleus (ARC). Networking of the central pacemaker to these hypothalamic brain regions is partly represented by close fiber appositions to specialized neurons, such as kisspeptin and gonadotropin-releasing hormone (GnRH) neurons; accounting for rhythmic release of gonadotropins and sex steroids. Numerous studies have attempted to dissect the neurochemical properties of GnRH neurons, which possess intrinsic oscillatory features through the presence of clock genes to regulate the pulsatile and circadian secretion. However, less attention has been given to kisspeptin, the upstream regulator of GnRH and a potent mediator of reproductive functions including puberty. Kisspeptin exerts its stimulatory effects on GnRH secretion via its cognate Kiss-1R receptor that is co-expressed on GnRH neurons. Emerging studies have found that kisspeptin neurons oscillate on a circadian basis and that these neurons also express clock genes that are thought to regulate its rhythmic activities. Based on the fiber networks between the SCN and reproductive nuclei such as the POA, AVPV, and ARC, it is suggested that interactions among the central biological clock and reproductive neurons ensure optimal reproductive functionality. Within this neuronal circuitry, kisspeptin neuronal system is likely to "time" reproduction in a long term during development and aging, in a medium term to regulate circadian or estrus cycle, and in a short term to regulate pulsatile GnRH secretion.
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Affiliation(s)
- Manish Putteeraj
- Brain Research Institute (BRIMS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Petaling Jaya, Malaysia
| | - Tomoko Soga
- Brain Research Institute (BRIMS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Petaling Jaya, Malaysia
| | - Takayoshi Ubuka
- Brain Research Institute (BRIMS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Petaling Jaya, Malaysia
| | - Ishwar S. Parhar
- Brain Research Institute (BRIMS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Petaling Jaya, Malaysia
- *Correspondence: Ishwar S. Parhar,
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39
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Takahashi JS. Molecular Architecture of the Circadian Clock in Mammals. RESEARCH AND PERSPECTIVES IN ENDOCRINE INTERACTIONS 2016. [DOI: 10.1007/978-3-319-27069-2_2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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40
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How is the inner circadian clock controlled by interactive clock proteins?: Structural analysis of clock proteins elucidates their physiological role. FEBS Lett 2015; 589:1516-29. [PMID: 25999309 DOI: 10.1016/j.febslet.2015.05.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/08/2015] [Accepted: 05/11/2015] [Indexed: 12/12/2022]
Abstract
Most internationally travelled researchers will have encountered jetlag. If not, working odd hours makes most of us feel somehow dysfunctional. How can all this be linked to circadian rhythms and circadian clocks? In this review, we define circadian clocks, their composition and underlying molecular mechanisms. We describe and discuss recent crystal structures of Drosophila and mammalian core clock components and the enormous impact they had on the understanding of circadian clock mechanisms. Finally, we highlight the importance of circadian clocks for the daily regulation of human/mammalian physiology and show connections to overall fitness, health and disease.
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41
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Wallach T, Kramer A. Chemical chronobiology: Toward drugs manipulating time. FEBS Lett 2015; 589:1530-8. [DOI: 10.1016/j.febslet.2015.04.059] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 04/29/2015] [Accepted: 04/29/2015] [Indexed: 01/01/2023]
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42
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Crane BR, Young MW. Interactive features of proteins composing eukaryotic circadian clocks. Annu Rev Biochem 2015; 83:191-219. [PMID: 24905781 DOI: 10.1146/annurev-biochem-060713-035644] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Research into the molecular mechanisms of eukaryotic circadian clocks has proceeded at an electrifying pace. In this review, we discuss advances in our understanding of the structures of central molecular players in the timing oscillators of fungi, insects, and mammals. A series of clock protein structures demonstrate that the PAS (Per/Arnt/Sim) domain has been used with great variation to formulate the transcriptional activators and repressors of the clock. We discuss how posttranslational modifications and external cues, such as light, affect the conformation and function of core clock components. Recent breakthroughs have also revealed novel interactions among clock proteins and new partners that couple the clock to metabolic and developmental pathways. Overall, a picture of clock function has emerged wherein conserved motifs and structural platforms have been elaborated into a highly dynamic collection of interacting molecules that undergo orchestrated changes in chemical structure, conformational state, and partners.
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Affiliation(s)
- Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853;
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43
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Gustafson CL, Partch CL. Emerging models for the molecular basis of mammalian circadian timing. Biochemistry 2014; 54:134-49. [PMID: 25303119 PMCID: PMC4303291 DOI: 10.1021/bi500731f] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mammalian circadian timekeeping arises from a transcription-based feedback loop driven by a set of dedicated clock proteins. At its core, the heterodimeric transcription factor CLOCK:BMAL1 activates expression of Period, Cryptochrome, and Rev-Erb genes, which feed back to repress transcription and create oscillations in gene expression that confer circadian timing cues to cellular processes. The formation of different clock protein complexes throughout this transcriptional cycle helps to establish the intrinsic ∼24 h periodicity of the clock; however, current models of circadian timekeeping lack the explanatory power to fully describe this process. Recent studies confirm the presence of at least three distinct regulatory complexes: a transcriptionally active state comprising the CLOCK:BMAL1 heterodimer with its coactivator CBP/p300, an early repressive state containing PER:CRY complexes, and a late repressive state marked by a poised but inactive, DNA-bound CLOCK:BMAL1:CRY1 complex. In this review, we analyze high-resolution structures of core circadian transcriptional regulators and integrate biochemical data to suggest how remodeling of clock protein complexes may be achieved throughout the 24 h cycle. Defining these detailed mechanisms will provide a foundation for understanding the molecular basis of circadian timing and help to establish new platforms for the discovery of therapeutics to manipulate the clock.
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Affiliation(s)
- Chelsea L Gustafson
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
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44
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Levy RC, Kozak GM, Wadsworth CB, Coates BS, Dopman EB. Explaining the sawtooth: latitudinal periodicity in a circadian gene correlates with shifts in generation number. J Evol Biol 2014; 28:40-53. [DOI: 10.1111/jeb.12562] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 11/21/2014] [Accepted: 11/24/2014] [Indexed: 01/03/2023]
Affiliation(s)
- R. C. Levy
- Department of Biology; Tufts University; Medford MA USA
| | - G. M. Kozak
- Department of Biology; Tufts University; Medford MA USA
| | | | - B. S. Coates
- USDA-ARS; Corn Insects and Crop Genetics Research Unit; Genetics Laboratory; Iowa State University; Ames IA USA
| | - E. B. Dopman
- Department of Biology; Tufts University; Medford MA USA
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45
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Abstract
Structural approaches have provided insight into the mechanisms of circadian clock oscillators. This review focuses upon the myriad structural methods that have been applied to the molecular architecture of cyanobacterial circadian proteins, their interactions with each other, and the mechanism of the KaiABC posttranslational oscillator. X-ray crystallography and solution NMR were deployed to gain an understanding of the three-dimensional structures of the three proteins KaiA, KaiB, and KaiC that make up the inner timer in cyanobacteria. A hybrid structural biology approach including crystallography, electron microscopy, and solution scattering has shed light on the shapes of binary and ternary Kai protein complexes. Structural studies of the cyanobacterial oscillator demonstrate both the strengths and the limitations of the divide-and-conquer strategy. Thus, investigations of complexes involving domains and/or peptides have afforded valuable information into Kai protein interactions. However, high-resolution structural data are still needed at the level of complexes between the 360-kDa KaiC hexamer that forms the heart of the clock and its KaiA and KaiB partners.
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46
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ZHU LITING, YU JUN, ZHANG WENYI, XIE BIN, ZHU YI. Research progress on the central mechanism underlying regulation of visceral biological rhythm by per2 (Review). Mol Med Rep 2014; 10:2241-8. [DOI: 10.3892/mmr.2014.2559] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 04/25/2014] [Indexed: 11/05/2022] Open
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47
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Öllinger R, Korge S, Korte T, Koller B, Herrmann A, Kramer A. Dynamics of the circadian clock protein PERIOD2 in living cells. J Cell Sci 2014; 127:4322-8. [PMID: 25074809 DOI: 10.1242/jcs.156612] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In mammals, circadian rhythms are generated by delayed negative feedback, in which period (PER1-PER3) and cryptochrome (CRY1, CRY2) proteins gradually accumulate in the nucleus to suppress the transcription of their own genes. Although the importance of nuclear import and export signals for the subcellular localization of clock proteins is well established, little is known about the dynamics of these processes as well as their importance for the generation of circadian rhythms. We show by pharmacological perturbations of oscillating cells that nuclear import and export are of crucial importance for the circadian period. Live-cell fluorescence microscopy revealed that nuclear import of the key circadian protein PER2 is fast and further accelerated by CRY1. Moreover, PER2 nuclear import is crucially dependent on a specific nuclear-receptor-binding motif in PER2 that also mediates nuclear immobility. Nuclear export, however, is relatively slow, supporting a model of PER2 nuclear accumulation by rapid import, slow export and substantial nuclear degradation.
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Affiliation(s)
- Rupert Öllinger
- Laboratory of Chronobiology, Charité - Universitätsmedizin Berlin, Hessische Strasse 3-4, 10115 Berlin, Germany
| | - Sandra Korge
- Laboratory of Chronobiology, Charité - Universitätsmedizin Berlin, Hessische Strasse 3-4, 10115 Berlin, Germany
| | - Thomas Korte
- Department of Biology, Molecular Biophysics, Humboldt-University Berlin, Invalidenstrasse 43, 10115 Berlin, Germany
| | - Barbara Koller
- Laboratory of Chronobiology, Charité - Universitätsmedizin Berlin, Hessische Strasse 3-4, 10115 Berlin, Germany
| | - Andreas Herrmann
- Department of Biology, Molecular Biophysics, Humboldt-University Berlin, Invalidenstrasse 43, 10115 Berlin, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Charité - Universitätsmedizin Berlin, Hessische Strasse 3-4, 10115 Berlin, Germany
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48
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Interaction of Circadian Clock Proteins CRY1 and PER2 Is Modulated by Zinc Binding and Disulfide Bond Formation. Cell 2014; 157:1203-15. [DOI: 10.1016/j.cell.2014.03.057] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 02/06/2014] [Accepted: 03/17/2014] [Indexed: 11/22/2022]
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Evolution of PAS domains and PAS-containing genes in eukaryotes. Chromosoma 2014; 123:385-405. [PMID: 24699836 DOI: 10.1007/s00412-014-0457-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/21/2014] [Accepted: 03/11/2014] [Indexed: 01/18/2023]
Abstract
The PAS domains are signal modules, which are widely distributed in proteins across all kingdoms of life. They are common in photoreceptors and transcriptional regulators of eukaryotic circadian clocks q(bHLH-PAS proteins and PER in animals; PHY and ZTL in plants; and WC-1, 2, and VVD in fungi) and possess mainly protein-protein interaction and light-sensing functions. We conducted several evolutionary analyses of the PAS superfamily. Although the whole superfamily evolved primarily under strong purifying selection (average ω ranges from 0.0030 to 0.1164), some lineages apparently experienced strong episodic positive selection at some periods of the evolution. Although the PAS domains from different proteins vary in sequence and length, but they maintain a fairly conserved 3D structure, which is determined by only eight residues. The WC-1 and WC- 2, bHLH-PAS, and P er genes probably originated in the Neoproterozoic Era (1000-542 Mya), plant P hy and ZTL evolved in the Paleozoic (541-252 Mya), which might be a result of adaptation to the major climate and global light regime changes having occurred in those eras.
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Heintz U, Meinhart A, Winkler A. Multi-PAS domain-mediated protein oligomerization of PpsR from Rhodobacter sphaeroides. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:863-76. [PMID: 24598755 PMCID: PMC3949515 DOI: 10.1107/s1399004713033634] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 12/12/2013] [Indexed: 01/04/2023]
Abstract
Per-ARNT-Sim (PAS) domains are essential modules of many multi-domain signalling proteins that mediate protein interaction and/or sense environmental stimuli. Frequently, multiple PAS domains are present within single polypeptide chains, where their interplay is required for protein function. Although many isolated PAS domain structures have been reported over the last decades, only a few structures of multi-PAS proteins are known. Therefore, the molecular mechanism of multi-PAS domain-mediated protein oligomerization and function is poorly understood. The transcription factor PpsR from Rhodobacter sphaeroides is such a multi-PAS domain protein that, in addition to its three PAS domains, contains a glutamine-rich linker and a C-terminal helix-turn-helix DNA-binding motif. Here, crystal structures of two N-terminally and C-terminally truncated PpsR variants that comprise a single (PpsRQ-PAS1) and two (PpsRN-Q-PAS1) PAS domains, respectively, are presented and the multi-step strategy required for the phasing of a triple PAS domain construct (PpsRΔHTH) is illustrated. While parts of the biologically relevant dimerization interface can already be observed in the two shorter constructs, the PpsRΔHTH structure reveals how three PAS domains enable the formation of multiple oligomeric states (dimer, tetramer and octamer), highlighting that not only the PAS cores but also their α-helical extensions are essential for protein oligomerization. The results demonstrate that the long helical glutamine-rich linker of PpsR results from a direct fusion of the N-cap of the PAS1 domain with the C-terminal extension of the N-domain that plays an important role in signal transduction.
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Affiliation(s)
- Udo Heintz
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Anton Meinhart
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Andreas Winkler
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
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