1
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Gabriel CH, Del Olmo M, Rizki Widini A, Roshanbin R, Woyde J, Hamza E, Gutu NN, Zehtabian A, Ewers H, Granada A, Herzel H, Kramer A. Circadian period is compensated for repressor protein turnover rates in single cells. Proc Natl Acad Sci U S A 2024; 121:e2404738121. [PMID: 39141353 DOI: 10.1073/pnas.2404738121] [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: 03/06/2024] [Accepted: 07/07/2024] [Indexed: 08/15/2024] Open
Abstract
Most mammalian cells have molecular circadian clocks that generate widespread rhythms in transcript and protein abundance. While circadian clocks are robust to fluctuations in the cellular environment, little is known about the mechanisms by which the circadian period compensates for fluctuating metabolic states. Here, we exploit the heterogeneity of single cells both in circadian period and a metabolic parameter-protein stability-to study their interdependence without the need for genetic manipulation. We generated cells expressing key circadian proteins (CRYPTOCHROME1/2 (CRY1/2) and PERIOD1/2 (PER1/2)) as endogenous fusions with fluorescent proteins and simultaneously monitored circadian rhythms and degradation in thousands of single cells. We found that the circadian period compensates for fluctuations in the turnover rates of circadian repressor proteins and uncovered possible mechanisms using a mathematical model. In addition, the stabilities of the repressor proteins are circadian phase dependent and correlate with the circadian period in a phase-dependent manner, in contrast to the prevailing model.
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Affiliation(s)
- Christian H Gabriel
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin 10117, Germany
| | - Marta Del Olmo
- Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin, Berlin 10115, Germany
| | - Arunya Rizki Widini
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin 10117, Germany
| | - Rashin Roshanbin
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin 10117, Germany
| | - Jonas Woyde
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin 10117, Germany
| | - Ebrahim Hamza
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin 10117, Germany
| | - Nica-Nicoleta Gutu
- Charité Comprehensive Cancer Center, Charité-Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Amin Zehtabian
- Department of Biology, Chemistry and Pharmacy, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin 14195, Germany
| | - Helge Ewers
- Department of Biology, Chemistry and Pharmacy, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin 14195, Germany
| | - Adrian Granada
- Charité Comprehensive Cancer Center, Charité-Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin, Berlin 10115, Germany
| | - Achim Kramer
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin 10117, Germany
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2
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Delisle BP, Prabhat A, Burgess DE, Ono M, Esser KA, Schroder EA. Circadian Regulation of Cardiac Arrhythmias and Electrophysiology. Circ Res 2024; 134:659-674. [PMID: 38484028 PMCID: PMC11177776 DOI: 10.1161/circresaha.123.323513] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Circadian rhythms in physiology and behavior are ≈24-hour biological cycles regulated by internal biological clocks (ie, circadian clocks) that optimize organismal homeostasis in response to predictable environmental changes. These clocks are present in virtually all cells in the body, including cardiomyocytes. Many decades ago, clinicians and researchers became interested in studying daily patterns of triggers for sudden cardiac death, the incidence of sudden cardiac death, and cardiac arrhythmias. This review highlights historical and contemporary studies examining the role of day/night rhythms in the timing of cardiovascular events, delves into changes in the timing of these events over the last few decades, and discusses cardiovascular disease-specific differences in the timing of cardiovascular events. The current understanding of the environmental, behavioral, and circadian mechanisms that regulate cardiac electrophysiology is examined with a focus on the circadian regulation of cardiac ion channels and ion channel regulatory genes. Understanding the contribution of environmental, behavioral, and circadian rhythms on arrhythmia susceptibility and the incidence of sudden cardiac death will be essential in developing future chronotherapies.
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Affiliation(s)
- Brian P. Delisle
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Abhilash Prabhat
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Don E. Burgess
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Makoto Ono
- Division of Cardiology and Rehabilitation, Tamaki Hospital, Japan
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3
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Choi SB, Vatan T, Alexander TA, Zhang C, Mitchell SM, Speer CM, Nemes P. Microanalytical Mass Spectrometry with Super-Resolution Microscopy Reveals a Proteome Transition During Development of the Brain's Circadian Pacemaker. Anal Chem 2023; 95:15208-15216. [PMID: 37792996 PMCID: PMC10728713 DOI: 10.1021/acs.analchem.3c01987] [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] [Indexed: 10/06/2023]
Abstract
During brain development, neuronal proteomes are regulated in part by changes in spontaneous and sensory-driven activity in immature neural circuits. A longstanding model for studying activity-dependent circuit refinement is the developing mouse visual system where the formation of axonal projections from the eyes to the brain is influenced by spontaneous retinal activity prior to the onset of vision and by visual experience after eye-opening. The precise proteomic changes in retinorecipient targets that occur during this developmental transition are unknown. Here, we developed a microanalytical proteomics pipeline using capillary electrophoresis (CE) electrospray ionization (ESI) mass spectrometry (MS) in the discovery setting to quantify developmental changes in the chief circadian pacemaker, the suprachiasmatic nucleus (SCN), before and after the onset of photoreceptor-dependent visual function. Nesting CE-ESI with trapped ion mobility spectrometry time-of-flight (TOF) mass spectrometry (TimsTOF PRO) doubled the number of identified and quantified proteins compared to the TOF-only control on the same analytical platform. From 10 ng of peptide input, corresponding to <∼0.5% of the total local tissue proteome, technical triplicate analyses identified 1894 proteins and quantified 1066 proteins, including many with important canonical functions in axon guidance, synapse function, glial cell maturation, and extracellular matrix refinement. Label-free quantification revealed differential regulation for 166 proteins over development, with enrichment of axon guidance-associated proteins prior to eye-opening and synapse-associated protein enrichment after eye-opening. Super-resolution imaging of select proteins using STochastic Optical Reconstruction Microscopy (STORM) corroborated the MS results and showed that increased presynaptic protein abundance pre/post eye-opening in the SCN reflects a developmental increase in synapse number, but not presynaptic size or extrasynaptic protein expression. This work marks the first development and systematic application of TimsTOF PRO for CE-ESI-based microproteomics and the first integration of microanalytical CE-ESI TimsTOF PRO with volumetric super-resolution STORM imaging to expand the repertoire of technologies supporting analytical neuroscience.
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Affiliation(s)
- Sam B. Choi
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Tarlan Vatan
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
| | | | - Chenghang Zhang
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
| | | | - Colenso M. Speer
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
| | - Peter Nemes
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
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4
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Ragozzino FJ, Peterson B, Karatsoreos IN, Peters JH. Circadian regulation of glutamate release pathways shapes synaptic throughput in the brainstem nucleus of the solitary tract (NTS). J Physiol 2023; 601:1881-1896. [PMID: 36975145 PMCID: PMC10192157 DOI: 10.1113/jp284370] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
Circadian regulation of autonomic reflex pathways pairs physiological function with the daily light cycle. The brainstem nucleus of the solitary tract (NTS) is a key candidate for rhythmic control of the autonomic nervous system. Here we investigated circadian regulation of NTS neurotransmission and synaptic throughput using patch-clamp electrophysiology in brainstem slices from mice. We found that spontaneous quantal glutamate release onto NTS neurons showed strong circadian rhythmicity, with the highest rate of release during the light phase and the lowest in the dark, that were sufficient to drive day/night differences in constitutive postsynaptic action potential firing. In contrast, afferent evoked action potential throughput was enhanced during the dark and diminished in the light. Afferent-driven synchronous release pathways showed a similar decrease in release probability that did not explain the enhanced synaptic throughput during the night. However, analysis of postsynaptic membrane properties revealed diurnal changes in conductance, which, when coupled with the circadian changes in glutamate release pathways, tuned synaptic throughput between the light and dark phases. These coordinated pre-/postsynaptic changes encode nuanced control over synaptic performance and pair NTS action potential firing and vagal throughput with time of day. KEY POINTS: Vagal afferent neurons relay information from peripheral organs to the brainstem nucleus of the solitary tract (NTS) to initiate autonomic reflex pathways as well as providing important controls of food intake, digestive function and energy balance. Vagally mediated reflexes and behaviours are under strong circadian regulation. Diurnal fluctuations in presynaptic vesicle release pathways and postsynaptic membrane conductances provide nuanced control over NTS action potential firing and vagal synaptic throughput. Coordinated pre-/postsynaptic changes represent a fundamental mechanism mediating daily changes in vagal afferent signalling and autonomic function.
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Affiliation(s)
- Forrest J. Ragozzino
- Department of Integrative Physiology and Neuroscience, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - BreeAnne Peterson
- Department of Integrative Physiology and Neuroscience, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Ilia N. Karatsoreos
- Department of Psychological and Brain Sciences, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - James H. Peters
- Department of Integrative Physiology and Neuroscience, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
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5
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Wang Y, Guo H, He F. Circadian disruption: from mouse models to molecular mechanisms and cancer therapeutic targets. Cancer Metastasis Rev 2023; 42:297-322. [PMID: 36513953 DOI: 10.1007/s10555-022-10072-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022]
Abstract
The circadian clock is a timekeeping system for numerous biological rhythms that contribute to the regulation of numerous homeostatic processes in humans. Disruption of circadian rhythms influences physiology and behavior and is associated with adverse health outcomes, especially cancer. However, the underlying molecular mechanisms of circadian disruption-associated cancer initiation and development remain unclear. It is essential to construct good circadian disruption models to uncover and validate the detailed molecular clock framework of circadian disruption in cancer development and progression. Mouse models are the most widely used in circadian studies due to their relatively small size, fast reproduction cycle, easy genome manipulation, and economic practicality. Here, we reviewed the current mouse models of circadian disruption, including suprachiasmatic nuclei destruction, genetic engineering, light disruption, sleep deprivation, and other lifestyle factors in our understanding of the crosstalk between circadian rhythms and oncogenic signaling, as well as the molecular mechanisms of circadian disruption that promotes cancer growth. We focused on the discoveries made with the nocturnal mouse, diurnal human being, and cell culture and provided several circadian rhythm-based cancer therapeutic strategies.
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Affiliation(s)
- Yu Wang
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Haidong Guo
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
- Department of Anatomy, School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Feng He
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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6
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Abstract
Our physiology and behavior follow precise daily programs that adapt us to the alternating opportunities and challenges of day and night. Under experimental isolation, these rhythms persist with a period of approximately one day (circadian), demonstrating their control by an internal autonomous clock. Circadian time is created at the cellular level by a transcriptional/translational feedback loop (TTFL) in which the protein products of the Period and Cryptochrome genes inhibit their own transcription. Because the accumulation of protein is slow and delayed, the system oscillates spontaneously with a period of ∼24 hours. This cell-autonomous TTFL controls cycles of gene expression in all major tissues and these cycles underpin our daily metabolic programs. In turn, our innumerable cellular clocks are coordinated by a central pacemaker, the suprachiasmatic nucleus (SCN) of the hypothalamus. When isolated in slice culture, the SCN TTFL and its dependent cycles of neural activity persist indefinitely, operating as "a clock in a dish". In vivo, SCN time is synchronized to solar time by direct innervation from specialized retinal photoreceptors. In turn, the precise circadian cycle of action potential firing signals SCN-generated time to hypothalamic and brain stem targets, which co-ordinate downstream autonomic, endocrine, and behavioral (feeding) cues to synchronize and sustain the distributed cellular clock network. Circadian time therefore pervades every level of biological organization, from molecules to society. Understanding its mechanisms offers important opportunities to mitigate the consequences of circadian disruption, so prevalent in modern societies, that arise from shiftwork, aging, and neurodegenerative diseases, not least Huntington's disease.
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Affiliation(s)
- Andrew P. Patton
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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7
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Greiner P, Houdek P, Sládek M, Sumová A. Early rhythmicity in the fetal suprachiasmatic nuclei in response to maternal signals detected by omics approach. PLoS Biol 2022; 20:e3001637. [PMID: 35609026 PMCID: PMC9129005 DOI: 10.1371/journal.pbio.3001637] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/19/2022] [Indexed: 11/18/2022] Open
Abstract
The suprachiasmatic nuclei (SCN) of the hypothalamus harbor the central clock of the circadian system, which gradually matures during the perinatal period. In this study, time-resolved transcriptomic and proteomic approaches were used to describe fetal SCN tissue-level rhythms before rhythms in clock gene expression develop. Pregnant rats were maintained in constant darkness and had intact SCN, or their SCN were lesioned and behavioral rhythm was imposed by temporal restriction of food availability. Model-selecting tools dryR and CompareRhythms identified sets of genes in the fetal SCN that were rhythmic in the absence of the fetal canonical clock. Subsets of rhythmically expressed genes were assigned to groups of fetuses from mothers with either intact or lesioned SCN, or both groups. Enrichment analysis for GO terms and signaling pathways revealed that neurodevelopment and cell-to-cell signaling were significantly enriched within the subsets of genes that were rhythmic in response to distinct maternal signals. The findings discovered a previously unexpected breadth of rhythmicity in the fetal SCN at a developmental stage when the canonical clock has not yet developed at the tissue level and thus likely represents responses to rhythmic maternal signals.
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Affiliation(s)
- Philipp Greiner
- Laboratory of Biological Rhythms, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Pavel Houdek
- Laboratory of Biological Rhythms, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martin Sládek
- Laboratory of Biological Rhythms, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alena Sumová
- Laboratory of Biological Rhythms, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
- * E-mail:
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8
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Wong DCS, Seinkmane E, Zeng A, Stangherlin A, Rzechorzek NM, Beale AD, Day J, Reed M, Peak‐Chew SY, Styles CT, Edgar RS, Putker M, O’Neill JS. CRYPTOCHROMES promote daily protein homeostasis. EMBO J 2022; 41:e108883. [PMID: 34842284 PMCID: PMC8724739 DOI: 10.15252/embj.2021108883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 11/29/2022] Open
Abstract
The daily organisation of most mammalian cellular functions is attributed to circadian regulation of clock-controlled protein expression, driven by daily cycles of CRYPTOCHROME-dependent transcriptional feedback repression. To test this, we used quantitative mass spectrometry to compare wild-type and CRY-deficient fibroblasts under constant conditions. In CRY-deficient cells, we found that temporal variation in protein, phosphopeptide, and K+ abundance was at least as great as wild-type controls. Most strikingly, the extent of temporal variation within either genotype was much smaller than overall differences in proteome composition between WT and CRY-deficient cells. This proteome imbalance in CRY-deficient cells and tissues was associated with increased susceptibility to proteotoxic stress, which impairs circadian robustness, and may contribute to the wide-ranging phenotypes of CRY-deficient mice. Rather than generating large-scale daily variation in proteome composition, we suggest it is plausible that the various transcriptional and post-translational functions of CRY proteins ultimately act to maintain protein and osmotic homeostasis against daily perturbation.
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Affiliation(s)
| | | | - Aiwei Zeng
- MRC Laboratory of Molecular BiologyCambridgeUK
| | | | | | | | - Jason Day
- Department of Earth SciencesUniversity of CambridgeCambridgeUK
| | - Martin Reed
- MRC Laboratory of Molecular BiologyCambridgeUK
| | | | | | - Rachel S Edgar
- Department of Infectious DiseasesImperial CollegeLondonUK
| | - Marrit Putker
- MRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
Crown BioscienceUtrechtthe Netherlands
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Lu X, Zhou M, Liu N, Zhang C, Zhao Z, Cai D. Synaptic Protein Phosphorylation Networks Are Associated With Electroacupuncture-Induced Circadian Control in the Suprachiasmatic Nucleus. Front Genet 2021; 12:762557. [PMID: 34976011 PMCID: PMC8717940 DOI: 10.3389/fgene.2021.762557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 11/29/2021] [Indexed: 11/23/2022] Open
Abstract
Phosphorylation is one of the most important posttranslational modifications and regulates the physiological process. While recent studies highlight a major role of phosphorylation in the regulation of sleep–wake cycles to a lesser extent, the phosphoproteome in the suprachiasmatic nucleus (SCN) is not well-understood. Herein, we reported that the EA treatment elicits partial reparation of circadian rhythmicity when mice were exposure to constant darkness for long time. We investigated the effects of EA on circadian rhythms in constant darkness between EA stimulation and free-running control. Next, mass spectrometry–based phosphoproteome was utilized to explore the molecular characteristics of EA-induced phosphorylation modification in the SCN. A total of 6,192 distinct phosphosites on 2,488 proteins were quantified. Functional annotation analysis and protein–protein interaction networks demonstrated the most significant enriched phosphor-proteins and phosphosites involved in postsynapse and glutamatergic synapse. The current data indicated that most of the altered molecules are structural proteins. The target proteins, NMDAR and CAMK2, were selected for verification, consistent with the results of LC–MS/MS. These findings revealed a complete profile of phosphorylation modification in response to EA.
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Affiliation(s)
| | | | | | | | | | - Dingjun Cai
- *Correspondence: Zhengyu Zhao, ; Dingjun Cai,
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10
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Compensatory ion transport buffers daily protein rhythms to regulate osmotic balance and cellular physiology. Nat Commun 2021; 12:6035. [PMID: 34654800 PMCID: PMC8520019 DOI: 10.1038/s41467-021-25942-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/04/2021] [Indexed: 01/15/2023] Open
Abstract
Between 6-20% of the cellular proteome is under circadian control and tunes mammalian cell function with daily environmental cycles. For cell viability, and to maintain volume within narrow limits, the daily variation in osmotic potential exerted by changes in the soluble proteome must be counterbalanced. The mechanisms and consequences of this osmotic compensation have not been investigated before. In cultured cells and in tissue we find that compensation involves electroneutral active transport of Na+, K+, and Cl- through differential activity of SLC12A family cotransporters. In cardiomyocytes ex vivo and in vivo, compensatory ion fluxes confer daily variation in electrical activity. Perturbation of soluble protein abundance has commensurate effects on ion composition and cellular function across the circadian cycle. Thus, circadian regulation of the proteome impacts ion homeostasis with substantial consequences for the physiology of electrically active cells such as cardiomyocytes.
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11
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Phosphorylation of GAPVD1 Is Regulated by the PER Complex and Linked to GAPVD1 Degradation. Int J Mol Sci 2021; 22:ijms22073787. [PMID: 33917494 PMCID: PMC8038846 DOI: 10.3390/ijms22073787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 03/29/2021] [Accepted: 04/03/2021] [Indexed: 11/16/2022] Open
Abstract
Repressor protein period (PER) complexes play a central role in the molecular oscillator mechanism of the mammalian circadian clock. While the main role of nuclear PER complexes is transcriptional repression, much less is known about the functions of cytoplasmic PER complexes. We found with a biochemical screen for PER2-interacting proteins that the small GTPase regulator GTPase-activating protein and VPS9 domain-containing protein 1 (GAPVD1), which has been identified previously as a component of cytoplasmic PER complexes in mice, is also a bona fide component of human PER complexes. We show that in situ GAPVD1 is closely associated with casein kinase 1 delta (CSNK1D), a kinase that regulates PER2 levels through a phosphoswitch mechanism, and that CSNK1D regulates the phosphorylation of GAPVD1. Moreover, phosphorylation determines the kinetics of GAPVD1 degradation and is controlled by PER2 and a C-terminal autoinhibitory domain in CSNK1D, indicating that the regulation of GAPVD1 phosphorylation is a novel function of cytoplasmic PER complexes and might be part of the oscillator mechanism or an output function of the circadian clock.
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12
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Wu G, Ruben MD, Lee Y, Li J, Hughes ME, Hogenesch JB. Genome-wide studies of time of day in the brain: Design and analysis. BRAIN SCIENCE ADVANCES 2020. [DOI: 10.26599/bsa.2020.9050005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Transcriptome profiling at different times of day is powerful for studying circadian regulation in model organisms and humans. To date, 24 h profiles from many tissue types suggest that about half of all genes are circadian-expressed somewhere in the body. However, few of these studies focused on the brain. Thus, despite known links between circadian disruption and neurological disease, we have virtually no mechanistic understanding. In the coming decade, we expect more genome-wide studies of time of day in different brain diseases, regions, and cell types. We expect just as many different approaches to the design and analysis of these studies. This review considers key principles of circadian tran scriptomics, with the goal of maximizing utility and reproducibility of future studies in the nervous system.
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Affiliation(s)
- Gang Wu
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH 45229, U.S.A
| | - Marc D. Ruben
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH 45229, U.S.A
| | - Yinyeng Lee
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH 45229, U.S.A
| | - Jiajia Li
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO 63310, U.S.A
| | - Michael E. Hughes
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO 63310, U.S.A
| | - John B. Hogenesch
- Divisions of Human Genetics and Immunobiology, Center for Chronobiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, 240 Albert Sabin Way, Cincinnati, OH 45229, U.S.A
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13
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Marcheva B, Perelis M, Weidemann BJ, Taguchi A, Lin H, Omura C, Kobayashi Y, Newman MV, Wyatt EJ, McNally EM, Fox JEM, Hong H, Shankar A, Wheeler EC, Ramsey KM, MacDonald PE, Yeo GW, Bass J. A role for alternative splicing in circadian control of exocytosis and glucose homeostasis. Genes Dev 2020; 34:1089-1105. [PMID: 32616519 PMCID: PMC7397853 DOI: 10.1101/gad.338178.120] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/10/2020] [Indexed: 11/24/2022]
Abstract
The circadian clock is encoded by a negative transcriptional feedback loop that coordinates physiology and behavior through molecular programs that remain incompletely understood. Here, we reveal rhythmic genome-wide alternative splicing (AS) of pre-mRNAs encoding regulators of peptidergic secretion within pancreatic β cells that are perturbed in Clock-/- and Bmal1-/- β-cell lines. We show that the RNA-binding protein THRAP3 (thyroid hormone receptor-associated protein 3) regulates circadian clock-dependent AS by binding to exons at coding sequences flanking exons that are more frequently skipped in clock mutant β cells, including transcripts encoding Cask (calcium/calmodulin-dependent serine protein kinase) and Madd (MAP kinase-activating death domain). Depletion of THRAP3 restores expression of the long isoforms of Cask and Madd, and mimicking exon skipping in these transcripts through antisense oligonucleotide delivery in wild-type islets reduces glucose-stimulated insulin secretion. Finally, we identify shared networks of alternatively spliced exocytic genes from islets of rodent models of diet-induced obesity that significantly overlap with clock mutants. Our results establish a role for pre-mRNA alternative splicing in β-cell function across the sleep/wake cycle.
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Affiliation(s)
- Biliana Marcheva
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Mark Perelis
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Benjamin J Weidemann
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Akihiko Taguchi
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Haopeng Lin
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Chiaki Omura
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Yumiko Kobayashi
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Marsha V Newman
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Eugene J Wyatt
- Center for Genetic Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Jocelyn E Manning Fox
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Heekyung Hong
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Archana Shankar
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Emily C Wheeler
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Kathryn Moynihan Ramsey
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Patrick E MacDonald
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Joseph Bass
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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14
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Castelo-Szekely V, Gatfield D. Emerging Roles of Translational Control in Circadian Timekeeping. J Mol Biol 2020; 432:3483-3497. [PMID: 32246961 DOI: 10.1016/j.jmb.2020.03.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 01/07/2023]
Abstract
A large part of mammalian physiology and behaviour shows regular daily variations. This temporal organisation is driven by the activity of an endogenous circadian clock, whose molecular basis consists of diurnal waves in gene expression. Circadian transcription is the major driver of these rhythms, yet post-transcriptional mechanisms, some of which occur in response to systemic cues and in a tissue-specific fashion, have central roles in ultimately establishing the oscillatory gene expression programme as well. Regulatory control that occurs at the level of translation is emerging as an important player in the generation and modulation of protein accumulation rhythms. As a mechanism, translation lies at a privileged position to integrate genetically encoded rhythmic signals with other, external and internal stimuli, including nutrient-derived cues. In this review, we summarise our current knowledge of how diurnal control of translation affects both bulk protein levels and gene-specific protein biosynthesis. We discuss mechanisms of regulation, in particular with regard to the complex interplay between circadian cycles and feeding/fasting cycles, as well as emerging roles for upstream open reading frames in clock control.
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Affiliation(s)
- Violeta Castelo-Szekely
- Center for Integrative Genomics, University of Lausanne, Genopode, 1015 Lausanne, Switzerland
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, Genopode, 1015 Lausanne, Switzerland.
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15
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Takemura S, Nagano M, Isonishi A, Tanaka T, Tatsumi K, Yamano M, Minami Y, Shigeyoshi Y, Wanaka A. Circadian rhythms of sorting nexin 25 in the mouse suprachiasmatic nucleus. Neurosci Lett 2020; 727:134897. [PMID: 32156614 DOI: 10.1016/j.neulet.2020.134897] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 12/27/2022]
Abstract
Entrainment of mammalian circadian rhythms requires receptor-mediated signaling in the hypothalamic suprachiasmatic nucleus (SCN), the site of the master circadian pacemaker. Receptor-mediated signaling is regulated by endocytosis, indicating that endocytosis-related proteins contribute to SCN pacemaking. Sorting nexin 25 (SNX25) belongs to the sorting nexin superfamily, whose members are responsible for membrane attachment to organelles of the endocytic system. In this study, we showed that Snx25 mRNA and SNX25 protein are highly expressed and exhibit remarkable circadian rhythms in the SCN of adult mice. Expression was maximal at about zeitgeber time (ZT) 16 in the subjective night and minimal at ZT8 in the subjective day. Prominent SNX25 immunoreactivity was found in the arginine vasopressin-positive neurons of the SCN. These findings suggest that SNX25 is a new actor in endocytic signaling, perhaps contributing to the circadian pacemaking system.
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Affiliation(s)
- Shoko Takemura
- Department of Anatomy & Neuroscience, Faculty of Medicine, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan.
| | - Mamoru Nagano
- Department of Anatomy and Neurobiology, Faculty of Medicine, Kindai University, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Ayami Isonishi
- Department of Anatomy & Neuroscience, Faculty of Medicine, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Tatsuhide Tanaka
- Department of Anatomy & Neuroscience, Faculty of Medicine, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Kouko Tatsumi
- Department of Anatomy & Neuroscience, Faculty of Medicine, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Mariko Yamano
- Department of Anatomy & Neuroscience, Faculty of Medicine, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
| | - Yoichi Minami
- Department of Anatomy and Neurobiology, Faculty of Medicine, Kindai University, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Yasufumi Shigeyoshi
- Department of Anatomy and Neurobiology, Faculty of Medicine, Kindai University, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Akio Wanaka
- Department of Anatomy & Neuroscience, Faculty of Medicine, Nara Medical University, 840 Shijo-cho, Kashihara, Nara, 634-8521, Japan
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16
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Hastings MH, Smyllie NJ, Patton AP. Molecular-genetic Manipulation of the Suprachiasmatic Nucleus Circadian Clock. J Mol Biol 2020; 432:3639-3660. [PMID: 31996314 DOI: 10.1016/j.jmb.2020.01.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/10/2020] [Accepted: 01/15/2020] [Indexed: 01/08/2023]
Abstract
Circadian (approximately daily) rhythms of physiology and behaviour adapt organisms to the alternating environments of day and night. The suprachiasmatic nucleus (SCN) of the hypothalamus is the principal circadian timekeeper of mammals. The mammalian cell-autonomous circadian clock is built around a self-sustaining transcriptional-translational negative feedback loop (TTFL) in which the negative regulators Per and Cry suppress their own expression, which is driven by the positive regulators Clock and Bmal1. Importantly, such TTFL-based clocks are present in all major tissues across the organism, and the SCN is their central co-ordinator. First, we analyse SCN timekeeping at the cell-autonomous and the circuit-based levels of organisation. We consider how molecular-genetic manipulations have been used to probe cell-autonomous timing in the SCN, identifying the integral components of the clock. Second, we consider new approaches that enable real-time monitoring of the activity of these clock components and clock-driven cellular outputs. Finally, we review how intersectional genetic manipulations of the cell-autonomous clockwork can be used to determine how SCN cells interact to generate an ensemble circadian signal. Critically, it is these network-level interactions that confer on the SCN its emergent properties of robustness, light-entrained phase and precision- properties that are essential for its role as the central co-ordinator. Remaining gaps in knowledge include an understanding of how the TTFL proteins behave individually and in complexes: whether particular SCN neuronal populations act as pacemakers, and if so, by which signalling mechanisms, and finally the nature of the recently discovered role of astrocytes within the SCN network.
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Affiliation(s)
- Michael H Hastings
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
| | - Nicola J Smyllie
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Andrew P Patton
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
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17
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Adler P, Chiang CK, Mayne J, Ning Z, Zhang X, Xu B, Cheng HYM, Figeys D. Aging Disrupts the Circadian Patterns of Protein Expression in the Murine Hippocampus. Front Aging Neurosci 2020; 11:368. [PMID: 32009941 PMCID: PMC6974521 DOI: 10.3389/fnagi.2019.00368] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 12/16/2019] [Indexed: 12/29/2022] Open
Abstract
Aging is associated with cognitive decline and dysregulation of the circadian system, which modulates hippocampal-dependent memory as well as biological processes underlying hippocampal function. While circadian dysfunction and memory impairment are common features of aging and several neurodegenerative brain disorders, how aging impacts the circadian expression patterns of proteins involved in processes that underlie hippocampal-dependent memory is not well understood. In this study, we profiled the hippocampal proteomes of young and middle-aged mice across two circadian cycles using quantitative mass spectrometry in order to explore aging-associated changes in the temporal orchestration of biological pathways. Of the ∼1,420 proteins that were accurately quantified, 15% (214 proteins) displayed circadian rhythms in abundance in the hippocampus of young mice, while only 1.6% (23 proteins) were rhythmic in middle-aged mice. Remarkably, aging disrupted the circadian regulation of proteins involved in cellular functions critical for hippocampal function and memory, including dozens of proteins participating in pathways of energy metabolism, neurotransmission, and synaptic plasticity. These included processes such as glycolysis, the tricarboxylic acid cycle, synaptic vesicle cycling, long-term potentiation, and cytoskeletal organization. Moreover, aging altered the daily expression rhythms of proteins implicated in hallmarks of aging and the pathogenesis of several age-related neurodegenerative brain disorders affecting the hippocampus. Notably, we identified age-related alterations in the rhythmicity of proteins involved in mitochondrial dysfunction and loss of proteostasis, as well as proteins involved in the pathogenesis of disorders such as Alzheimer’s disease and Parkinson’s disease. These insights into aging-induced changes in the hippocampal proteome provide a framework for understanding how the age-dependent circadian decline may contribute to cognitive impairment and the development of neurodegenerative diseases during aging.
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Affiliation(s)
- Paula Adler
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Cheng-Kang Chiang
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Janice Mayne
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Zhibin Ning
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Xu Zhang
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Bo Xu
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Hai-Ying Mary Cheng
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Daniel Figeys
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Canadian Institute for Advanced Research, Toronto, ON, Canada
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18
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Mauvoisin D, Gachon F. Proteomics in Circadian Biology. J Mol Biol 2019; 432:3565-3577. [PMID: 31843517 DOI: 10.1016/j.jmb.2019.12.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/09/2019] [Accepted: 12/09/2019] [Indexed: 02/06/2023]
Abstract
The circadian clock is an endogenous molecular timekeeping system that allows organisms to adjust their physiology and behavior to the time of day in an anticipatory fashion. In different organisms, the circadian clock coordinates physiology and metabolism through regulation of gene expression at the transcriptional and post-transcriptional levels. Until now, circadian gene expression studies have mostly focused primarily on transcriptomics approaches. This type of analyses revealed that many protein-encoding genes show circadian expression in a tissue-specific manner. During the last three decades, a long way has been traveled since the pioneering work on dinoflagellates, and new advances in mass spectrometry offered new perspectives in the characterization of the circadian dynamics of the proteome. Altogether, these efforts highlighted that rhythmic protein oscillation is driven equally by gene transcription, post-transcriptional and post-translational regulations. The determination of the role of the circadian clock in these three levels of regulation appears to be the next major challenge in the field.
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Affiliation(s)
- Daniel Mauvoisin
- L'institut Du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France.
| | - Frédéric Gachon
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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19
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Ubiquitylation Dynamics of the Clock Cell Proteome and TIMELESS during a Circadian Cycle. Cell Rep 2019; 23:2273-2282. [PMID: 29791839 DOI: 10.1016/j.celrep.2018.04.064] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 02/10/2018] [Accepted: 04/13/2018] [Indexed: 12/14/2022] Open
Abstract
Circadian clocks have evolved as time-measuring molecular devices to help organisms adapt their physiology to daily changes in light and temperature. Transcriptional oscillations account for a large fraction of rhythmic protein abundance. However, cycling of various posttranslational modifications, such as ubiquitylation, also contributes to shape the rhythmic protein landscape. In this study, we used an in vivo ubiquitin labeling assay to investigate the circadian ubiquitylated proteome of Drosophila melanogaster. We find that cyclic ubiquitylation affects MEGATOR (MTOR), a chromatin-associated nucleoporin that, in turn, feeds back to regulate the core molecular oscillator. Furthermore, we show that the ubiquitin ligase subunits CULLIN-3 (CUL-3) and SUPERNUMERARY LIMBS (SLMB) cooperate for ubiquitylating the TIMELESS protein. These findings stress the importance of ubiquitylation pathways in the Drosophila circadian clock and reveal a key component of this system.
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20
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Abstract
The suprachiasmatic nucleus (SCN) of the hypothalamus is remarkable. Despite numbering only about 10,000 neurons on each side of the third ventricle, the SCN is our principal circadian clock, directing the daily cycles of behaviour and physiology that set the tempo of our lives. When this nucleus is isolated in organotypic culture, its autonomous timing mechanism can persist indefinitely, with precision and robustness. The discovery of the cell-autonomous transcriptional and post-translational feedback loops that drive circadian activity in the SCN provided a powerful exemplar of the genetic specification of complex mammalian behaviours. However, the analysis of circadian time-keeping is moving beyond single cells. Technical and conceptual advances, including intersectional genetics, multidimensional imaging and network theory, are beginning to uncover the circuit-level mechanisms and emergent properties that make the SCN a uniquely precise and robust clock. However, much remains unknown about the SCN, not least the intrinsic properties of SCN neurons, its circuit topology and the neuronal computations that these circuits support. Moreover, the convention that the SCN is a neuronal clock has been overturned by the discovery that astrocytes are an integral part of the timepiece. As a test bed for examining the relationships between genes, cells and circuits in sculpting complex behaviours, the SCN continues to offer powerful lessons and opportunities for contemporary neuroscience.
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21
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Abstract
Fundamental aspects of neurobiology are time-of-day regulated. Therefore, it is not surprising that neurodegenerative and psychiatric diseases are accompanied by sleep and circadian rhythm disruption. Although the direction of causation remains unclear, abnormal sleep-wake patterns often occur early in disease, exacerbate progression, and are a common primary complaint from patients. Circadian medicine incorporates knowledge of 24-hour biological rhythms to improve treatment. This article highlights how research and technologic advances in circadian biology might translate to improved patient care.
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22
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Mauvoisin D. Circadian rhythms and proteomics: It's all about posttranslational modifications! WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2019; 11:e1450. [PMID: 31034157 DOI: 10.1002/wsbm.1450] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 12/23/2022]
Abstract
The circadian clock is a molecular endogenous timekeeping system and allows organisms to adjust their physiology and behavior to the geophysical time. Organized hierarchically, the master clock in the suprachiasmatic nuclei, coordinates peripheral clocks, via direct, or indirect signals. In peripheral organs, such as the liver, the circadian clock coordinates gene expression, notably metabolic gene expression, from transcriptional to posttranslational level. The metabolism in return feeds back on the molecular circadian clock via posttranslational-based mechanisms. During the last two decades, circadian gene expression studies have mostly been relying primarily on genomics or transcriptomics approaches and transcriptome analyses of multiple organs/tissues have revealed that the majority of protein-coding genes display circadian rhythms in a tissue specific manner. More recently, new advances in mass spectrometry offered circadian proteomics new perspectives, that is, the possibilities of performing large scale proteomic studies at cellular and subcellular levels, but also at the posttranslational modification level. With important implications in metabolic health, cell signaling has been shown to be highly relevant to circadian rhythms. Moreover, comprehensive characterization studies of posttranslational modifications are emerging and as a result, cell signaling processes are expected to be more deeply characterized and understood in the coming years with the use of proteomics. This review summarizes the work studying diurnally rhythmic or circadian gene expression performed at the protein level. Based on the knowledge brought by circadian proteomics studies, this review will also discuss the role of posttranslational modification events as an important link between the molecular circadian clock and metabolic regulation. This article is categorized under: Laboratory Methods and Technologies > Proteomics Methods Physiology > Mammalian Physiology in Health and Disease Biological Mechanisms > Cell Signaling.
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Affiliation(s)
- Daniel Mauvoisin
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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23
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El Cheikh Hussein L, Mollard P, Bonnefont X. Molecular and Cellular Networks in The Suprachiasmatic Nuclei. Int J Mol Sci 2019; 20:ijms20082052. [PMID: 31027315 PMCID: PMC6514755 DOI: 10.3390/ijms20082052] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 12/20/2022] Open
Abstract
Why do we experience the ailments of jetlag when we travel across time zones? Why is working night-shifts so detrimental to our health? In other words, why can’t we readily choose and stick to non-24 h rhythms? Actually, our daily behavior and physiology do not simply result from the passive reaction of our organism to the external cycle of days and nights. Instead, an internal clock drives the variations in our bodily functions with a period close to 24 h, which is supposed to enhance fitness to regular and predictable changes of our natural environment. This so-called circadian clock relies on a molecular mechanism that generates rhythmicity in virtually all of our cells. However, the robustness of the circadian clock and its resilience to phase shifts emerge from the interaction between cell-autonomous oscillators within the suprachiasmatic nuclei (SCN) of the hypothalamus. Thus, managing jetlag and other circadian disorders will undoubtedly require extensive knowledge of the functional organization of SCN cell networks. Here, we review the molecular and cellular principles of circadian timekeeping, and their integration in the multi-cellular complexity of the SCN. We propose that new, in vivo imaging techniques now enable to address these questions directly in freely moving animals.
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Affiliation(s)
- Lama El Cheikh Hussein
- Institut de Génomique Fonctionnelle (IGF), University Montpellier, CNRS, INSERM, 34094 Montpellier, France.
| | - Patrice Mollard
- Institut de Génomique Fonctionnelle (IGF), University Montpellier, CNRS, INSERM, 34094 Montpellier, France.
| | - Xavier Bonnefont
- Institut de Génomique Fonctionnelle (IGF), University Montpellier, CNRS, INSERM, 34094 Montpellier, France.
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24
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Plumel M, Dumont S, Maes P, Sandu C, Felder-Schmittbuhl MP, Challet E, Bertile F. Circadian Analysis of the Mouse Cerebellum Proteome. Int J Mol Sci 2019; 20:ijms20081852. [PMID: 30991638 PMCID: PMC6515515 DOI: 10.3390/ijms20081852] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 02/07/2023] Open
Abstract
The cerebellum contains a circadian clock, generating internal temporal signals. The daily oscillations of cerebellar proteins were investigated in mice using a large-scale two-dimensional difference in gel electrophoresis (2D-DIGE). Analysis of 2D-DIGE gels highlighted the rhythmic variation in the intensity of 27/588 protein spots (5%) over 24 h based on cosinor regression. Notably, the rhythmic expression of most abundant cerebellar proteins was clustered in two main phases (i.e., midday and midnight), leading to bimodal distribution. Only six proteins identified here to be rhythmic in the cerebellum are also known to oscillate in the suprachiasmatic nuclei, including two proteins involved in the synapse activity (Synapsin 2 [SYN2] and vesicle-fusing ATPase [NSF]), two others participating in carbohydrate metabolism (triosephosphate isomerase (TPI1] and alpha-enolase [ENO1]), Glutamine synthetase (GLUL), as well as Tubulin alpha (TUBA4A). Most oscillating cerebellar proteins were not previously identified in circadian proteomic analyses of any tissue. Strikingly, the daily accumulation of mitochondrial proteins was clustered to the mid-resting phase, as previously observed for distinct mitochondrial proteins in the liver. Moreover, a number of rhythmic proteins, such as SYN2, NSF and TPI1, were associated with non-rhythmic mRNAs, indicating widespread post-transcriptional control in cerebellar oscillations. Thus, this study highlights extensive rhythmic aspects of the cerebellar proteome.
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Affiliation(s)
- Marine Plumel
- Institut Pluridisciplinaire Hubert Curien, LSMBO, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 67087 Strasbourg, France.
| | - Stéphanie Dumont
- Institute of Cellular and Integrative Neurosciences, CNRS, Université de Strasbourg, 67000 Strasbourg, France.
| | - Pauline Maes
- Institut Pluridisciplinaire Hubert Curien, LSMBO, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 67087 Strasbourg, France.
| | - Cristina Sandu
- Institute of Cellular and Integrative Neurosciences, CNRS, Université de Strasbourg, 67000 Strasbourg, France.
| | | | - Etienne Challet
- Institute of Cellular and Integrative Neurosciences, CNRS, Université de Strasbourg, 67000 Strasbourg, France.
| | - Fabrice Bertile
- Institut Pluridisciplinaire Hubert Curien, LSMBO, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 67087 Strasbourg, France.
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25
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Hastings MH, Maywood ES, Brancaccio M. The Mammalian Circadian Timing System and the Suprachiasmatic Nucleus as Its Pacemaker. BIOLOGY 2019; 8:E13. [PMID: 30862123 PMCID: PMC6466121 DOI: 10.3390/biology8010013] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/05/2019] [Accepted: 03/08/2019] [Indexed: 11/16/2022]
Abstract
The past twenty years have witnessed the most remarkable breakthroughs in our understanding of the molecular and cellular mechanisms that underpin circadian (approximately one day) time-keeping. Across model organisms in diverse taxa: cyanobacteria (Synechococcus), fungi (Neurospora), higher plants (Arabidopsis), insects (Drosophila) and mammals (mouse and humans), a common mechanistic motif of delayed negative feedback has emerged as the Deus ex machina for the cellular definition of ca. 24 h cycles. This review will consider, briefly, comparative circadian clock biology and will then focus on the mammalian circadian system, considering its molecular genetic basis, the properties of the suprachiasmatic nucleus (SCN) as the principal circadian clock in mammals and its role in synchronising a distributed peripheral circadian clock network. Finally, it will consider new directions in analysing the cell-autonomous and circuit-level SCN clockwork and will highlight the surprising discovery of a central role for SCN astrocytes as well as SCN neurons in controlling circadian behaviour.
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Affiliation(s)
- Michael H Hastings
- MRC Laboratory of Molecular Biology, Division of Neurobiology, CB2 0QH Cambridge, UK.
| | - Elizabeth S Maywood
- MRC Laboratory of Molecular Biology, Division of Neurobiology, CB2 0QH Cambridge, UK.
| | - Marco Brancaccio
- UK Dementia Research Institute at Imperial College London, Division of Brain Sciences, Department of Medicine, W12 0NN London, UK.
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26
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Schenk S, Bannister SC, Sedlazeck FJ, Anrather D, Minh BQ, Bileck A, Hartl M, von Haeseler A, Gerner C, Raible F, Tessmar-Raible K. Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase. eLife 2019; 8:e41556. [PMID: 30767890 PMCID: PMC6377233 DOI: 10.7554/elife.41556] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/15/2019] [Indexed: 12/15/2022] Open
Abstract
Many marine animals, ranging from corals to fishes, synchronise reproduction to lunar cycles. In the annelid Platynereis dumerilii, this timing is orchestrated by an endogenous monthly (circalunar) clock entrained by moonlight. Whereas daily (circadian) clocks cause extensive transcriptomic and proteomic changes, the quality and quantity of regulations by circalunar clocks have remained largely elusive. By establishing a combined transcriptomic and proteomic profiling approach, we provide first systematic insight into the molecular changes in Platynereis heads between circalunar phases, and across sexual differentiation and maturation. Whereas maturation elicits large transcriptomic and proteomic changes, the circalunar clock exhibits only minor transcriptomic, but strong proteomic regulation. Our study provides a versatile extraction technique and comprehensive resources. It corroborates that circadian and circalunar clock effects are likely distinct and identifies key molecular brain signatures for reproduction, sex and circalunar clock phase. Examples include prepro-whitnin/proctolin and ependymin-related proteins as circalunar clock targets.
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Affiliation(s)
- Sven Schenk
- Max F Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria
- Research Platform 'Rhythms of Life', University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Stephanie C Bannister
- Max F Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria
- Research Platform 'Rhythms of Life', University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Fritz J Sedlazeck
- Center of Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Dorothea Anrather
- Max F Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria
- Mass Spectrometry Facility, Max F Perutz Laboratories, Vienna, Austria
| | - Bui Quang Minh
- Center of Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Andrea Bileck
- Research Platform 'Rhythms of Life', University of Vienna, Vienna BioCenter, Vienna, Austria
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Markus Hartl
- Max F Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria
- Mass Spectrometry Facility, Max F Perutz Laboratories, Vienna, Austria
| | - Arndt von Haeseler
- Research Platform 'Rhythms of Life', University of Vienna, Vienna BioCenter, Vienna, Austria
- Center of Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna BioCenter, Vienna, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Christopher Gerner
- Research Platform 'Rhythms of Life', University of Vienna, Vienna BioCenter, Vienna, Austria
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Florian Raible
- Max F Perutz Laboratories, University of Vienna, Vienna BioCenter, Vienna, Austria
- Research Platform 'Rhythms of Life', University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Kristin Tessmar-Raible
- Research Platform 'Rhythms of Life', University of Vienna, Vienna BioCenter, Vienna, Austria
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27
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Hannou L, Roy P, Ballester Roig MN, Mongrain V. Transcriptional control of synaptic components by the clock machinery. Eur J Neurosci 2019; 51:241-267. [DOI: 10.1111/ejn.14294] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/01/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Lydia Hannou
- Center for Advanced Research in Sleep Medicine and Research CenterHôpital du Sacré‐Cœur de Montréal (CIUSSS‐NIM) Montreal Quebec Canada
- Department of PsychiatryUniversité de Montréal Montreal Quebec Canada
| | - Pierre‐Gabriel Roy
- Center for Advanced Research in Sleep Medicine and Research CenterHôpital du Sacré‐Cœur de Montréal (CIUSSS‐NIM) Montreal Quebec Canada
- Department of NeuroscienceUniversité de Montréal Montreal Quebec Canada
| | - Maria Neus Ballester Roig
- Center for Advanced Research in Sleep Medicine and Research CenterHôpital du Sacré‐Cœur de Montréal (CIUSSS‐NIM) Montreal Quebec Canada
- Department of NeuroscienceUniversité de Montréal Montreal Quebec Canada
| | - Valérie Mongrain
- Center for Advanced Research in Sleep Medicine and Research CenterHôpital du Sacré‐Cœur de Montréal (CIUSSS‐NIM) Montreal Quebec Canada
- Department of NeuroscienceUniversité de Montréal Montreal Quebec Canada
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28
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Maywood ES. Synchronization and maintenance of circadian timing in the mammalian clockwork. Eur J Neurosci 2018; 51:229-240. [DOI: 10.1111/ejn.14279] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/19/2018] [Accepted: 10/30/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Elizabeth S. Maywood
- Neurobiology DivisionMedical Research Council Laboratory of Molecular Biology Cambridge UK
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29
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Carmona-Alcocer V, Rohr KE, Joye DAM, Evans JA. Circuit development in the master clock network of mammals. Eur J Neurosci 2018; 51:82-108. [PMID: 30402923 DOI: 10.1111/ejn.14259] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/08/2018] [Accepted: 10/31/2018] [Indexed: 12/24/2022]
Abstract
Daily rhythms are generated by the circadian timekeeping system, which is orchestrated by the master circadian clock in the suprachiasmatic nucleus (SCN) of mammals. Circadian timekeeping is endogenous and does not require exposure to external cues during development. Nevertheless, the circadian system is not fully formed at birth in many mammalian species and it is important to understand how SCN development can affect the function of the circadian system in adulthood. The purpose of the current review is to discuss the ontogeny of cellular and circuit function in the SCN, with a focus on work performed in model rodent species (i.e., mouse, rat, and hamster). Particular emphasis is placed on the spatial and temporal patterns of SCN development that may contribute to the function of the master clock during adulthood. Additional work aimed at decoding the mechanisms that guide circadian development is expected to provide a solid foundation upon which to better understand the sources and factors contributing to aberrant maturation of clock function.
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Affiliation(s)
| | - Kayla E Rohr
- Department of Biomedical Sciences, Marquette University, Milwaukee, Wisconsin
| | - Deborah A M Joye
- Department of Biomedical Sciences, Marquette University, Milwaukee, Wisconsin
| | - Jennifer A Evans
- Department of Biomedical Sciences, Marquette University, Milwaukee, Wisconsin
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30
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Hatcher KM, Royston SE, Mahoney MM. Modulation of circadian rhythms through estrogen receptor signaling. Eur J Neurosci 2018; 51:217-228. [PMID: 30270552 DOI: 10.1111/ejn.14184] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/06/2018] [Accepted: 09/17/2018] [Indexed: 01/11/2023]
Abstract
Circadian rhythms are physiological and behavioral processes that exhibit a 24-hr cycle. These daily rhythms are essential for living organisms to align their behavior and physiology with the environment to increase the likelihood of survival. In mammals, circadian rhythms synchronize with the environment primarily by the suprachiasmatic nucleus, a hypothalamic brain region that integrates exogenous and endogenous timing cues. Sex steroid hormones, including estrogens, are thought to modulate sexually dimorphic behaviors through developmental programming of the brain (i.e., organization), as well as acute receptor signaling during adulthood (i.e., activation). Importantly, there are known sex differences in the expression of circadian locomotor activity and molecular organization of the suprachiasmatic nucleus, likely due, in part, to the actions of circulating estrogens. Circadian locomotor rhythms, which are coordinated by the suprachiasmatic nucleus, have been shown to be regulated by developmental and adult levels of circulating estrogens. Further, increasing evidence suggests that estrogens can modulate expression of circadian clock genes that are essential for orchestration of circadian rhythms by the suprachiasmatic nucleus. In this review, we will discuss the organizational and activational modulation of the circadian timekeeping system by estrogens through estrogen receptor signaling.
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Affiliation(s)
- Katherine M Hatcher
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Sara E Royston
- Department of Anesthesiology, Perioperative Medicine and Pain, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Department of Spine and Pain Management, Christie Clinic, Champaign, Illinois
| | - Megan M Mahoney
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
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31
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Du J, Zhang Y, Xue Y, Zhao X, Zhao X, Wei Y, Li Z, Zhang Y, Zhao Z. Diurnal protein oscillation profiles in Drosophila head. FEBS Lett 2018; 592:3736-3749. [PMID: 30311939 DOI: 10.1002/1873-3468.13267] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 09/23/2018] [Accepted: 10/02/2018] [Indexed: 11/08/2022]
Abstract
Circadian clocks control daily rhythms in physiology, metabolism and behaviour in most organisms. Proteome-wide analysis of protein oscillations is still lacking in Drosophila. In this study, the total protein and phosphorylated protein in Drosophila heads in a 24-h daily time-course were assayed by using the isobaric tags for relative and absolute quantitation (iTRAQ) method, and 10 and 7 oscillating proteins as well as 19 and 22 oscillating phosphoproteins in the w1118 control and ClkJrk mutant strains were separately identified. Lastly, we performed a mini screen to investigate the functions of some oscillating proteins in circadian locomotion rhythms. This study provides the first proteomic profiling of diurnally oscillating proteins in fly heads, thereby providing a basis for further mechanistic studies of these proteins in circadian rhythm.
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Affiliation(s)
- Juan Du
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yifan Zhang
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yongbo Xue
- Department of Biology, University of Nevada, Reno, NV, USA
| | - Xiaoyun Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xianguo Zhao
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yu Wei
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhen Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yong Zhang
- Department of Biology, University of Nevada, Reno, NV, USA
| | - Zhangwu Zhao
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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32
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Wong DCS, O’Neill JS. Non-transcriptional processes in circadian rhythm generation. CURRENT OPINION IN PHYSIOLOGY 2018; 5:117-132. [PMID: 30596188 PMCID: PMC6302373 DOI: 10.1016/j.cophys.2018.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
'Biological clocks' orchestrate mammalian biology to a daily rhythm. Whilst 'clock gene' transcriptional circuits impart rhythmic regulation to myriad cellular systems, our picture of the biochemical mechanisms that determine their circadian (∼24 hour) period is incomplete. Here we consider the evidence supporting different models for circadian rhythm generation in mammalian cells in light of evolutionary factors. We find it plausible that the circadian timekeeping mechanism in mammalian cells is primarily protein-based, signalling biological timing information to the nucleus by the post-translational regulation of transcription factor activity, with transcriptional feedback imparting robustness to the oscillation via hysteresis. We conclude by suggesting experiments that might distinguish this model from competing paradigms.
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33
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Mistimed food intake and sleep alters 24-hour time-of-day patterns of the human plasma proteome. Proc Natl Acad Sci U S A 2018; 115:E5390-E5399. [PMID: 29784788 DOI: 10.1073/pnas.1714813115] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Proteomics holds great promise for understanding human physiology, developing health biomarkers, and precision medicine. However, how much the plasma proteome varies with time of day and is regulated by the master circadian suprachiasmatic nucleus brain clock, assessed here by the melatonin rhythm, is largely unknown. Here, we assessed 24-h time-of-day patterns of human plasma proteins in six healthy men during daytime food intake and nighttime sleep in phase with the endogenous circadian clock (i.e., circadian alignment) versus daytime sleep and nighttime food intake out of phase with the endogenous circadian clock (i.e., circadian misalignment induced by simulated nightshift work). We identified 24-h time-of-day patterns in 573 of 1,129 proteins analyzed, with 30 proteins showing strong regulation by the circadian cycle. Relative to circadian alignment, the average abundance and/or 24-h time-of-day patterns of 127 proteins were altered during circadian misalignment. Altered proteins were associated with biological pathways involved in immune function, metabolism, and cancer. Of the 30 circadian-regulated proteins, the majority peaked between 1400 hours and 2100 hours, and these 30 proteins were associated with basic pathways involved in extracellular matrix organization, tyrosine kinase signaling, and signaling by receptor tyrosine-protein kinase erbB-2. Furthermore, circadian misalignment altered multiple proteins known to regulate glucose homeostasis and/or energy metabolism, with implications for altered metabolic physiology. Our findings demonstrate the circadian clock, the behavioral wake-sleep/food intake-fasting cycle, and interactions between these processes regulate 24-h time-of-day patterns of human plasma proteins and help identify mechanisms of circadian misalignment that may contribute to metabolic dysregulation.
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34
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Khan AM, Grant AH, Martinez A, Burns GAPC, Thatcher BS, Anekonda VT, Thompson BW, Roberts ZS, Moralejo DH, Blevins JE. Mapping Molecular Datasets Back to the Brain Regions They are Extracted from: Remembering the Native Countries of Hypothalamic Expatriates and Refugees. ADVANCES IN NEUROBIOLOGY 2018; 21:101-193. [PMID: 30334222 PMCID: PMC6310046 DOI: 10.1007/978-3-319-94593-4_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This article focuses on approaches to link transcriptomic, proteomic, and peptidomic datasets mined from brain tissue to the original locations within the brain that they are derived from using digital atlas mapping techniques. We use, as an example, the transcriptomic, proteomic and peptidomic analyses conducted in the mammalian hypothalamus. Following a brief historical overview, we highlight studies that have mined biochemical and molecular information from the hypothalamus and then lay out a strategy for how these data can be linked spatially to the mapped locations in a canonical brain atlas where the data come from, thereby allowing researchers to integrate these data with other datasets across multiple scales. A key methodology that enables atlas-based mapping of extracted datasets-laser-capture microdissection-is discussed in detail, with a view of how this technology is a bridge between systems biology and systems neuroscience.
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Affiliation(s)
- Arshad M Khan
- UTEP Systems Neuroscience Laboratory, University of Texas at El Paso, El Paso, TX, USA.
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA.
- Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, USA.
| | - Alice H Grant
- UTEP Systems Neuroscience Laboratory, University of Texas at El Paso, El Paso, TX, USA
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
- Graduate Program in Pathobiology, University of Texas at El Paso, El Paso, TX, USA
| | - Anais Martinez
- UTEP Systems Neuroscience Laboratory, University of Texas at El Paso, El Paso, TX, USA
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
- Graduate Program in Pathobiology, University of Texas at El Paso, El Paso, TX, USA
| | - Gully A P C Burns
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Marina del Rey, CA, USA
| | - Brendan S Thatcher
- VA Puget Sound Health Care System, Office of Research and Development Medical Research Service, Department of Veterans Affairs Medical Center, Seattle, WA, USA
| | - Vishwanath T Anekonda
- VA Puget Sound Health Care System, Office of Research and Development Medical Research Service, Department of Veterans Affairs Medical Center, Seattle, WA, USA
| | - Benjamin W Thompson
- VA Puget Sound Health Care System, Office of Research and Development Medical Research Service, Department of Veterans Affairs Medical Center, Seattle, WA, USA
| | - Zachary S Roberts
- VA Puget Sound Health Care System, Office of Research and Development Medical Research Service, Department of Veterans Affairs Medical Center, Seattle, WA, USA
| | - Daniel H Moralejo
- Division of Neonatology, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - James E Blevins
- VA Puget Sound Health Care System, Office of Research and Development Medical Research Service, Department of Veterans Affairs Medical Center, Seattle, WA, USA
- Division of Metabolism, Endocrinology, and Nutrition, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
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35
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O'Callaghan EK, Green EW, Franken P, Mongrain V. Omics Approaches in Sleep-Wake Regulation. Handb Exp Pharmacol 2018; 253:59-81. [PMID: 29796779 DOI: 10.1007/164_2018_125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Although sleep seems an obvious and simple behaviour, it is extremely complex involving numerous interactions both at the neuronal and the molecular levels. While we have gained detailed insight into the molecules and neuronal networks responsible for the circadian organization of sleep and wakefulness, the molecular underpinnings of the homeostatic aspect of sleep regulation are still unknown and the focus of a considerable research effort. In the last 20 years, the development of techniques allowing the simultaneous measurement of hundreds to thousands of molecular targets (i.e. 'omics' approaches) has enabled the unbiased study of the molecular pathways regulated by and regulating sleep. In this chapter, we will review how the different omics approaches, including transcriptomics, epigenomics, proteomics, and metabolomics, have advanced sleep research. We present relevant data in the framework of the two-process model in which circadian and homeostatic processes interact to regulate sleep. The integration of the different omics levels, known as 'systems genetics', will eventually lead to a better understanding of how information flows from the genome, to molecules, to networks, and finally to sleep both in health and disease.
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Affiliation(s)
- Emma K O'Callaghan
- Center for Advanced Research in Sleep Medicine and Research Center, Hôpital du Sacré-Coeur de Montréal, Montreal, QC, Canada.,Department of Neuroscience, Université de Montréal, Montreal, QC, Canada
| | - Edward W Green
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul Franken
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Valérie Mongrain
- Center for Advanced Research in Sleep Medicine and Research Center, Hôpital du Sacré-Coeur de Montréal, Montreal, QC, Canada. .,Department of Neuroscience, Université de Montréal, Montreal, QC, Canada.
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36
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Brown LA, Williams J, Taylor L, Thomson RJ, Nolan PM, Foster RG, Peirson SN. Meta-analysis of transcriptomic datasets identifies genes enriched in the mammalian circadian pacemaker. Nucleic Acids Res 2017; 45:9860-9873. [PMID: 28973476 PMCID: PMC5737434 DOI: 10.1093/nar/gkx714] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 08/04/2017] [Indexed: 12/14/2022] Open
Abstract
The master circadian pacemaker in mammals is located in the suprachiasmatic nuclei (SCN) which regulate physiology and behaviour, as well as coordinating peripheral clocks throughout the body. Investigating the function of the SCN has often focused on the identification of rhythmically expressed genes. However, not all genes critical for SCN function are rhythmically expressed. An alternative strategy is to characterize those genes that are selectively enriched in the SCN. Here, we examined the transcriptome of the SCN and whole brain (WB) of mice using meta-analysis of publicly deposited data across a range of microarray platforms and RNA-Seq data. A total of 79 microarrays were used (24 SCN and 55 WB samples, 4 different microarray platforms), alongside 17 RNA-Seq data files (7 SCN and 10 WB). 31 684 MGI gene symbols had data for at least one platform. Meta-analysis using a random effects model for weighting individual effect sizes (derived from differential expression between relevant SCN and WB samples) reliably detected known SCN markers. SCN-enriched transcripts identified in this study provide novel insights into SCN function, including identifying genes which may play key roles in SCN physiology or provide SCN-specific drivers.
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Affiliation(s)
- Laurence A Brown
- Sleep and Circadian Neuroscience Institute (SCNi), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX1 3RE, UK
| | - John Williams
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Lewis Taylor
- Sleep and Circadian Neuroscience Institute (SCNi), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX1 3RE, UK
| | - Ross J Thomson
- Sleep and Circadian Neuroscience Institute (SCNi), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX1 3RE, UK
| | - Patrick M Nolan
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Russell G Foster
- Sleep and Circadian Neuroscience Institute (SCNi), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX1 3RE, UK
| | - Stuart N Peirson
- Sleep and Circadian Neuroscience Institute (SCNi), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX1 3RE, UK
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37
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Comas M, Gordon CJ, Oliver BG, Stow NW, King G, Sharma P, Ammit AJ, Grunstein RR, Phillips CL. A circadian based inflammatory response – implications for respiratory disease and treatment. SLEEP SCIENCE AND PRACTICE 2017. [DOI: 10.1186/s41606-017-0019-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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38
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Jagota A, Mattam U. Daily chronomics of proteomic profile in aging and rotenone-induced Parkinson’s disease model in male Wistar rat and its modulation by melatonin. Biogerontology 2017; 18:615-630. [DOI: 10.1007/s10522-017-9711-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 05/11/2017] [Indexed: 02/08/2023]
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39
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Chiang CK, Xu B, Mehta N, Mayne J, Sun WYL, Cheng K, Ning Z, Dong J, Zou H, Cheng HYM, Figeys D. Phosphoproteome Profiling Reveals Circadian Clock Regulation of Posttranslational Modifications in the Murine Hippocampus. Front Neurol 2017; 8:110. [PMID: 28382018 PMCID: PMC5360755 DOI: 10.3389/fneur.2017.00110] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/08/2017] [Indexed: 12/20/2022] Open
Abstract
The circadian clock is an endogenous oscillator that drives daily rhythms in physiology, behavior, and gene expression. The underlying mechanisms of circadian timekeeping are cell-autonomous and involve oscillatory expression of core clock genes that is driven by interconnecting transcription–translation feedback loops (TTFLs). Circadian clock TTFLs are further regulated by posttranslational modifications, in particular, phosphorylation. The hippocampus plays an important role in spatial memory and the conversion of short- to long-term memory. Several studies have reported the presence of a peripheral oscillator in the hippocampus and have highlighted the importance of circadian regulation in memory formation. Given the general importance of phosphorylation in circadian clock regulation, we performed global quantitative proteome and phosphoproteome analyses of the murine hippocampus across the circadian cycle, applying spiked-in labeled reference and high accuracy mass spectrometry (MS). Of the 3,052 proteins and 2,868 phosphosites on 1,368 proteins that were accurately quantified, 1.7% of proteins and 5.2% of phosphorylation events exhibited time-of-day-dependent expression profiles. The majority of circadian phosphopeptides displayed abrupt fluctuations at mid-to-late day without underlying rhythms of protein abundance. Bioinformatic analysis of cyclic phosphorylation events revealed their diverse distribution in different biological pathways, most notably, cytoskeletal organization and neuronal morphogenesis. This study provides the first large-scale, quantitative MS analysis of the circadian phosphoproteome and proteome of the murine hippocampus and highlights the significance of rhythmic regulation at the posttranslational level in this peripheral oscillator. In addition to providing molecular insights into the hippocampal circadian clock, our results will assist in the understanding of genetic factors that underlie rhythms-associated pathological states of the hippocampus.
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Affiliation(s)
- Cheng-Kang Chiang
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada; Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien, Taiwan
| | - Bo Xu
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa , Ottawa, ON , Canada
| | - Neel Mehta
- Department of Biology, University of Toronto Mississauga , Mississauga, ON , Canada
| | - Janice Mayne
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa , Ottawa, ON , Canada
| | - Warren Y L Sun
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa , Ottawa, ON , Canada
| | - Kai Cheng
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa , Ottawa, ON , Canada
| | - Zhibin Ning
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa , Ottawa, ON , Canada
| | - Jing Dong
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , China
| | - Hanfa Zou
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian , China
| | - Hai-Ying Mary Cheng
- Department of Biology, University of Toronto Mississauga , Mississauga, ON , Canada
| | - Daniel Figeys
- Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada; Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada; Canadian Institute for Advanced Research, Toronto, ON, Canada
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40
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Taylor SR, Wang TJ, Granados-Fuentes D, Herzog ED. Resynchronization Dynamics Reveal that the Ventral Entrains the Dorsal Suprachiasmatic Nucleus. J Biol Rhythms 2017; 32:35-47. [PMID: 28326909 PMCID: PMC5483321 DOI: 10.1177/0748730416680904] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Although the suprachiasmatic nucleus (SCN) has long been considered the master circadian clock in mammals, the topology of the connections that synchronize daily rhythms among SCN cells is not well understood. We combined experimental and computational methods to infer the directed interactions that mediate circadian synchrony between regions of the SCN. We analyzed PERIOD2 (PER2) expression from SCN slices during and after treatment with tetrodotoxin, allowing us to map connections as cells resynchronized their daily cycling following blockade and restoration of cell-cell communication. Using automated analyses, we found that cells in the dorsal SCN stabilized their periods slower than those in the ventral SCN. A phase-amplitude computational model of the SCN revealed that, to reproduce the experimental results: (1) the ventral SCN had to be more densely connected than the dorsal SCN and (2) the ventral SCN needed strong connections to the dorsal SCN. Taken together, these results provide direct evidence that the ventral SCN entrains the dorsal SCN in constant conditions.
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Affiliation(s)
| | - Thomas J. Wang
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | | | - Erik D. Herzog
- Department of Biology, Washington University, St. Louis, Missouri, USA
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41
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Herzog ED, Hermanstyne T, Smyllie NJ, Hastings MH. Regulating the Suprachiasmatic Nucleus (SCN) Circadian Clockwork: Interplay between Cell-Autonomous and Circuit-Level Mechanisms. Cold Spring Harb Perspect Biol 2017; 9:9/1/a027706. [PMID: 28049647 DOI: 10.1101/cshperspect.a027706] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The suprachiasmatic nucleus (SCN) is the principal circadian clock of the brain, directing daily cycles of behavior and physiology. SCN neurons contain a cell-autonomous transcription-based clockwork but, in turn, circuit-level interactions synchronize the 20,000 or so SCN neurons into a robust and coherent daily timer. Synchronization requires neuropeptide signaling, regulated by a reciprocal interdependence between the molecular clockwork and rhythmic electrical activity, which in turn depends on a daytime Na+ drive and nighttime K+ drag. Recent studies exploiting intersectional genetics have started to identify the pacemaking roles of particular neuronal groups in the SCN. They support the idea that timekeeping involves nonlinear and hierarchical computations that create and incorporate timing information through the interactions between key groups of neurons within the SCN circuit. The field is now poised to elucidate these computations, their underlying cellular mechanisms, and how the SCN clock interacts with subordinate circadian clocks across the brain to determine the timing and efficiency of the sleep-wake cycle, and how perturbations of this coherence contribute to neurological and psychiatric illness.
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Affiliation(s)
- Erik D Herzog
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130-4899
| | - Tracey Hermanstyne
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130-4899
| | - Nicola J Smyllie
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Michael H Hastings
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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42
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Atger F, Mauvoisin D, Weger B, Gobet C, Gachon F. Regulation of Mammalian Physiology by Interconnected Circadian and Feeding Rhythms. Front Endocrinol (Lausanne) 2017; 8:42. [PMID: 28337174 PMCID: PMC5340782 DOI: 10.3389/fendo.2017.00042] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/17/2017] [Indexed: 12/29/2022] Open
Abstract
Circadian clocks are endogenous timekeeping systems that adapt in an anticipatory fashion the physiology and behavior of most living organisms. In mammals, the master pacemaker resides in the suprachiasmatic nucleus and entrains peripheral clocks using a wide range of signals that differentially schedule physiology and gene expression in a tissue-specific manner. The peripheral clocks, such as those found in the liver, are particularly sensitive to rhythmic external cues like feeding behavior, which modulate the phase and amplitude of rhythmic gene expression. Consequently, the liver clock temporally tunes the expression of many genes involved in metabolism and physiology. However, the circadian modulation of cellular functions also relies on multiple layers of posttranscriptional and posttranslational regulation. Strikingly, these additional regulatory events may happen independently of any transcriptional oscillations, showing that complex regulatory networks ultimately drive circadian output functions. These rhythmic events also integrate feeding-related cues and adapt various metabolic processes to food availability schedules. The importance of such temporal regulation of metabolism is illustrated by metabolic dysfunctions and diseases resulting from circadian clock disruption or inappropriate feeding patterns. Therefore, the study of circadian clocks and rhythmic feeding behavior should be of interest to further advance our understanding of the prevention and therapy of metabolic diseases.
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Affiliation(s)
- Florian Atger
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, Lausanne, Switzerland
- Department of Pharmacology and Toxicology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Mauvoisin
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, Lausanne, Switzerland
- School of Life Sciences, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Benjamin Weger
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Cédric Gobet
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, Lausanne, Switzerland
- School of Life Sciences, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Frédéric Gachon
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- *Correspondence: Frédéric Gachon,
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Subramanian P, Jayapalan JJ, Abdul-Rahman PS, Arumugam M, Hashim OH. Temporal regulation of proteome profile in the fruit fly, Drosophila melanogaster. PeerJ 2016; 4:e2080. [PMID: 27257555 PMCID: PMC4888302 DOI: 10.7717/peerj.2080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 05/03/2016] [Indexed: 12/11/2022] Open
Abstract
Background. Diurnal rhythms of protein synthesis controlled by the biological clock underlie the rhythmic physiology in the fruit fly, Drosophila melanogaster. In this study, we conducted a proteome-wide investigation of rhythmic protein accumulation in D. melanogaster. Materials and Methods. Total protein collected from fly samples harvested at 4 h intervals over the 24 h period were subjected to two-dimensional gel electrophoresis, trypsin digestion and MS/MS analysis. Protein spots/clusters were identified with MASCOT search engine and Swiss-Prot database. Expression of proteins was documented as percentage of volume contribution using the Image Master 2D Platinum software. Results. A total of 124 protein spots/clusters were identified using MS/MS analysis. Significant variation in the expression of 88 proteins over the 24-h period was observed. A relatively higher number of proteins was upregulated during the night compared to the daytime. The complexity of temporal regulation of the D. melanogaster proteome was further reflected from functional annotations of the differently expressed proteins, with those that were upregulated at night being restricted to the heat shock proteins and proteins involved in metabolism, muscle activity, protein synthesis/folding/degradation and apoptosis, whilst those that were overexpressed in the daytime were apparently involved in metabolism, muscle activity, ion-channel/cellular transport, protein synthesis/folding/degradation, redox homeostasis, development and transcription. Conclusion. Our data suggests that a wide range of proteins synthesized by the fruit fly, D. melanogaster, is under the regulation of the biological clock.
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Affiliation(s)
- Perumal Subramanian
- Department of Biochemistry and Biotechnology, Annamalai University , Chidambaram, Tamil Nadu , India
| | - Jaime J Jayapalan
- University of Malaya Centre for Proteomics Research (UMCPR), Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia
| | - Puteri S Abdul-Rahman
- University of Malaya Centre for Proteomics Research (UMCPR), Department of Molecular Medicine, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia
| | - Manjula Arumugam
- Department of Biochemistry and Biotechnology, Annamalai University , Chidambaram, Tamil Nadu , India
| | - Onn H Hashim
- University of Malaya Centre for Proteomics Research (UMCPR), Department of Molecular Medicine, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia
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Johnston JD, Ordovás JM, Scheer FA, Turek FW. Circadian Rhythms, Metabolism, and Chrononutrition in Rodents and Humans. Adv Nutr 2016; 7:399-406. [PMID: 26980824 PMCID: PMC4785478 DOI: 10.3945/an.115.010777] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Chrononutrition is an emerging discipline that builds on the intimate relation between endogenous circadian (24-h) rhythms and metabolism. Circadian regulation of metabolic function can be observed from the level of intracellular biochemistry to whole-organism physiology and even postprandial responses. Recent work has elucidated the metabolic roles of circadian clocks in key metabolic tissues, including liver, pancreas, white adipose, and skeletal muscle. For example, tissue-specific clock disruption in a single peripheral organ can cause obesity or disruption of whole-organism glucose homeostasis. This review explains mechanistic insights gained from transgenic animal studies and how these data are being translated into the study of human genetics and physiology. The principles of chrononutrition have already been demonstrated to improve human weight loss and are likely to benefit the health of individuals with metabolic disease, as well as of the general population.
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Affiliation(s)
| | - José M Ordovás
- Tufts University, Boston, MA;,Madrid Institutes of Advanced Studies-Food, Madrid, Spain
| | - Frank A Scheer
- Brigham and Women's Hospital, Boston, MA;,Harvard Medical School, Boston, MA; and
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Ray S, Reddy AB. Cross-talk between circadian clocks, sleep-wake cycles, and metabolic networks: Dispelling the darkness. Bioessays 2016; 38:394-405. [PMID: 26866932 PMCID: PMC4817226 DOI: 10.1002/bies.201500056] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Integration of knowledge concerning circadian rhythms, metabolic networks, and sleep‐wake cycles is imperative for unraveling the mysteries of biological cycles and their underlying mechanisms. During the last decade, enormous progress in circadian biology research has provided a plethora of new insights into the molecular architecture of circadian clocks. However, the recent identification of autonomous redox oscillations in cells has expanded our view of the clockwork beyond conventional transcription/translation feedback loop models, which have been dominant since the first circadian period mutants were identified in fruit fly. Consequently, non‐transcriptional timekeeping mechanisms have been proposed, and the antioxidant peroxiredoxin proteins have been identified as conserved markers for 24‐hour rhythms. Here, we review recent advances in our understanding of interdependencies amongst circadian rhythms, sleep homeostasis, redox cycles, and other cellular metabolic networks. We speculate that systems‐level investigations implementing integrated multi‐omics approaches could provide novel mechanistic insights into the connectivity between daily cycles and metabolic systems.
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Affiliation(s)
- Sandipan Ray
- Department of Clinical Neurosciences, University of Cambridge Metabolic Research Laboratories, National Institutes of Health Biomedical Research Centre, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Akhilesh B Reddy
- Department of Clinical Neurosciences, University of Cambridge Metabolic Research Laboratories, National Institutes of Health Biomedical Research Centre, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
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Benleulmi-Chaachoua A, Chen L, Sokolina K, Wong V, Jurisica I, Emerit MB, Darmon M, Espin A, Stagljar I, Tafelmeyer P, Zamponi GW, Delagrange P, Maurice P, Jockers R. Protein interactome mining defines melatonin MT1 receptors as integral component of presynaptic protein complexes of neurons. J Pineal Res 2016; 60:95-108. [PMID: 26514267 DOI: 10.1111/jpi.12294] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 10/26/2015] [Indexed: 01/11/2023]
Abstract
In mammals, the hormone melatonin is mainly produced by the pineal gland with nocturnal peak levels. Its peripheral and central actions rely either on its intrinsic antioxidant properties or on binding to melatonin MT1 and MT2 receptors, belonging to the G protein-coupled receptor (GPCR) super-family. Melatonin has been reported to be involved in many functions of the central nervous system such as circadian rhythm regulation, neurotransmission, synaptic plasticity, memory, sleep, and also in Alzheimer's disease and depression. However, little is known about the subcellular localization of melatonin receptors and the molecular aspects involved in neuronal functions of melatonin. Identification of protein complexes associated with GPCRs has been shown to be a valid approach to improve our understanding of their function. By combining proteomic and genomic approaches we built an interactome of MT1 and MT2 receptors, which comprises 378 individual proteins. Among the proteins interacting with MT1 , but not with MT2 , we identified several presynaptic proteins, suggesting a potential role of MT1 in neurotransmission. Presynaptic localization of MT1 receptors in the hypothalamus, striatum, and cortex was confirmed by subcellular fractionation experiments and immunofluorescence microscopy. MT1 physically interacts with the voltage-gated calcium channel Cav 2.2 and inhibits Cav 2.2-promoted Ca(2+) entry in an agonist-independent manner. In conclusion, we show that MT1 is part of the presynaptic protein network and negatively regulates Cav 2.2 activity, providing a first hint for potential synaptic functions of MT1.
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Affiliation(s)
- Abla Benleulmi-Chaachoua
- Inserm, U1016, Institut Cochin, Paris, France
- CNRS UMR 8104, Paris, France
- Sorbonne Paris Cité, Université Paris Descartes, Paris, France
| | - Lina Chen
- Department of Physiology and Pharmacology, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Kate Sokolina
- Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Victoria Wong
- Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Igor Jurisica
- Princess Margaret Cancer Centre, University Health Network and TECHNA Institute for the Advancement of Technology for Health, Toronto, ON, Canada
| | - Michel Boris Emerit
- Sorbonne Paris Cité, Université Paris Descartes, Paris, France
- Centre de Psychiatrie et Neurosciences, INSERM U894, Paris, France
| | - Michèle Darmon
- Sorbonne Paris Cité, Université Paris Descartes, Paris, France
- Centre de Psychiatrie et Neurosciences, INSERM U894, Paris, France
| | - Almudena Espin
- Inserm, U1016, Institut Cochin, Paris, France
- CNRS UMR 8104, Paris, France
- Sorbonne Paris Cité, Université Paris Descartes, Paris, France
| | - Igor Stagljar
- Donnelly Centre, Department of Biochemistry, Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | | | - Gerald W Zamponi
- Department of Physiology and Pharmacology, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | | | - Pascal Maurice
- Inserm, U1016, Institut Cochin, Paris, France
- CNRS UMR 8104, Paris, France
- Sorbonne Paris Cité, Université Paris Descartes, Paris, France
| | - Ralf Jockers
- Inserm, U1016, Institut Cochin, Paris, France
- CNRS UMR 8104, Paris, France
- Sorbonne Paris Cité, Université Paris Descartes, Paris, France
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Choudhary MK, Nomura Y, Shi H, Nakagami H, Somers DE. Circadian Profiling of the Arabidopsis Proteome Using 2D-DIGE. FRONTIERS IN PLANT SCIENCE 2016; 7:1007. [PMID: 27462335 PMCID: PMC4940426 DOI: 10.3389/fpls.2016.01007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 06/27/2016] [Indexed: 05/18/2023]
Abstract
Clock-generated biological rhythms provide an adaptive advantage to an organism, resulting in increased fitness and survival. To better elucidate the plant response to the circadian system, we surveyed protein oscillations in Arabidopsis seedlings under constant light. Using large-scale two-dimensional difference in gel electrophoresis (2D-DIGE) the abundance of more than 1000 proteins spots was reproducibly resolved quantified and profiled across a circadian time series. A comparison between phenol-extracted samples and RuBisCO-depleted extracts identified 71 and 40 rhythmically-expressed proteins, respectively, and between 30 and 40% of these derive from non-rhythmic transcripts. These included proteins influencing transcriptional regulation, translation, metabolism, photosynthesis, protein chaperones, and stress-mediated responses. The phasing of maximum expression for the cyclic proteins was similar for both datasets, with a nearly even distribution of peak phases across the time series. STRING clustering analysis identified two interaction networks with a notable number of oscillating proteins: plastid-based and cytosolic chaperones and 10 proteins involved in photosynthesis. The oscillation of the ABA receptor, PYR1/RCAR11, with peak expression near dusk adds to a growing body of evidence that intimately ties ABA signaling to the circadian system. Taken together, this study provides new insights into the importance of post-transcriptional circadian control of plant physiology and metabolism.
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Affiliation(s)
- Mani K. Choudhary
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and TechnologyPohang, South Korea
| | - Yuko Nomura
- Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Hua Shi
- Department of Molecular Genetics, Ohio State UniversityColumbus, OH, USA
| | - Hirofumi Nakagami
- Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - David E. Somers
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and TechnologyPohang, South Korea
- Department of Molecular Genetics, Ohio State UniversityColumbus, OH, USA
- *Correspondence: David E. Somers
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Montenegro-Montero A, Larrondo LF. In the Driver's Seat: The Case for Transcriptional Regulation and Coupling as Relevant Determinants of the Circadian Transcriptome and Proteome in Eukaryotes. J Biol Rhythms 2015; 31:37-47. [PMID: 26446874 DOI: 10.1177/0748730415607321] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Circadian clocks drive daily oscillations in a variety of biological processes through the coordinate orchestration of precise gene expression programs. Global expression profiling experiments have suggested that a significant fraction of the transcriptome and proteome is under circadian control, and such output rhythms have historically been assumed to rely on the rhythmic transcription of these genes. Recent genome-wide studies, however, have challenged this long-held view and pointed to a major contribution of posttranscriptional regulation in driving oscillations at the messenger RNA (mRNA) level, while others have highlighted extensive clock translational regulation, regardless of mRNA rhythms. There are various examples of genes that are uniformly transcribed throughout the day but that exhibit rhythmic mRNA levels, and of flat mRNAs, with oscillating protein levels, and such observations have largely been considered to result from independent regulation at each step. These studies have thereby obviated any connections, or coupling, that might exist between the different steps of gene expression and the impact that any of them could have on subsequent ones. Here, we argue that due to both biological and technical reasons, the jury is still out on the determination of the relative contributions of each of the different stages of gene expression in regulating output molecular rhythms. In addition, we propose that through a variety of coupling mechanisms, gene transcription (even when apparently arrhythmic) might play a much relevant role in determining oscillations in gene expression than currently estimated, regulating rhythms at downstream steps. Furthermore, we posit that eukaryotic genomes regulate daily RNA polymerase II (RNAPII) recruitment and histone modifications genome-wide, setting the stage for global nascent transcription, but that tissue-specific mechanisms locally specify the different processes under clock control.
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Affiliation(s)
- Alejandro Montenegro-Montero
- Millennium Nucleus for Fungal Integrative and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luis F Larrondo
- Millennium Nucleus for Fungal Integrative and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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Choudhary MK, Nomura Y, Wang L, Nakagami H, Somers DE. Quantitative Circadian Phosphoproteomic Analysis of Arabidopsis Reveals Extensive Clock Control of Key Components in Physiological, Metabolic, and Signaling Pathways. Mol Cell Proteomics 2015; 14:2243-60. [PMID: 26091701 DOI: 10.1074/mcp.m114.047183] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Indexed: 01/01/2023] Open
Abstract
The circadian clock provides adaptive advantages to an organism, resulting in increased fitness and survival. The phosphorylation events that regulate circadian-dependent signaling and the processes which post-translationally respond to clock-gated signals are largely unknown. To better elucidate post-translational events tied to the circadian system we carried out a survey of circadian-regulated protein phosphorylation events in Arabidopsis seedlings. A large-scale mass spectrometry-based quantitative phosphoproteomics approach employing TiO2-based phosphopeptide enrichment techniques identified and quantified 1586 phosphopeptides on 1080 protein groups. A total of 102 phosphopeptides displayed significant changes in abundance, enabling the identification of specific patterns of response to circadian rhythms. Our approach was sensitive enough to quantitate oscillations in the phosphorylation of low abundance clock proteins (early flowering4; ELF4 and pseudoresponse regulator3; PRR3) as well as other transcription factors and kinases. During constant light, extensive cyclic changes in phosphorylation status occurred in critical regulators, implicating direct or indirect regulation by the circadian system. These included proteins influencing transcriptional regulation, translation, metabolism, stress and phytohormones-mediated responses. We validated our analysis using the elf4-211 allele, in which an S45L transition removes the phosphorylation herein identified. We show that removal of this phosphorylatable site diminishes interaction with early flowering3 (ELF3), a key partner in a tripartite evening complex required for circadian cycling. elf4-211 lengthens period, which increases with increasing temperature, relative to the wild type, resulting in a more stable temperature compensation of circadian period over a wider temperature range.
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Affiliation(s)
- Mani Kant Choudhary
- From the ‡Division of Integrative Biosciences and Biotechnology, POSTECH, Hyojadong, Pohang, Kyungbuk, 790-784, Republic of Korea
| | - Yuko Nomura
- ¶Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan
| | - Lei Wang
- From the ‡Division of Integrative Biosciences and Biotechnology, POSTECH, Hyojadong, Pohang, Kyungbuk, 790-784, Republic of Korea §Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210; ‖Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hirofumi Nakagami
- ¶Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan
| | - David E Somers
- From the ‡Division of Integrative Biosciences and Biotechnology, POSTECH, Hyojadong, Pohang, Kyungbuk, 790-784, Republic of Korea §Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210;
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Bhardwaj SK, Stojkovic K, Kiessling S, Srivastava LK, Cermakian N. Constant light uncovers behavioral effects of a mutation in the schizophrenia risk gene Dtnbp1 in mice. Behav Brain Res 2015; 284:58-68. [DOI: 10.1016/j.bbr.2015.01.048] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/23/2015] [Accepted: 01/26/2015] [Indexed: 10/24/2022]
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