101
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Redox and Metabolic Oscillations in the Clockwork. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-3-319-27069-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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102
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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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103
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Lück S, Westermark PO. Circadian mRNA expression: insights from modeling and transcriptomics. Cell Mol Life Sci 2016; 73:497-521. [PMID: 26496725 PMCID: PMC11108398 DOI: 10.1007/s00018-015-2072-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 01/08/2023]
Abstract
Circadian clocks synchronize organisms to the 24 h rhythms of the environment. These clocks persist under constant conditions, have their origin at the cellular level, and produce an output of rhythmic mRNA expression affecting thousands of transcripts in many mammalian cell types. Here, we review the charting of circadian output rhythms in mRNA expression, focusing on mammals. We emphasize the challenges in statistics, interpretation, and quantitative descriptions that such investigations have faced and continue to face, and outline remaining outstanding questions.
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Affiliation(s)
- Sarah Lück
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Invalidenstrasse 43, 10115, Berlin, Germany
| | - Pål O Westermark
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Invalidenstrasse 43, 10115, Berlin, Germany.
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104
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Putker M, O’Neill JS. Reciprocal Control of the Circadian Clock and Cellular Redox State - a Critical Appraisal. Mol Cells 2016; 39:6-19. [PMID: 26810072 PMCID: PMC4749875 DOI: 10.14348/molcells.2016.2323] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 11/26/2015] [Indexed: 12/16/2022] Open
Abstract
Redox signalling comprises the biology of molecular signal transduction mediated by reactive oxygen (or nitrogen) species. By specific and reversible oxidation of redox-sensitive cysteines, many biological processes sense and respond to signals from the intracellular redox environment. Redox signals are therefore important regulators of cellular homeostasis. Recently, it has become apparent that the cellular redox state oscillates in vivo and in vitro, with a period of about one day (circadian). Circadian time-keeping allows cells and organisms to adapt their biology to resonate with the 24-hour cycle of day/night. The importance of this innate biological time-keeping is illustrated by the association of clock disruption with the early onset of several diseases (e.g. type II diabetes, stroke and several forms of cancer). Circadian regulation of cellular redox balance suggests potentially two distinct roles for redox signalling in relation to the cellular clock: one where it is regulated by the clock, and one where it regulates the clock. Here, we introduce the concepts of redox signalling and cellular timekeeping, and then critically appraise the evidence for the reciprocal regulation between cellular redox state and the circadian clock. We conclude there is a substantial body of evidence supporting circadian regulation of cellular redox state, but that it would be premature to conclude that the converse is also true. We therefore propose some approaches that might yield more insight into redox control of cellular timekeeping.
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Affiliation(s)
- Marrit Putker
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH,
UK
| | - John Stuart O’Neill
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH,
UK
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105
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Burnetti AJ, Aydin M, Buchler NE. Cell cycle Start is coupled to entry into the yeast metabolic cycle across diverse strains and growth rates. Mol Biol Cell 2016; 27:64-74. [PMID: 26538026 PMCID: PMC4694762 DOI: 10.1091/mbc.e15-07-0454] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/21/2015] [Accepted: 10/27/2015] [Indexed: 01/30/2023] Open
Abstract
Cells have evolved oscillators with different frequencies to coordinate periodic processes. Here we studied the interaction of two oscillators, the cell division cycle (CDC) and the yeast metabolic cycle (YMC), in budding yeast. Previous work suggested that the CDC and YMC interact to separate high oxygen consumption (HOC) from DNA replication to prevent genetic damage. To test this hypothesis, we grew diverse strains in chemostat and measured DNA replication and oxygen consumption with high temporal resolution at different growth rates. Our data showed that HOC is not strictly separated from DNA replication; rather, cell cycle Start is coupled with the initiation of HOC and catabolism of storage carbohydrates. The logic of this YMC-CDC coupling may be to ensure that DNA replication and cell division occur only when sufficient cellular energy reserves have accumulated. Our results also uncovered a quantitative relationship between CDC period and YMC period across different strains. More generally, our approach shows how studies in genetically diverse strains efficiently identify robust phenotypes and steer the experimentalist away from strain-specific idiosyncrasies.
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Affiliation(s)
- Anthony J Burnetti
- Program in Cellular & Molecular Biology, Duke University, Durham, NC 27708 University Program in Genetics & Genomics, Duke University, Durham, NC 27708 Center for Genomic & Computational Biology, Duke University, Durham, NC 22710 Department of Biology, Duke University, Durham, NC 27708
| | - Mert Aydin
- Center for Genomic & Computational Biology, Duke University, Durham, NC 22710 Department of Biology, Duke University, Durham, NC 27708
| | - Nicolas E Buchler
- Center for Genomic & Computational Biology, Duke University, Durham, NC 22710 Department of Biology, Duke University, Durham, NC 27708
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106
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Shultzaberger RK, Boyd JS, Diamond S, Greenspan RJ, Golden SS. Giving Time Purpose: The Synechococcus elongatus Clock in a Broader Network Context. Annu Rev Genet 2015; 49:485-505. [PMID: 26442846 DOI: 10.1146/annurev-genet-111212-133227] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Early research on the cyanobacterial clock focused on characterizing the genes needed to keep, entrain, and convey time within the cell. As the scope of assays used in molecular genetics has expanded to capture systems-level properties (e.g., RNA-seq, ChIP-seq, metabolomics, high-throughput screening of genetic variants), so has our understanding of how the clock fits within and influences a broader cellular context. Here we review the work that has established a global perspective of the clock, with a focus on (a) an emerging network-centric view of clock architecture, (b) mechanistic insights into how temporal and environmental cues are transmitted and integrated within this network,
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Affiliation(s)
- Ryan K Shultzaberger
- Center for Circadian Biology, University of California San Diego, La Jolla, USA, 92093.,Kavli Institute for Brain and Mind, University of California San Diego, La Jolla, USA, 92093
| | - Joseph S Boyd
- Center for Circadian Biology, University of California San Diego, La Jolla, USA, 92093.,Division of Biological Sciences, University of California San Diego, La Jolla, USA, 92093
| | - Spencer Diamond
- Center for Circadian Biology, University of California San Diego, La Jolla, USA, 92093.,Division of Biological Sciences, University of California San Diego, La Jolla, USA, 92093
| | - Ralph J Greenspan
- Center for Circadian Biology, University of California San Diego, La Jolla, USA, 92093.,Kavli Institute for Brain and Mind, University of California San Diego, La Jolla, USA, 92093
| | - Susan S Golden
- Center for Circadian Biology, University of California San Diego, La Jolla, USA, 92093.,Division of Biological Sciences, University of California San Diego, La Jolla, USA, 92093
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107
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108
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Mei Q, Dvornyk V. Evolutionary History of the Photolyase/Cryptochrome Superfamily in Eukaryotes. PLoS One 2015; 10:e0135940. [PMID: 26352435 PMCID: PMC4564169 DOI: 10.1371/journal.pone.0135940] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/28/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Photolyases and cryptochromes are evolutionarily related flavoproteins, which however perform distinct physiological functions. Photolyases (PHR) are evolutionarily ancient enzymes. They are activated by light and repair DNA damage caused by UV radiation. Although cryptochromes share structural similarity with DNA photolyases, they lack DNA repair activity. Cryptochrome (CRY) is one of the key elements of the circadian system in animals. In plants, CRY acts as a blue light receptor to entrain circadian rhythms, and mediates a variety of light responses, such as the regulation of flowering and seedling growth. RESULTS We performed a comprehensive evolutionary analysis of the CRY/PHR superfamily. The superfamily consists of 7 major subfamilies: CPD class I and CPD class II photolyases, (6-4) photolyases, CRY-DASH, plant PHR2, plant CRY and animal CRY. Although the whole superfamily evolved primarily under strong purifying selection (average ω = 0.0168), some subfamilies did experience strong episodic positive selection during their evolution. Photolyases were lost in higher animals that suggests natural selection apparently became weaker in the late stage of evolutionary history. The evolutionary time estimates suggested that plant and animal CRYs evolved in the Neoproterozoic Era (~1000-541 Mya), which might be a result of adaptation to the major climate and global light regime changes occurred in that period of the Earth's geological history.
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Affiliation(s)
- Qiming Mei
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Volodymyr Dvornyk
- School of Biological Sciences, the University of Hong Kong, Pokfulam Rd., Hong Kong SAR, People’s Republic of China
- Department of Life Sciences, College of Science and General Studies, Alfaisal University, Riyadh, Kingdom of Saudi Arabia
- * E-mail:
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109
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Herrero A, Romanowski A, Meelkop E, Caldart CS, Schoofs L, Golombek DA. Pigment-dispersing factor signaling in the circadian system ofCaenorhabditis elegans. GENES BRAIN AND BEHAVIOR 2015; 14:493-501. [DOI: 10.1111/gbb.12231] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 06/18/2015] [Accepted: 06/24/2015] [Indexed: 11/29/2022]
Affiliation(s)
- A. Herrero
- Laboratorio de Cronobiología, Departamento de Ciencia y Tecnología; Universidad Nacional de Quilmes; Buenos Aires Argentina
| | - A. Romanowski
- Laboratorio de Cronobiología, Departamento de Ciencia y Tecnología; Universidad Nacional de Quilmes; Buenos Aires Argentina
| | - E. Meelkop
- Animal Physiology and Neurobiology Section, Department of Biology; KU Leuven; Leuven Belgium
| | - C. S. Caldart
- Laboratorio de Cronobiología, Departamento de Ciencia y Tecnología; Universidad Nacional de Quilmes; Buenos Aires Argentina
| | - L. Schoofs
- Animal Physiology and Neurobiology Section, Department of Biology; KU Leuven; Leuven Belgium
| | - D. A. Golombek
- Laboratorio de Cronobiología, Departamento de Ciencia y Tecnología; Universidad Nacional de Quilmes; Buenos Aires Argentina
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110
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Cao R, Gkogkas CG, de Zavalia N, Blum ID, Yanagiya A, Tsukumo Y, Xu H, Lee C, Storch KF, Liu AC, Amir S, Sonenberg N. Light-regulated translational control of circadian behavior by eIF4E phosphorylation. Nat Neurosci 2015; 18:855-62. [PMID: 25915475 PMCID: PMC4446158 DOI: 10.1038/nn.4010] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 03/28/2015] [Indexed: 12/14/2022]
Abstract
The circadian (~24 h) clock is continuously entrained (reset) by ambient light so that endogenous rhythms are synchronized with daily changes in the environment. Light-induced gene expression is thought to be the molecular mechanism underlying clock entrainment. mRNA translation is a key step of gene expression, but how clock entrainment is controlled at the mRNA translation level is not understood. Here we report that a light- and circadian clock-regulated MAPK/MNK pathway leads to phosphorylation of the cap-binding protein eIF4E in the mouse suprachiasmatic nucleus (SCN) of the hypothalamus, the locus of the master circadian clock in mammals. Phosphorylation of eIF4E specifically promotes translation of Period (Per) 1 and 2 mRNAs and increases the abundance of basal and inducible PER proteins, which facilitates circadian clock resetting and precise timekeeping. Together, these results highlight a critical role for light-regulated translational control in the physiology of the circadian clock.
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Affiliation(s)
- Ruifeng Cao
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Canada
| | - Christos G Gkogkas
- Patrick Wild Centre, Centre for Integrative Physiology, University of Edinburgh, Edinburgh, UK
| | - Nuria de Zavalia
- Center for Studies in Behavioral Neurobiology, Concordia University, Montreal, Canada
| | - Ian D Blum
- Douglas Mental Health University Institute and Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - Akiko Yanagiya
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Canada
| | - Yoshinori Tsukumo
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Canada
| | - Haiyan Xu
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee, USA
| | - Choogon Lee
- Department of Biomedical Sciences, Neuroscience Program, College of Medicine, Florida State University, Tallahassee, Florida, USA
| | - Kai-Florian Storch
- Douglas Mental Health University Institute and Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - Andrew C Liu
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee, USA
| | - Shimon Amir
- Center for Studies in Behavioral Neurobiology, Concordia University, Montreal, Canada
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Canada
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111
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Larrondo LF, Olivares-Yañez C, Baker CL, Loros JJ, Dunlap JC. Circadian rhythms. Decoupling circadian clock protein turnover from circadian period determination. Science 2015; 347:1257277. [PMID: 25635104 DOI: 10.1126/science.1257277] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The mechanistic basis of eukaryotic circadian oscillators in model systems as diverse as Neurospora, Drosophila, and mammalian cells is thought to be a transcription-and-translation-based negative feedback loop, wherein progressive and controlled phosphorylation of one or more negative elements ultimately elicits their own proteasome-mediated degradation, thereby releasing negative feedback and determining circadian period length. The Neurospora crassa circadian negative element FREQUENCY (FRQ) exemplifies such proteins; it is progressively phosphorylated at more than 100 sites, and strains bearing alleles of frq with anomalous phosphorylation display abnormal stability of FRQ that is well correlated with altered periods or apparent arrhythmicity. Unexpectedly, we unveiled normal circadian oscillations that reflect the allelic state of frq but that persist in the absence of typical degradation of FRQ. This manifest uncoupling of negative element turnover from circadian period length determination is not consistent with the consensus eukaryotic circadian model.
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Affiliation(s)
- 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, Casilla 114-D, Santiago, Chile. Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.
| | - Consuelo Olivares-Yañez
- Millennium Nucleus for Fungal Integrative and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile
| | - Christopher L Baker
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jennifer J Loros
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA. Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jay C Dunlap
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.
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112
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Plikus MV, Van Spyk EN, Pham K, Geyfman M, Kumar V, Takahashi JS, Andersen B. The circadian clock in skin: implications for adult stem cells, tissue regeneration, cancer, aging, and immunity. J Biol Rhythms 2015; 30:163-82. [PMID: 25589491 DOI: 10.1177/0748730414563537] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Historically, work on peripheral circadian clocks has been focused on organs and tissues that have prominent metabolic functions, such as the liver, fat, and muscle. In recent years, skin has emerged as a model for studying circadian clock regulation of cell proliferation, stem cell functions, tissue regeneration, aging, and carcinogenesis. Morphologically, skin is complex, containing multiple cell types and structures, and there is evidence for a functional circadian clock in most, if not all, of its cell types. Despite the complexity, skin stem cell populations are well defined, experimentally tractable, and exhibit prominent daily cell proliferation cycles. Hair follicle stem cells also participate in recurrent, long-lasting cycles of regeneration: the hair growth cycles. Among other advantages of skin is a broad repertoire of available genetic tools enabling the creation of cell type-specific circadian mutants. Also, due to the accessibility of skin, in vivo imaging techniques can be readily applied to study the circadian clock and its outputs in real time, even at the single-cell level. Skin provides the first line of defense against many environmental and stress factors that exhibit dramatic diurnal variations such as solar ultraviolet (UV) radiation and temperature. Studies have already linked the circadian clock to the control of UVB-induced DNA damage and skin cancers. Due to the important role that skin plays in the defense against microorganisms, it also represents a promising model system to further explore the role of the clock in the regulation of the body's immune functions. To that end, recent studies have already linked the circadian clock to psoriasis, one of the most common immune-mediated skin disorders. Skin also provides opportunities to interrogate the clock regulation of tissue metabolism in the context of stem cells and regeneration. Furthermore, many animal species feature prominent seasonal hair molt cycles, offering an attractive model for investigating the role of the clock in seasonal organismal behaviors.
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Affiliation(s)
- Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA Center for Complex Biological Systems, University of California, Irvine, Irvine, CA
| | - Elyse N Van Spyk
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA Department of Biological Chemistry, University of California, Irvine, Irvine, CA Division of Endocrinology, Department of Medicine, University of California, Irvine, Irvine, CA
| | - Kim Pham
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA
| | | | - Vivek Kumar
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Joseph S Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Bogi Andersen
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA Department of Biological Chemistry, University of California, Irvine, Irvine, CA Division of Endocrinology, Department of Medicine, University of California, Irvine, Irvine, CA
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113
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Abstract
Circadian clocks have evolved a slowing-down mechanism. Temperature may be the original and universal time-giver to the organism. Brown adipose tissue generates heat and guides the circadian rhythm of core body temperature. The cryptochrome proteins regulate the temperature entrainability, and their dysfunction may let the activation of brown adipose tissue affect the brain more easily. Therefore, the activity of brown adipose tissue may compromise the slowing-down mechanism and thereby contribute to the emergence of mood disorders and the increase in suicide mortality around the time of puberty.
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Affiliation(s)
- Timo Partonen
- a National Institute for Health and Welfare , Department of Health , Helsinki , Finland
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114
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Hoyle NP, O'Neill JS. Oxidation-reduction cycles of peroxiredoxin proteins and nontranscriptional aspects of timekeeping. Biochemistry 2014; 54:184-93. [PMID: 25454580 PMCID: PMC4302831 DOI: 10.1021/bi5008386] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The circadian clock allows organisms to accurately predict the earth's rotation and modify their behavior as a result. Genetic analyses in a variety of organisms have defined a mechanism based largely on gene expression feedback loops. However, as we delve more deeply into the mechanisms of circadian timekeeping, we are discovering that post-translational mechanisms play a key role in defining the character of the clock. We are also discovering that these modifications are inextricably linked to cellular metabolism, including redox homeostasis. A robust circadian oscillation in the redox status of the peroxiredoxins (a major class of cellular antioxidants) was recently shown to be remarkably conserved from archaea and cyanobacteria all the way to plants and animals. Furthermore, recent findings indicate that cellular redox status is coupled not only to canonical circadian gene expression pathways but also to a noncanonical transcript-independent circadian clock. The redox rhythms observed in peroxiredoxins in the absence of canonical clock mechanisms may hint at the nature of this new and hitherto unknown aspect of circadian timekeeping.
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Affiliation(s)
- Nathaniel P Hoyle
- Laboratory of Molecular Biology, Medical Research Council , Francis Crick Avenue, Cambridge CB2 0QH, U.K
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115
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Wildenberg GA, Murray AW. Evolving a 24-hr oscillator in budding yeast. eLife 2014; 3. [PMID: 25383925 PMCID: PMC4270073 DOI: 10.7554/elife.04875] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 11/07/2014] [Indexed: 01/10/2023] Open
Abstract
We asked how a new, complex trait evolves by selecting for diurnal oscillations in the budding yeast, Saccharomyces cerevisiae. We expressed yellow fluorescent protein (YFP) from a yeast promoter and selected for a regular alternation between low and high fluorescence over a 24-hr period. This selection produced changes in cell adhesion rather than YFP expression: clonal populations oscillated between single cells and multicellular clumps. The oscillations are not a response to environmental cues and continue for at least three cycles in a constant environment. We identified eight putative causative mutations in one clone and recreated the evolved phenotype in the ancestral strain. The mutated genes lack obvious relationships to each other, but multiple lineages change from the haploid to the diploid pattern of gene expression. We show that a novel, complex phenotype can evolve by small sets of mutations in genes whose molecular functions appear to be unrelated to each other.
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Affiliation(s)
- Gregg A Wildenberg
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, United States
| | - Andrew W Murray
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, United States
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116
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Cleal JK, Shepherd JN, Shearer JL, Bruce KD, Cagampang FR. Sensitivity of housekeeping genes in the suprachiasmatic nucleus of the mouse brain to diet and the daily light–dark cycle. Brain Res 2014; 1575:72-7. [DOI: 10.1016/j.brainres.2014.05.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/20/2014] [Accepted: 05/21/2014] [Indexed: 02/07/2023]
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117
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Craig DPA, Varnon CA, Sokolowski MBC, Wells H, Abramson CI. An assessment of fixed interval timing in free-flying honey bees (Apis mellifera ligustica): an analysis of individual performance. PLoS One 2014; 9:e101262. [PMID: 24983960 PMCID: PMC4077790 DOI: 10.1371/journal.pone.0101262] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 06/04/2014] [Indexed: 11/19/2022] Open
Abstract
Interval timing is a key element of foraging theory, models of predator avoidance, and competitive interactions. Although interval timing is well documented in vertebrate species, it is virtually unstudied in invertebrates. In the present experiment, we used free-flying honey bees (Apis mellifera ligustica) as a model for timing behaviors. Subjects were trained to enter a hole in an automated artificial flower to receive a nectar reinforcer (i.e. reward). Responses were continuously reinforced prior to exposure to either a fixed interval (FI) 15-sec, FI 30-sec, FI 60-sec, or FI 120-sec reinforcement schedule. We measured response rate and post-reinforcement pause within each fixed interval trial between reinforcers. Honey bees responded at higher frequencies earlier in the fixed interval suggesting subject responding did not come under traditional forms of temporal control. Response rates were lower during FI conditions compared to performance on continuous reinforcement schedules, and responding was more resistant to extinction when previously reinforced on FI schedules. However, no "scalloped" or "break-and-run" patterns of group or individual responses reinforced on FI schedules were observed; no traditional evidence of temporal control was found. Finally, longer FI schedules eventually caused all subjects to cease returning to the operant chamber indicating subjects did not tolerate the longer FI schedules.
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Affiliation(s)
| | - Christopher A. Varnon
- Department of Psychology, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | | | - Harrington Wells
- Department of Biology, University of Tulsa, Tulsa, Oklahoma, United States of America
| | - Charles I. Abramson
- Department of Psychology, Oklahoma State University, Stillwater, Oklahoma, United States of America
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118
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Gillette MU, Wang TA. Brain circadian oscillators and redox regulation in mammals. Antioxid Redox Signal 2014; 20:2955-65. [PMID: 24111727 PMCID: PMC4038987 DOI: 10.1089/ars.2013.5598] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 10/10/2013] [Indexed: 11/12/2022]
Abstract
SIGNIFICANCE Functional states of organisms vary rhythmically with a period of about a day (i.e., circadian). This endogenous dynamic is shaped by day-night alternations in light and energy. Mammalian circadian rhythms are orchestrated by the hypothalamic suprachiasmatic nucleus (SCN), a brain region specialized for timekeeping. These autonomous ~24-h oscillations are cell-based, requiring transcription-translation-based regulation. SCN circadian oscillations include the maintenance of intrinsic rhythms, sensitivities to input signals, and generation of output signals. These change predictably as time proceeds from dawn to day, dusk, and through the night. SCN neuronal excitability, a highly energy-demanding process, also oscillates over ~24 h. The nature of the relationship of cellular metabolism and excitability had been unknown. RECENT ADVANCES Global SCN redox state was found to undergo an autonomous circadian rhythm. Redox state is relatively reduced in daytime, when neuronal activity is high, and oxidized during nighttime, when neurons are relatively inactive. Redox modulates neuronal excitability via tight coupling: imposed reducing or oxidizing shifts immediately alter membrane excitability. Whereas an intact transcription-translation oscillator is necessary for the redox oscillation, metabolic modulation of excitability is too rapid to be under clockwork control. CRITICAL ISSUES Our observations lead to the hypothesis that redox state and neuronal activity are coupled nontranscriptional circadian oscillators in SCN neurons. Critical issues include discovering molecular and cellular substrates and functional consequences of this redox oscillator. FUTURE DIRECTIONS Understanding interdependencies between cellular energy metabolism, neuronal activity, and circadian rhythms is critical to developing therapeutic strategies for treating neurodegenerative diseases and brain metabolic syndromes.
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Affiliation(s)
- Martha U. Gillette
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Tongfei A. Wang
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois
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119
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Abstract
Circadian clocks that comprise clock genes exist throughout the body and control daily physiological events. The central clock that dominates activity rhythms is entrained by light/dark cycles, whereas peripheral clocks regulating local metabolic rhythms are determined by feeding/fasting cycles. Nutrients reset peripheral circadian clocks and the local clock genes control downstream metabolic processes. Metabolic states also affect the clockworks in feedback manners. Because the circadian system organizes whole energy homeostasis, including food intake, fat accumulation, and caloric expenditure, the disruption of circadian clocks leads to metabolic disorders. Recent findings show that time-restricted feeding during the active phase amplifies circadian clocks and improves metabolic disorders induced by a high-fat diet without caloric reduction, whereas unusual/irregular food intake induces various metabolic dysfunctions. Such evidence from nutrition studies that consider circadian system (chrononutrition) has rapidly accumulated. We review molecular relationships between circadian clocks and nutrition as well as recent chrononutrition findings.
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Affiliation(s)
- Hideaki Oike
- Food Function Division, National Food Research Institute (NFRI), National Agriculture and Food Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642 Japan ; Biological Clock Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 Japan
| | - Katsutaka Oishi
- Biological Clock Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 Japan ; Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan ; Department of Applied Biological Science, Graduate School of Science and Technology, Tokyo University of Science, Noda, Japan
| | - Masuko Kobori
- Food Function Division, National Food Research Institute (NFRI), National Agriculture and Food Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642 Japan
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120
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Circadian clocks in symbiotic corals: The duet between Symbiodinium algae and their coral host. Mar Genomics 2014; 14:47-57. [DOI: 10.1016/j.margen.2014.01.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 11/11/2013] [Accepted: 01/13/2014] [Indexed: 12/15/2022]
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121
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Hardy JG, Mouser DJ, Arroyo-Currás N, Geissler S, Chow JK, Nguy L, Kim JM, Schmidt CE. Biodegradable electroactive polymers for electrochemically-triggered drug delivery. J Mater Chem B 2014; 2:6809-6822. [DOI: 10.1039/c4tb00355a] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report biodegradable electroactive polymer (EAP)-based materials and their application as drug delivery devices.
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Affiliation(s)
- John G. Hardy
- Department of Biomedical Engineering
- The University of Texas at Austin
- Austin, USA
- J. Crayton Pruitt Family Department of Biomedical Engineering
- University of Florida
| | - David J. Mouser
- Department of Biomedical Engineering
- The University of Texas at Austin
- Austin, USA
| | | | - Sydney Geissler
- Department of Biomedical Engineering
- The University of Texas at Austin
- Austin, USA
- J. Crayton Pruitt Family Department of Biomedical Engineering
- University of Florida
| | - Jacqueline K. Chow
- Department of Biomedical Engineering
- The University of Texas at Austin
- Austin, USA
| | - Lindsey Nguy
- Department of Biomedical Engineering
- The University of Texas at Austin
- Austin, USA
| | - Jong M. Kim
- Department of Biomedical Engineering
- The University of Texas at Austin
- Austin, USA
| | - Christine E. Schmidt
- Department of Biomedical Engineering
- The University of Texas at Austin
- Austin, USA
- J. Crayton Pruitt Family Department of Biomedical Engineering
- University of Florida
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122
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Beckwith EJ, Gorostiza EA, Berni J, Rezával C, Pérez-Santángelo A, Nadra AD, Ceriani MF. Circadian period integrates network information through activation of the BMP signaling pathway. PLoS Biol 2013; 11:e1001733. [PMID: 24339749 PMCID: PMC3858370 DOI: 10.1371/journal.pbio.1001733] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 10/30/2013] [Indexed: 11/18/2022] Open
Abstract
Circadian pacemaker neurons in the Drosophila brain gather network information through the highly conserved BMP signaling pathway to establish the daily period of locomotor behavior. Living organisms use biological clocks to maintain their internal temporal order and anticipate daily environmental changes. In Drosophila, circadian regulation of locomotor behavior is controlled by ∼150 neurons; among them, neurons expressing the PIGMENT DISPERSING FACTOR (PDF) set the period of locomotor behavior under free-running conditions. To date, it remains unclear how individual circadian clusters integrate their activity to assemble a distinctive behavioral output. Here we show that the BONE MORPHOGENETIC PROTEIN (BMP) signaling pathway plays a crucial role in setting the circadian period in PDF neurons in the adult brain. Acute deregulation of BMP signaling causes period lengthening through regulation of dClock transcription, providing evidence for a novel function of this pathway in the adult brain. We propose that coherence in the circadian network arises from integration in PDF neurons of both the pace of the cell-autonomous molecular clock and information derived from circadian-relevant neurons through release of BMP ligands. The circadian clock controls rhythms in behavior, physiology, and metabolism in all living organisms. The molecular components as well as the neuronal network required to keep this clock running have been identified in several species. In the Drosophila brain this neuronal network is represented by an ensemble of 150 neurons, and among them, those expressing the Pigment Dispersing Factor (PDF) neuropeptide encompass the “central oscillator”—also called master clock as it ensures 24-hour periods—of the fly brain. In this study we show that the widely conserved Bone Morphogenetic Protein (BMP) signaling pathway is present in PDF neurons, and upon adult-specific activation it lengthens the endogenous period of locomotor behavior. We find that period lengthening correlates with delayed accumulation of nuclear PERIOD, a core component of the molecular clock. We also identified a putative DNA binding motif for the BMP pathway nuclear components within the regulatory region of the Clock (Clk) promoter, another core component of the circadian machinery. Interestingly, upon BMP pathway activation endogenous CLK levels are downregulated, thus accounting for the lengthening of the endogenous period. We propose that the endogenous period is a network property commanded by PDF neurons that results from integration of information from both the autonomous molecular clock and the nonautonomous BMP signaling pathway.
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Affiliation(s)
- Esteban J. Beckwith
- Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir, IIB-BA-CONICET, Buenos Aires, Argentina
| | - E. Axel Gorostiza
- Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir, IIB-BA-CONICET, Buenos Aires, Argentina
| | - Jimena Berni
- Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir, IIB-BA-CONICET, Buenos Aires, Argentina
| | - Carolina Rezával
- Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir, IIB-BA-CONICET, Buenos Aires, Argentina
| | - Agustín Pérez-Santángelo
- Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir, IIB-BA-CONICET, Buenos Aires, Argentina
| | - Alejandro D. Nadra
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, UBA. IQUIBICEN-CONICET, Buenos Aires, Argentina
| | - María Fernanda Ceriani
- Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir, IIB-BA-CONICET, Buenos Aires, Argentina
- * E-mail:
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123
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Abstract
Animals, plants, and microorganisms exhibit numerous biological rhythms that are generated by numerous biological clocks. This article summarizes experimental data pertinent to the often-ignored issue of integration of multiple rhythms. Five contexts of integration are discussed: (i) integration of circadian rhythms of multiple processes within an individual organism, (ii) integration of biological rhythms operating in different time scales (such as tidal, daily, and seasonal), (iii) integration of rhythms across multiple species, (iv) integration of rhythms of different members of a species, and (v) integration of rhythmicity and physiological homeostasis. Understanding of these multiple rhythmic interactions is an important first step in the eventual thorough understanding of how organisms arrange their vital functions temporally within and without their bodies.
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Affiliation(s)
- Roberto Refinetti
- Circadian Rhythm Laboratory, University of South Carolina, Walterboro, South Carolina, USA.
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124
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Cao R, Robinson B, Xu H, Gkogkas C, Khoutorsky A, Alain T, Yanagiya A, Nevarko T, Liu AC, Amir S, Sonenberg N. Translational control of entrainment and synchrony of the suprachiasmatic circadian clock by mTOR/4E-BP1 signaling. Neuron 2013; 79:712-24. [PMID: 23972597 DOI: 10.1016/j.neuron.2013.06.026] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2013] [Indexed: 11/28/2022]
Abstract
Protein synthesis is critical for circadian clock function, but little is known of how translational regulation controls the master pacemaker in mammals, the suprachiasmatic nucleus (SCN). Here we demonstrate that the pivotal translational repressor, the eukaryotic translational initiation factor 4E binding protein 1 (4E-BP1), is rhythmically regulated via the mechanistic target of rapamycin (mTOR) signaling in the SCN and preferentially represses vasoactive intestinal peptide (Vip) mRNA translation. Knockout (KO) of Eif4ebp1 (gene encoding 4E-BP1) leads to upregulation of VIP and higher amplitude of molecular rhythms in the SCN. Consequently, the 4E-BP1 null mice exhibit accelerated re-entrainment to a shifted light/dark cycle and are more resistant to the rhythm-disruptive effects of constant light. Conversely, in Mtor(+/-) mice VIP expression is decreased and susceptibility to the effects of constant light is increased. These results reveal a key role for mTOR/4E-BP1-mediated translational control in regulating entrainment and synchrony of the master clock.
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Affiliation(s)
- Ruifeng Cao
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, QC H3A 1A3, Canada
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125
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LNK genes integrate light and clock signaling networks at the core of the Arabidopsis oscillator. Proc Natl Acad Sci U S A 2013; 110:12120-5. [PMID: 23818596 DOI: 10.1073/pnas.1302170110] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Light signaling pathways and the circadian clock interact to help organisms synchronize physiological and developmental processes with periodic environmental cycles. The plant photoreceptors responsible for clock resetting have been characterized, but signaling components that link the photoreceptors to the clock remain to be identified. Here we describe a family of night light-inducible and clock-regulated genes (LNK) that play a key role linking light regulation of gene expression to the control of daily and seasonal rhythms in Arabidopsis thaliana. A genomewide transcriptome analysis revealed that most light-induced genes respond more strongly to light during the subjective day, which is consistent with the diurnal nature of most physiological processes in plants. However, a handful of genes, including the homologous genes LNK1 and LNK2, are more strongly induced by light in the middle of the night, when the clock is most responsive to this signal. Further analysis revealed that the morning phased LNK1 and LNK2 genes control circadian rhythms, photomorphogenic responses, and photoperiodic dependent flowering, most likely by regulating a subset of clock and flowering time genes in the afternoon. LNK1 and LNK2 themselves are directly repressed by members of the TIMING OF CAB1 EXPRESSION/PSEUDO RESPONSE REGULATOR family of core-clock genes in the afternoon and early night. Thus, LNK1 and LNK2 integrate early light signals with temporal information provided by core oscillator components to control the expression of afternoon genes, allowing plants to keep track of seasonal changes in day length.
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126
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Itoh TQ, Matsumoto A, Tanimura T. C-terminal binding protein (CtBP) activates the expression of E-box clock genes with CLOCK/CYCLE in Drosophila. PLoS One 2013; 8:e63113. [PMID: 23646183 PMCID: PMC3640014 DOI: 10.1371/journal.pone.0063113] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 04/02/2013] [Indexed: 12/21/2022] Open
Abstract
In Drosophila, CLOCK/CYCLE heterodimer (CLK/CYC) is the primary activator of circadian clock genes that contain the E-box sequence in their promoter regions (hereafter referred to as "E-box clock genes"). Although extensive studies have investigated the feedback regulation of clock genes, little is known regarding other factors acting with CLK/CYC. Here we show that Drosophila C-terminal binding protein (dCtBP), a transcriptional co-factor, is involved in the regulation of the E-box clock genes. In vivo overexpression of dCtBP in clock cells lengthened or abolished circadian locomotor rhythm with up-regulation of a subset of the E-box clock genes, period (per), vrille (vri), and PAR domain protein 1ε (Pdp1ε). Co-expression of dCtBP with CLK in vitro also increased the promoter activity of per, vri, Pdp1ε and cwo depending on the amount of dCtBP expression, whereas no effect was observed without CLK. The activation of these clock genes in vitro was not observed when we used mutated dCtBP which carries amino acid substitutions in NAD+ domain. These results suggest that dCtBP generally acts as a putative co-activator of CLK/CYC through the E-box sequence.
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Affiliation(s)
- Taichi Q. Itoh
- Graduate School of Systems Life Sciences, Kyushu University, Hakozaki, Fukuoka, Japan
| | - Akira Matsumoto
- Department of Biology, Juntendo University School of Medicine, Inba-gun, Chiba, Japan
| | - Teiichi Tanimura
- Graduate School of Systems Life Sciences, Kyushu University, Hakozaki, Fukuoka, Japan
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127
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Reitzel AM, Tarrant AM, Levy O. Circadian clocks in the cnidaria: environmental entrainment, molecular regulation, and organismal outputs. Integr Comp Biol 2013; 53:118-30. [PMID: 23620252 DOI: 10.1093/icb/ict024] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The circadian clock is a molecular network that translates predictable environmental signals, such as light levels, into organismal responses, including behavior and physiology. Regular oscillations of the molecular components of the clock enable individuals to anticipate regularly fluctuating environmental conditions. Cnidarians play important roles in benthic and pelagic marine environments and also occupy a key evolutionary position as the likely sister group to the bilaterians. Together, these attributes make members of this phylum attractive as models for testing hypotheses on roles for circadian clocks in regulating behavior, physiology, and reproduction as well as those regarding the deep evolutionary conservation of circadian regulatory pathways in animal evolution. Here, we review and synthesize the field of cnidarian circadian biology by discussing the diverse effects of daily light cycles on cnidarians, summarizing the molecular evidence for the conservation of a bilaterian-like circadian clock in anthozoan cnidarians, and presenting new empirical data supporting the presence of a conserved feed-forward loop in the starlet sea anemone, Nematostella vectensis. Furthermore, we discuss critical gaps in our current knowledge about the cnidarian clock, including the functions directly regulated by the clock and the precise molecular interactions that drive the oscillating gene-expression patterns. We conclude that the field of cnidarian circadian biology is moving rapidly toward linking molecular mechanisms with physiology and behavior.
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Affiliation(s)
- Adam M Reitzel
- Department of Biology, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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128
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Gutu A, O'Shea EK. Two antagonistic clock-regulated histidine kinases time the activation of circadian gene expression. Mol Cell 2013; 50:288-94. [PMID: 23541768 PMCID: PMC3674810 DOI: 10.1016/j.molcel.2013.02.022] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 02/04/2013] [Accepted: 02/20/2013] [Indexed: 01/13/2023]
Abstract
The cyanobacterial circadian pacemaker consists of a three-protein clock--KaiA, KaiB, and KaiC--that generates oscillations in the phosphorylation state of KaiC. Here we investigate how temporal information encoded in KaiC phosphorylation is transduced to RpaA, a transcription factor required for circadian gene expression. We show that phosphorylation of RpaA is regulated by two antagonistic histidine kinases, SasA and CikA, which are sequentially activated at distinct times by the Kai clock complex. SasA acts as a kinase toward RpaA, whereas CikA, previously implicated in clock input, acts as a phosphatase that dephosphorylates RpaA. CikA and SasA cooperate to generate an oscillation of RpaA activity that is distinct from that generated by either enzyme alone and offset from the rhythm of KaiC phosphorylation. Our observations reveal how circadian clocks can precisely control the timing of output pathways via the concerted action of two oppositely acting enzymes.
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Affiliation(s)
- Andrian Gutu
- Howard Hughes Medical Institute, Harvard University Faculty of Arts and Sciences Center for Systems Biology, Northwest Labs, 52 Oxford Street, Cambridge, MA 02138, USA
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129
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Abstract
Circadian rhythms are believed to be an evolutionary adaptation to daily environmental cycles resulting from Earth's rotation about its axis. A trait evolved through a process of natural selection is considered as adaptation; therefore, rigorous demonstration of adaptation requires evidence suggesting evolution of a trait by natural selection. Like any other adaptive trait, circadian rhythms are believed to be advantageous to living beings through some perceived function. Circadian rhythms are thought to confer advantage to their owners through scheduling of biological functions at appropriate time of daily environmental cycle (extrinsic advantage), coordination of internal physiology (intrinsic advantage), and through their role in responses to seasonal changes. So far, the adaptive value of circadian rhythms has been tested in several studies and evidence indeed suggests that they confer advantage to their owners. In this review, we have discussed the background for development of the framework currently used to test the hypothesis of adaptive significance of circadian rhythms. Critical examination of evidence reveals that there are several lacunae in our understanding of circadian rhythms as adaptation. Although it is well known that demonstrating a given trait as adaptation (or setting the necessary criteria) is not a trivial task, here we recommend some of the basic criteria and suggest the nature of evidence required to comprehensively understand circadian rhythms as adaptation. Thus, we hope to create some awareness that may benefit future studies in this direction.
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Affiliation(s)
- Koustubh M Vaze
- Chronobiology Laboratory, Evolutionary and Organismal Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, Karnataka, India
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130
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McClung CR. Beyond Arabidopsis: the circadian clock in non-model plant species. Semin Cell Dev Biol 2013; 24:430-6. [PMID: 23466287 DOI: 10.1016/j.semcdb.2013.02.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 02/13/2013] [Accepted: 02/15/2013] [Indexed: 01/26/2023]
Abstract
Circadian clocks allow plants to temporally coordinate many aspects of their biology with the diurnal cycle derived from the rotation of Earth on its axis. Although there is a rich history of the study of clocks in many plant species, in recent years much progress in elucidating the architecture and function of the plant clock has emerged from studies of the model plant, Arabidopsis thaliana. There is considerable interest in extending this knowledge of the circadian clock into diverse plant species in order to address its role in topics as varied as agricultural productivity and the responses of individual species and plant communities to global climate change and environmental degradation. The analysis of circadian clocks in the green lineage provides insight into evolutionary processes in plants and throughout the eukaryotes.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Class of 1978 Life Sciences Center, Hanover, NH 03755, USA.
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131
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Gehring WJ. The evolution of vision. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2012; 3:1-40. [DOI: 10.1002/wdev.96] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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132
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Perez-Santangelo S, Schlaen RG, Yanovsky MJ. Genomic analysis reveals novel connections between alternative splicing and circadian regulatory networks. Brief Funct Genomics 2012; 12:13-24. [DOI: 10.1093/bfgp/els052] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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133
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Chen Z, Yoo SH, Takahashi JS. Small molecule modifiers of circadian clocks. Cell Mol Life Sci 2012; 70:2985-98. [PMID: 23161063 PMCID: PMC3760145 DOI: 10.1007/s00018-012-1207-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 10/26/2012] [Accepted: 10/29/2012] [Indexed: 12/11/2022]
Abstract
Circadian clocks orchestrate 24-h oscillations of essential physiological and behavioral processes in response to daily environmental changes. These clocks are remarkably precise under constant conditions yet highly responsive to resetting signals. With the molecular composition of the core oscillator largely established, recent research has increasingly focused on clock-modifying mechanisms/molecules. In particular, small molecule modifiers, intrinsic or extrinsic, are emerging as powerful tools for understanding basic clock biology as well as developing putative therapeutic agents for clock-associated diseases. In this review, we will focus on synthetic compounds capable of modifying the period, phase, or amplitude of circadian clocks, with particular emphasis on the mammalian clock. We will discuss the potential of exploiting these small molecule modifiers in both basic and translational research.
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Affiliation(s)
- Zheng Chen
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX 77030
- To whom correspondence should be addressed: ;
| | - Seung-Hee Yoo
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390
| | - Joseph S. Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390
- Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390
- To whom correspondence should be addressed: ;
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134
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Abstract
We studied the effects of increased sodium conductance on firing rate and gain in two populations of conductance-based, single-compartment model neurons. The first population consisted of 1000 model neurons with differing values of seven voltage-dependent conductances. In many of these models, increasing the sodium conductance threefold unexpectedly reduced the firing rate and divisively scaled the gain at high input current. In the second population, consisting of 1000 simplified model neurons, we found that enhanced sodium conductance changed the frequency-current (FI) curve in two computationally distinct ways, depending on the firing rate. In these models, increased sodium conductance produced a subtractive shift in the FI curve at low firing rates because the additional sodium conductance allowed the neuron to respond more strongly to equivalent input current. In contrast, at high input current, the increase in sodium conductance resulted in a divisive change in the gain because the increased conductance produced a proportionally larger activation of the delayed rectifier potassium conductance. The control and sodium-enhanced FI curves intersect at a point that delimits two regions in which the same biophysical manipulation produces two fundamentally different changes to the model neuron's computational properties. This suggests a potentially difficult problem for homeostatic regulation of intrinsic excitability.
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135
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Jones MA, Williams BA, McNicol J, Simpson CG, Brown JW, Harmer SL. Mutation of Arabidopsis spliceosomal timekeeper locus1 causes circadian clock defects. THE PLANT CELL 2012; 24:4066-82. [PMID: 23110899 PMCID: PMC3517236 DOI: 10.1105/tpc.112.104828] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2012] [Revised: 09/08/2012] [Accepted: 10/10/2012] [Indexed: 05/18/2023]
Abstract
The circadian clock plays a crucial role in coordinating plant metabolic and physiological functions with predictable environmental variables, such as dusk and dawn, while also modulating responses to biotic and abiotic challenges. Much of the initial characterization of the circadian system has focused on transcriptional initiation, but it is now apparent that considerable regulation is exerted after this key regulatory step. Transcript processing, protein stability, and cofactor availability have all been reported to influence circadian rhythms in a variety of species. We used a genetic screen to identify a mutation within a putative RNA binding protein (spliceosomal timekeeper locus1 [STIPL1]) that induces a long circadian period phenotype under constant conditions. STIPL1 is a homolog of the spliceosomal proteins TFP11 (Homo sapiens) and Ntr1p (Saccharomyces cerevisiae) involved in spliceosome disassembly. Analysis of general and alternative splicing using a high-resolution RT-PCR system revealed that mutation of this protein causes less efficient splicing of most but not all of the introns analyzed. In particular, the altered accumulation of circadian-associated transcripts may contribute to the observed mutant phenotype. Interestingly, mutation of a close homolog of STIPL1, STIP-LIKE2, does not cause a circadian phenotype, which suggests divergence in function between these family members. Our work highlights the importance of posttranscriptional control within the clock mechanism.
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Affiliation(s)
- Matthew A. Jones
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, 95616
| | - Brian A. Williams
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, 95616
| | - Jim McNicol
- Biomathematics and Statistics Scotland at Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom
| | - Craig G. Simpson
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, United Kingdom
| | - John W.S. Brown
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, United Kingdom
- Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, United Kingdom
| | - Stacey L. Harmer
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, 95616
- Address correspondence to
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136
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François P, Despierre N, Siggia ED. Adaptive temperature compensation in circadian oscillations. PLoS Comput Biol 2012; 8:e1002585. [PMID: 22807663 PMCID: PMC3395600 DOI: 10.1371/journal.pcbi.1002585] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 05/02/2012] [Indexed: 11/17/2022] Open
Abstract
A temperature independent period and temperature entrainment are two defining features of circadian oscillators. A default model of distributed temperature compensation satisfies these basic facts yet is not easily reconciled with other properties of circadian clocks, such as many mutants with altered but temperature compensated periods. The default model also suggests that the shape of the circadian limit cycle and the associated phase response curves (PRC) will vary since the average concentrations of clock proteins change with temperature. We propose an alternative class of models where the twin properties of a fixed period and entrainment are structural and arise from an underlying adaptive system that buffers temperature changes. These models are distinguished by a PRC whose shape is temperature independent and orbits whose extrema are temperature independent. They are readily evolved by local, hill climbing, optimization of gene networks for a common quality measure of biological clocks, phase anticipation. Interestingly a standard realization of the Goodwin model for temperature compensation displays properties of adaptive rather than distributed temperature compensation.
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Affiliation(s)
- Paul François
- Ernest Rutherford Physics Building, McGill University, Montreal, Quebec, Canada.
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137
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Abstract
Mammals have an endogenous timing system in the suprachiasmatic nuclei (SCN) of the hypothalamic region of the brain. This internal clock system is composed of an intracellular feedback loop that drives the expression of molecular components and their constitutive protein products to oscillate over a period of about 24 h (hence the term 'circadian'). These circadian oscillations bring about rhythmic changes in downstream molecular pathways and physiological processes such as those involved in nutrition and metabolism. It is now emerging that the molecular components of the clock system are also found within the cells of peripheral tissues, including the gastrointestinal tract, liver and pancreas. The present review examines their role in regulating nutritional and metabolic processes. In turn, metabolic status and feeding cycles are able to feed back onto the circadian clock in the SCN and in peripheral tissues. This feedback mechanism maintains the integrity and temporal coordination between various components of the circadian clock system. Thus, alterations in environmental cues could disrupt normal clock function, which may have profound effects on the health and well-being of an individual.
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138
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Edgar RS, Green EW, Zhao Y, van Ooijen G, Olmedo M, Qin X, Xu Y, Pan M, Valekunja UK, Feeney KA, Maywood ES, Hastings MH, Baliga NS, Merrow M, Millar AJ, Johnson CH, Kyriacou CP, O’Neill JS, Reddy AB. Peroxiredoxins are conserved markers of circadian rhythms. Nature 2012; 485:459-64. [PMID: 22622569 PMCID: PMC3398137 DOI: 10.1038/nature11088] [Citation(s) in RCA: 617] [Impact Index Per Article: 51.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 03/26/2012] [Indexed: 11/16/2022]
Abstract
Cellular life emerged ∼3.7 billion years ago. With scant exception, terrestrial organisms have evolved under predictable daily cycles owing to the Earth's rotation. The advantage conferred on organisms that anticipate such environmental cycles has driven the evolution of endogenous circadian rhythms that tune internal physiology to external conditions. The molecular phylogeny of mechanisms driving these rhythms has been difficult to dissect because identified clock genes and proteins are not conserved across the domains of life: Bacteria, Archaea and Eukaryota. Here we show that oxidation-reduction cycles of peroxiredoxin proteins constitute a universal marker for circadian rhythms in all domains of life, by characterizing their oscillations in a variety of model organisms. Furthermore, we explore the interconnectivity between these metabolic cycles and transcription-translation feedback loops of the clockwork in each system. Our results suggest an intimate co-evolution of cellular timekeeping with redox homeostatic mechanisms after the Great Oxidation Event ∼2.5 billion years ago.
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Affiliation(s)
- Rachel S. Edgar
- Department of Clinical Neurosciences, University of Cambridge Metabolic Research Laboratories, NIHR Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ,UK
| | - Edward W. Green
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Yuwei Zhao
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Gerben van Ooijen
- Synthetic and Systems Biology (SynthSys), Mayfield Road, EH9 3JD, Edinburgh, UK
| | - Maria Olmedo
- Department of Molecular Chronobiology, Center for Life Sciences, University of Groningen, The Netherlands
| | - Ximing Qin
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Yao Xu
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Min Pan
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Utham K. Valekunja
- Department of Clinical Neurosciences, University of Cambridge Metabolic Research Laboratories, NIHR Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ,UK
| | - Kevin A. Feeney
- Department of Clinical Neurosciences, University of Cambridge Metabolic Research Laboratories, NIHR Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ,UK
| | | | | | - Nitin S. Baliga
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
| | - Martha Merrow
- Department of Molecular Chronobiology, Center for Life Sciences, University of Groningen, The Netherlands
| | - Andrew J. Millar
- Synthetic and Systems Biology (SynthSys), Mayfield Road, EH9 3JD, Edinburgh, UK
- School of Biological Sciences, University of Edinburgh, Mayfield Road, EH9 3JR, Edinburgh, UK
| | - Carl H. Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | | | - John S. O’Neill
- Department of Clinical Neurosciences, University of Cambridge Metabolic Research Laboratories, NIHR Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ,UK
| | - Akhilesh B. Reddy
- Department of Clinical Neurosciences, University of Cambridge Metabolic Research Laboratories, NIHR Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ,UK
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139
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Donelson N, Kim EZ, Slawson JB, Vecsey CG, Huber R, Griffith LC. High-resolution positional tracking for long-term analysis of Drosophila sleep and locomotion using the "tracker" program. PLoS One 2012; 7:e37250. [PMID: 22615954 PMCID: PMC3352887 DOI: 10.1371/journal.pone.0037250] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 04/18/2012] [Indexed: 11/18/2022] Open
Abstract
Drosophila melanogaster has been used for decades in the study of circadian behavior, and more recently has become a popular model for the study of sleep. The classic method for monitoring fly activity involves counting the number of infrared beam crosses in individual small glass tubes. Incident recording methods such as this can measure gross locomotor activity, but they are unable to provide details about where the fly is located in space and do not detect small movements (i.e. anything less than half the enclosure size), which could lead to an overestimation of sleep and an inaccurate report of the behavior of the fly. This is especially problematic if the fly is awake, but is not moving distances that span the enclosure. Similarly, locomotor deficiencies could be incorrectly classified as sleep phenotypes. To address these issues, we have developed a locomotor tracking technique (the "Tracker" program) that records the exact location of a fly in real time. This allows for the detection of very small movements at any location within the tube. In addition to circadian locomotor activity, we are able to collect other information, such as distance, speed, food proximity, place preference, and multiple additional parameters that relate to sleep structure. Direct comparisons of incident recording and our motion tracking application using wild type and locomotor-deficient (CASK-β null) flies show that the increased temporal resolution in the data from the Tracker program can greatly affect the interpretation of the state of the fly. This is especially evident when a particular condition or genotype has strong effects on the behavior, and can provide a wealth of information previously unavailable to the investigator. The interaction of sleep with other behaviors can also be assessed directly in many cases with this method.
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Affiliation(s)
- Nathan Donelson
- Department of Biology, National Center for Behavioral Genomics and Volen Center for Complex Systems, Brandeis University, Waltham, Massachusetts, United States of America
| | - Eugene Z. Kim
- Department of Biology, National Center for Behavioral Genomics and Volen Center for Complex Systems, Brandeis University, Waltham, Massachusetts, United States of America
| | - Justin B. Slawson
- Department of Biology, National Center for Behavioral Genomics and Volen Center for Complex Systems, Brandeis University, Waltham, Massachusetts, United States of America
| | - Christopher G. Vecsey
- Department of Biology, National Center for Behavioral Genomics and Volen Center for Complex Systems, Brandeis University, Waltham, Massachusetts, United States of America
| | - Robert Huber
- Department of Biological Sciences, JP Scott Center for Neuroscience, Mind, & Behavior, Bowling Green State University, Bowling Green, Ohio, United States of America
| | - Leslie C. Griffith
- Department of Biology, National Center for Behavioral Genomics and Volen Center for Complex Systems, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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140
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Seay DJ, Thummel CS. The circadian clock, light, and cryptochrome regulate feeding and metabolism in Drosophila. J Biol Rhythms 2012; 26:497-506. [PMID: 22215608 DOI: 10.1177/0748730411420080] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Recent studies in mammals have demonstrated a central role for the circadian clock in maintaining metabolic homeostasis. In spite of these advances, however, little is known about how these complex pathways are coordinated. Here, we show that fundamental aspects of the circadian control of metabolism are conserved in the fruit fly Drosophila. We assay feeding behavior and basic metabolite levels in individual flies and show that, like mammals, Drosophila display a rapid increase in circulating sugar following a meal, which is subsequently stored in the form of glycogen. These daily rhythms in carbohydrate levels are disrupted in clock mutants, demonstrating a critical role for the circadian clock in the postprandial response to feeding. We also show that basic metabolite levels are coordinated in a clock-dependent manner and that clock function is required to maintain lipid homeostasis. By examining feeding behavior, we show that flies feed primarily during the first 4 hours of the day and that light suppresses a late day feeding bout through the cryptochrome photoreceptor. These studies demonstrate that central aspects of feeding and metabolism are dependent on the circadian clock in Drosophila. Our work also uncovers novel roles for light and cryptochrome on both feeding behavior and metabolism.
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Affiliation(s)
- Daniel J Seay
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112-5330, USA
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141
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Miyazaki Y, Nisimura T, Numata H. Circannual rhythm in the varied carpet beetle, Anthrenus verbasci. PROGRESS IN BRAIN RESEARCH 2012; 199:439-456. [PMID: 22877680 DOI: 10.1016/b978-0-444-59427-3.00025-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although circannual rhythms controlling different physiological processes and various aspects of behavior have been reported in numerous organisms, our understanding of the underlying biological mechanisms is still quite limited. We examined the mechanisms controlling the circannual pupation rhythm of the varied carpet beetle, Anthrenus verbasci. This rhythm is self-sustainable, exhibits temperature compensation of the periodicity, and is entrainable to environmental changes. In addition, the circannual phase response curves to a photoperiod pulse display Type 0 or Type 1 resetting, depending on the duration of the pulse. Thus, we infer that this rhythm is derived from a self-sustaining biological oscillator with a period of about a year, that is, a circannual clock, analogous to the circadian clock. Further, a circadian clock appears to mediate photoperiodic time measurement for phase resetting of the circannual clock. Based on these results and previous research performed in other organisms, we discuss the general characteristics of the physiological mechanisms underpinning circannual rhythmicity.
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Affiliation(s)
- Yosuke Miyazaki
- Faculty of Clinical Education, Ashiya University, Hyogo, Japan
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142
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Ripperger JA, Albrecht U. The circadian clock component PERIOD2: from molecular to cerebral functions. PROGRESS IN BRAIN RESEARCH 2012; 199:233-245. [PMID: 22877669 DOI: 10.1016/b978-0-444-59427-3.00014-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The circadian clock is based on a molecular oscillator, which simulates the external day within nearly all of a body's cells. This "internalized" day then defines activity and rest phases for the cells and the organism by generating precise rhythms in the metabolism, physiology, and behavior. In its perfect state, this timing system allows for the synchronization of an organism to its environment and this may optimize energy handling and responses to daily recurring challenges. However, nowadays, we believe that desynchronization of an organism due to its lifestyle or problems with its circadian clock not only causes discomfort but also may aggravate conditions such as depression, metabolic syndrome, addiction, or cancer. In this review, we focus on one simple cogwheel of the mammalian circadian clock, the PERIOD2 (PER2) protein. Originally identified as an integral part of the molecular mechanism that yields overt rhythms of about 24h, more recently multiple other functions have been identified. In essence, the PER proteins, in addition to their important function within the molecular oscillator, can be seen not only as integrators on the input side of the circadian clock but also as mediators of clock output. This diversity in their function is possible, because the PER proteins can interact with a multitude of other proteins transferring oscillator timing information to the latter. In this fashion, the circadian clock synchronizes many rhythmic processes.
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Affiliation(s)
- Jürgen A Ripperger
- Department of Biology, Unit of Biochemistry, University of Fribourg, Fribourg, Switzerland.
| | - Urs Albrecht
- Department of Biology, Unit of Biochemistry, University of Fribourg, Fribourg, Switzerland
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143
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Querfurth C, Diernfellner ACR, Gin E, Malzahn E, Höfer T, Brunner M. Circadian conformational change of the Neurospora clock protein FREQUENCY triggered by clustered hyperphosphorylation of a basic domain. Mol Cell 2011; 43:713-22. [PMID: 21884974 DOI: 10.1016/j.molcel.2011.06.033] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 01/31/2011] [Accepted: 06/26/2011] [Indexed: 10/17/2022]
Abstract
In the course of a day, the Neurospora clock protein FREQUENCY (FRQ) is progressively phosphorylated at up to 113 sites and eventually degraded. Phosphorylation and degradation are crucial for circadian time keeping, but it is not known how phosphorylation of a large number of sites correlates with circadian degradation of FRQ. We show that two amphipathic motifs in FRQ interact over a long distance, bringing the positively charged N-terminal portion in spatial proximity to the negatively charged middle and C-terminal portion of FRQ. The interaction is essential for the recruitment of casein kinase 1a (CK1a) into a stable complex with FRQ. FRQ-bound CK1a progressively phosphorylates the positively charged N-terminal domain of FRQ at up to 46 nonconsensus sites, triggering a conformational change, presumably by electrostatic repulsion, that commits the protein for degradation via the PEST1 signal in the negatively charged central portion of FRQ.
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Affiliation(s)
- Christina Querfurth
- University of Heidelberg Biochemistry Center, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
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144
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Itoh TQ, Tanimura T, Matsumoto A. Membrane-bound transporter controls the circadian transcription of clock genes in Drosophila. Genes Cells 2011; 16:1159-67. [PMID: 22077638 DOI: 10.1111/j.1365-2443.2011.01559.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Little is known about molecular mechanisms that control the Drosophila circadian clock beyond the transcriptional-translational feedback regulation of clock genes as an intracellular process. In this study, Early gene at 23 (E23) was identified as a novel clock gene that encodes the membrane-bound ABC transporter that is induced by the molting hormone ecdysone. E23 expresses in pacemaker neurons in fly head, and its knockdown flies lengthened circadian period with an increased expression of the clock gene vrille. E23 and vrille responded to both ecdysone and clock signals, whereas E23 protein specifically suppressed the ecdysone response and is necessary for rhythmicity. Thus, E23 forms its own feedback loop in the ecdysone response to control circadian oscillation through ecdysone-mediated vrille expression. The ecdysone signaling pathway with E23 is essential not only in developmental stage but also for the circadian behavior in adult fly.
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Affiliation(s)
- Taichi Q Itoh
- Graduate School of Systems Life Sciences, Kyushu University, Hakozaki, Fukuoka, Japan
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145
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Reaume CJ, Sokolowski MB. Conservation of gene function in behaviour. Philos Trans R Soc Lond B Biol Sci 2011; 366:2100-10. [PMID: 21690128 DOI: 10.1098/rstb.2011.0028] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Behaviour genetic research has shown that a given gene or gene pathway can influence categorically similar behaviours in different species. Questions about the conservation of gene function in behaviour are increasingly tractable. This is owing to the surge of DNA and 'omics data, bioinformatic tools, as well as advances in technologies for behavioural phenotyping. Here, we discuss how gene function, as a hierarchical biological phenomenon, can be used to examine behavioural homology across species. The question can be addressed independently using different levels of investigation including the DNA sequence, the gene's position in a genetic pathway, spatial-temporal tissue expression and neural circuitry. Selected examples from the literature are used to illustrate this point. We will also discuss how qualitative and quantitative comparisons of the behavioural phenotype, its function and the importance of environmental and social context should be used in cross-species comparisons. We conclude that (i) there are homologous behaviours, (ii) they are hard to define and (iii) neurogenetics and genomics investigations should help in this endeavour.
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Affiliation(s)
- Christopher J Reaume
- Department of Biology, University of Toronto, Mississauga, Ontario, Canada, L5L 1C6
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146
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Depetris-Chauvin A, Berni J, Aranovich EJ, Muraro NI, Beckwith EJ, Ceriani MF. Adult-specific electrical silencing of pacemaker neurons uncouples molecular clock from circadian outputs. Curr Biol 2011; 21:1783-93. [PMID: 22018542 DOI: 10.1016/j.cub.2011.09.027] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 09/09/2011] [Accepted: 09/13/2011] [Indexed: 01/24/2023]
Abstract
BACKGROUND Circadian rhythms regulate physiology and behavior through transcriptional feedback loops of clock genes running within specific pacemaker cells. In Drosophila, molecular oscillations in the small ventral lateral neurons (sLNvs) command rhythmic behavior under free-running conditions releasing the neuropeptide PIGMENT DISPERSING FACTOR (PDF) in a circadian fashion. Electrical activity in the sLNvs is also required for behavioral rhythmicity. Yet, how temporal information is transduced into behavior remains unclear. RESULTS Here we developed a new tool for temporal control of gene expression to obtain adult-restricted electrical silencing of the PDF circuit, which led to reversible behavioral arrhythmicity. Remarkably, PERIOD (PER) oscillations during the silenced phase remained unaltered, indicating that arrhythmicity is a direct consequence of the silenced activity. Accordingly, circadian axonal remodeling and PDF accumulation were severely affected during the silenced phase. CONCLUSIONS Although electrical activity of the sLNvs is not a clock component, it coordinates circuit outputs leading to rhythmic behavior.
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Affiliation(s)
- Ana Depetris-Chauvin
- Laboratorio de Genética del Comportamiento, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas-Buenos Aires, Av. Patricias Argentinas 435, 1405-BWE Buenos Aires, Argentina
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147
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Johnson CH, Stewart PL, Egli M. The cyanobacterial circadian system: from biophysics to bioevolution. Annu Rev Biophys 2011; 40:143-67. [PMID: 21332358 DOI: 10.1146/annurev-biophys-042910-155317] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Recent studies have unveiled the molecular machinery responsible for the biological clock in cyanobacteria and found that it exerts pervasive control over cellular processes including global gene expression. Indeed, the entire chromosome undergoes daily cycles of topology/compaction! The circadian system comprises both a posttranslational oscillator (PTO) and a transcriptional/translational feedback loop (TTFL). The PTO can be reconstituted in vitro with three purified proteins (KaiA, KaiB, and KaiC) and ATP. These are the only circadian proteins for which high-resolution structures are available. Phase in this nanoclockwork has been associated with key phosphorylations of KaiC. Structural considerations illuminate the mechanism by which the KaiABC oscillator ratchets unidirectionally. Models of the complete in vivo system have important implications for our understanding of circadian clocks in higher organisms, including mammals. The conjunction of structural, biophysical, and biochemical approaches to this system has brought our understanding of the molecular mechanisms of biological timekeeping to an unprecedented level.
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148
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Lefta M, Wolff G, Esser KA. Circadian rhythms, the molecular clock, and skeletal muscle. Curr Top Dev Biol 2011; 96:231-71. [PMID: 21621073 DOI: 10.1016/b978-0-12-385940-2.00009-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Almost all organisms ranging from single cell bacteria to humans exhibit a variety of behavioral, physiological, and biochemical rhythms. In mammals, circadian rhythms control the timing of many physiological processes over a 24-h period, including sleep-wake cycles, body temperature, feeding, and hormone production. This body of research has led to defined characteristics of circadian rhythms based on period length, phase, and amplitude. Underlying circadian behaviors is a molecular clock mechanism found in most, if not all, cell types including skeletal muscle. The mammalian molecular clock is a complex of multiple oscillating networks that are regulated through transcriptional mechanisms, timed protein turnover, and input from small molecules. At this time, very little is known about circadian aspects of skeletal muscle function/metabolism but some progress has been made on understanding the molecular clock in skeletal muscle. The goal of this chapter is to provide the basic terminology and concepts of circadian rhythms with a more detailed review of the current state of knowledge of the molecular clock, with reference to what is known in skeletal muscle. Research has demonstrated that the molecular clock is active in skeletal muscles and that the muscle-specific transcription factor, MyoD, is a direct target of the molecular clock. Skeletal muscle of clock-compromised mice, Bmal1(-/-) and Clock(Δ19) mice, are weak and exhibit significant disruptions in expression of many genes required for adult muscle structure and metabolism. We suggest that the interaction between the molecular clock, MyoD, and metabolic factors, such as PGC-1, provide a potential system of feedback loops that may be critical for both maintenance and adaptation of skeletal muscle.
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Affiliation(s)
- Mellani Lefta
- Center for Muscle Biology, Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
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149
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Hut RA, Beersma DGM. Evolution of time-keeping mechanisms: early emergence and adaptation to photoperiod. Philos Trans R Soc Lond B Biol Sci 2011; 366:2141-54. [PMID: 21690131 PMCID: PMC3130368 DOI: 10.1098/rstb.2010.0409] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Virtually all species have developed cellular oscillations and mechanisms that synchronize these cellular oscillations to environmental cycles. Such environmental cycles in biotic (e.g. food availability and predation risk) or abiotic (e.g. temperature and light) factors may occur on a daily, annual or tidal time scale. Internal timing mechanisms may facilitate behavioural or physiological adaptation to such changes in environmental conditions. These timing mechanisms commonly involve an internal molecular oscillator (a 'clock') that is synchronized ('entrained') to the environmental cycle by receptor mechanisms responding to relevant environmental signals ('Zeitgeber', i.e. German for time-giver). To understand the evolution of such timing mechanisms, we have to understand the mechanisms leading to selective advantage. Although major advances have been made in our understanding of the physiological and molecular mechanisms driving internal cycles (proximate questions), studies identifying mechanisms of natural selection on clock systems (ultimate questions) are rather limited. Here, we discuss the selective advantage of a circadian system and how its adaptation to day length variation may have a functional role in optimizing seasonal timing. We discuss various cases where selective advantages of circadian timing mechanisms have been shown and cases where temporarily loss of circadian timing may cause selective advantage. We suggest an explanation for why a circadian timing system has emerged in primitive life forms like cyanobacteria and we evaluate a possible molecular mechanism that enabled these bacteria to adapt to seasonal variation in day length. We further discuss how the role of the circadian system in photoperiodic time measurement may explain differential selection pressures on circadian period when species are exposed to changing climatic conditions (e.g. global warming) or when they expand their geographical range to different latitudes or altitudes.
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Affiliation(s)
- R A Hut
- University of Groningen, Chronobiology Research Unit, Life Science building, Nijenborgh 7, 9747AG Groningen, The Netherlands.
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150
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Jones MA, Harmer S. JMJD5 Functions in concert with TOC1 in the arabidopsis circadian system. PLANT SIGNALING & BEHAVIOR 2011; 6:445-8. [PMID: 21358285 PMCID: PMC3142435 DOI: 10.4161/psb.6.3.14654] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Accepted: 12/28/2010] [Indexed: 05/18/2023]
Abstract
The circadian clock modulates the expression of approximately one-third of Arabidopsis genes and as such plays a central role in the regulation of plant metabolism and responses to the environment. We have recently identified a novel component of the Arabidopsis circadian clock, JMJD5, based on its coexpression with TOC1, an evening-phased component of the molecular oscillator. We now examine the genetic interaction between TOC1 and JMJD5 in greater detail and demonstrate that toc1 is not epistatic to jmjd5, suggesting that these two proteins act in closely linked but parallel genetic pathways. The human homolog of JMJD5, KDM8, has been shown to have histone demethylation activity and is able to partially rescue the plant jmjd5 circadian phenotype. The potential role of JMJD5 as a histone demethylase within the circadian clock is discussed.
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Affiliation(s)
- Matthew A Jones
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California, USA
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