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Seinkmane E, Edmondson A, Peak-Chew SY, Zeng A, Rzechorzek NM, James NR, West J, Munns J, Wong DC, Beale AD, O'Neill JS. Circadian regulation of macromolecular complex turnover and proteome renewal. EMBO J 2024; 43:2813-2833. [PMID: 38778155 PMCID: PMC11217436 DOI: 10.1038/s44318-024-00121-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/04/2024] [Accepted: 04/15/2024] [Indexed: 05/25/2024] Open
Abstract
Although costly to maintain, protein homeostasis is indispensable for normal cellular function and long-term health. In mammalian cells and tissues, daily variation in global protein synthesis has been observed, but its utility and consequences for proteome integrity are not fully understood. Using several different pulse-labelling strategies, here we gain direct insight into the relationship between protein synthesis and abundance proteome-wide. We show that protein degradation varies in-phase with protein synthesis, facilitating rhythms in turnover rather than abundance. This results in daily consolidation of proteome renewal whilst minimising changes in composition. Coupled rhythms in synthesis and turnover are especially salient to the assembly of macromolecular protein complexes, particularly the ribosome, the most abundant species of complex in the cell. Daily turnover and proteasomal degradation rhythms render cells and mice more sensitive to proteotoxic stress at specific times of day, potentially contributing to daily rhythms in the efficacy of proteasomal inhibitors against cancer. Our findings suggest that circadian rhythms function to minimise the bioenergetic cost of protein homeostasis through temporal consolidation of protein turnover.
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Affiliation(s)
- Estere Seinkmane
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Anna Edmondson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Sew Y Peak-Chew
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Aiwei Zeng
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Nina M Rzechorzek
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Nathan R James
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - James West
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jack Munns
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - David Cs Wong
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Andrew D Beale
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - John S O'Neill
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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2
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Duong HA, Baba K, DeBruyne JP, Davidson AJ, Ehlen C, Powell M, Tosini G. Environmental circadian disruption re-writes liver circadian proteomes. Nat Commun 2024; 15:5537. [PMID: 38956413 PMCID: PMC11220080 DOI: 10.1038/s41467-024-49852-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024] Open
Abstract
Circadian gene expression is fundamental to the establishment and functions of the circadian clock, a cell-autonomous and evolutionary-conserved timing system. Yet, how it is affected by environmental-circadian disruption (ECD) such as shiftwork and jetlag are ill-defined. Here, we provided a comprehensive and comparative description of male liver circadian gene expression, encompassing transcriptomes, whole-cell proteomes and nuclear proteomes, under normal and after ECD conditions. Under both conditions, post-translation, rather than transcription, is the dominant contributor to circadian functional outputs. After ECD, post-transcriptional and post-translational processes are the major contributors to whole-cell or nuclear circadian proteome, respectively. Furthermore, ECD re-writes the rhythmicity of 64% transcriptome, 98% whole-cell proteome and 95% nuclear proteome. The re-writing, which is associated with changes of circadian regulatory cis-elements, RNA-processing and protein localization, diminishes circadian regulation of fat and carbohydrate metabolism and persists after one week of ECD-recovery.
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Affiliation(s)
- Hao A Duong
- Department of Pharmacology and Toxicology, Morehouse School of Medicine, Atlanta, GA, 30310, USA.
- Department of Neurobiology, Morehouse School of Medicine, Atlanta, GA, 30310, USA.
| | - Kenkichi Baba
- Department of Pharmacology and Toxicology, Morehouse School of Medicine, Atlanta, GA, 30310, USA
- Department of Neurobiology, Morehouse School of Medicine, Atlanta, GA, 30310, USA
| | - Jason P DeBruyne
- Department of Pharmacology and Toxicology, Morehouse School of Medicine, Atlanta, GA, 30310, USA
- Department of Neurobiology, Morehouse School of Medicine, Atlanta, GA, 30310, USA
| | - Alec J Davidson
- Department of Neurobiology, Morehouse School of Medicine, Atlanta, GA, 30310, USA
| | - Christopher Ehlen
- Department of Neurobiology, Morehouse School of Medicine, Atlanta, GA, 30310, USA
| | - Michael Powell
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, Atlanta, GA, 30310, USA
| | - Gianluca Tosini
- Department of Pharmacology and Toxicology, Morehouse School of Medicine, Atlanta, GA, 30310, USA
- Department of Neurobiology, Morehouse School of Medicine, Atlanta, GA, 30310, USA
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3
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Tsai SY. Lost in translation: challenges of current pharmacotherapy for sarcopenia. Trends Mol Med 2024:S1471-4914(24)00138-2. [PMID: 38880726 DOI: 10.1016/j.molmed.2024.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/21/2024] [Accepted: 05/28/2024] [Indexed: 06/18/2024]
Abstract
A healthy lifespan relies on independent living, in which active skeletal muscle is a critical element. The cost of not recognizing and acting earlier on unhealthy or aging muscle could be detrimental, since muscular weakness is inversely associated with all-cause mortality. Sarcopenia is characterized by a decline in skeletal muscle mass and strength and is associated with aging. Exercise is the only effective therapy to delay sarcopenia development and improve muscle health in older adults. Although numerous interventions have been proposed to reduce sarcopenia, none has yet succeeded in clinical trials. This review evaluates the biological gap between recent clinical trials targeting sarcopenia and the preclinical studies on which they are based, and suggests an alternative approach to bridge the discrepancy.
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Affiliation(s)
- Shih-Yin Tsai
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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4
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Nadimpalli HP, Katsioudi G, Arpa ES, Chikhaoui L, Arpat AB, Liechti A, Palais G, Tessmer C, Hofmann I, Galy B, Gatfield D. Diurnal control of iron responsive element containing mRNAs through iron regulatory proteins IRP1 and IRP2 is mediated by feeding rhythms. Genome Biol 2024; 25:128. [PMID: 38773499 PMCID: PMC11106963 DOI: 10.1186/s13059-024-03270-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/09/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Cellular iron homeostasis is regulated by iron regulatory proteins (IRP1 and IRP2) that sense iron levels (and other metabolic cues) and modulate mRNA translation or stability via interaction with iron regulatory elements (IREs). IRP2 is viewed as the primary regulator in the liver, yet our previous datasets showing diurnal rhythms for certain IRE-containing mRNAs suggest a nuanced temporal control mechanism. The purpose of this study is to gain insights into the daily regulatory dynamics across IRE-bearing mRNAs, specific IRP involvement, and underlying systemic and cellular rhythmicity cues in mouse liver. RESULTS We uncover high-amplitude diurnal oscillations in the regulation of key IRE-containing transcripts in the liver, compatible with maximal IRP activity at the onset of the dark phase. Although IRP2 protein levels also exhibit some diurnal variations and peak at the light-dark transition, ribosome profiling in IRP2-deficient mice reveals that maximal repression of target mRNAs at this timepoint still occurs. We further find that diurnal regulation of IRE-containing mRNAs can continue in the absence of a functional circadian clock as long as feeding is rhythmic. CONCLUSIONS Our findings suggest temporally controlled redundancy in IRP activities, with IRP2 mediating regulation of IRE-containing transcripts in the light phase and redundancy, conceivably with IRP1, at dark onset. Moreover, we highlight the significance of feeding-associated signals in driving rhythmicity. Our work highlights the dynamic nature and regulatory complexity in a metabolic pathway that had previously been considered well-understood.
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Affiliation(s)
| | - Georgia Katsioudi
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Enes Salih Arpa
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Lies Chikhaoui
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Alaaddin Bulak Arpat
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Angelica Liechti
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Gaël Palais
- German Cancer Research Center (DKFZ), Division of Virus-Associated Carcinogenesis, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Claudia Tessmer
- German Cancer Research Center (DKFZ), Core Facility Antibodies, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Ilse Hofmann
- German Cancer Research Center (DKFZ), Core Facility Antibodies, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Bruno Galy
- German Cancer Research Center (DKFZ), Division of Virus-Associated Carcinogenesis, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland.
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5
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Bass J. Interorgan rhythmicity as a feature of healthful metabolism. Cell Metab 2024; 36:655-669. [PMID: 38335957 PMCID: PMC10990795 DOI: 10.1016/j.cmet.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 02/12/2024]
Abstract
The finding that animals with circadian gene mutations exhibit diet-induced obesity and metabolic syndrome with hypoinsulinemia revealed a distinct role for the clock in the brain and peripheral tissues. Obesogenic diets disrupt rhythmic sleep/wake patterns, feeding behavior, and transcriptional networks, showing that metabolic signals reciprocally control the clock. Providing access to high-fat diet only during the sleep phase (light period) in mice accelerates weight gain, whereas isocaloric time-restricted feeding during the active period enhances energy expenditure due to circadian induction of adipose thermogenesis. This perspective focuses on advances and unanswered questions in understanding the interorgan circadian control of healthful metabolism.
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Affiliation(s)
- Joseph Bass
- Department of Medicine, Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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6
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Llewellyn J, Hubbard SJ, Swift J. Translation is an emerging constraint on protein homeostasis in ageing. Trends Cell Biol 2024:S0962-8924(24)00024-2. [PMID: 38423854 DOI: 10.1016/j.tcb.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/23/2024] [Accepted: 02/01/2024] [Indexed: 03/02/2024]
Abstract
Proteins are molecular machines that provide structure and perform vital transport, signalling and enzymatic roles. Proteins expressed by cells require tight regulation of their concentration, folding, localisation, and modifications; however, this state of protein homeostasis is continuously perturbed by tissue-level stresses. While cells in healthy tissues are able to buffer against these perturbations, for example, by expression of chaperone proteins, protein homeostasis is lost in ageing, and can lead to protein aggregation characteristic of protein folding diseases. Here, we review reports of a progressive disconnect between transcriptomic and proteomic regulation during cellular ageing. We discuss how age-associated changes to cellular responses to specific stressors in the tissue microenvironment are exacerbated by loss of ribosomal proteins, ribosomal pausing, and mistranslation.
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Affiliation(s)
- Jack Llewellyn
- Wellcome Centre for Cell-Matrix Research, Oxford Road, Manchester, M13 9PT, UK; Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PT, UK
| | - Simon J Hubbard
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PT, UK.
| | - Joe Swift
- Wellcome Centre for Cell-Matrix Research, Oxford Road, Manchester, M13 9PT, UK; Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PT, UK.
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7
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Liu X, Cai YD, Chiu JC. Regulation of protein O-GlcNAcylation by circadian, metabolic, and cellular signals. J Biol Chem 2024; 300:105616. [PMID: 38159854 PMCID: PMC10810748 DOI: 10.1016/j.jbc.2023.105616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024] Open
Abstract
O-linked β-N-acetylglucosamine (O-GlcNAcylation) is a dynamic post-translational modification that regulates thousands of proteins and almost all cellular processes. Aberrant O-GlcNAcylation has been associated with numerous diseases, including cancer, neurodegenerative diseases, cardiovascular diseases, and type 2 diabetes. O-GlcNAcylation is highly nutrient-sensitive since it is dependent on UDP-GlcNAc, the end product of the hexosamine biosynthetic pathway (HBP). We previously observed daily rhythmicity of protein O-GlcNAcylation in a Drosophila model that is sensitive to the timing of food consumption. We showed that the circadian clock is pivotal in regulating daily O-GlcNAcylation rhythms given its control of the feeding-fasting cycle and hence nutrient availability. Interestingly, we reported that the circadian clock also modulates daily O-GlcNAcylation rhythm by regulating molecular mechanisms beyond the regulation of food consumption time. A large body of work now indicates that O-GlcNAcylation is likely a generalized cellular status effector as it responds to various cellular signals and conditions, such as ER stress, apoptosis, and infection. In this review, we summarize the metabolic regulation of protein O-GlcNAcylation through nutrient availability, HBP enzymes, and O-GlcNAc processing enzymes. We discuss the emerging roles of circadian clocks in regulating daily O-GlcNAcylation rhythm. Finally, we provide an overview of other cellular signals or conditions that impact O-GlcNAcylation. Many of these cellular pathways are themselves regulated by the clock and/or metabolism. Our review highlights the importance of maintaining optimal O-GlcNAc rhythm by restricting eating activity to the active period under physiological conditions and provides insights into potential therapeutic targets of O-GlcNAc homeostasis under pathological conditions.
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Affiliation(s)
- Xianhui Liu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California, USA
| | - Yao D Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, California, USA.
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8
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Chaloupsky P, Kolackova M, Dobesova M, Pencik O, Tarbajova V, Capal P, Svec P, Ridoskova A, Bytesnikova Z, Pelcova P, Adam V, Huska D. Mechanistic transcriptome comprehension of Chlamydomonas reinhardtii subjected to black phosphorus. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 270:115823. [PMID: 38176180 DOI: 10.1016/j.ecoenv.2023.115823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 12/08/2023] [Accepted: 12/10/2023] [Indexed: 01/06/2024]
Abstract
Two-dimensional materials have recently gained significant awareness. A representative of such materials, black phosphorous (BP), earned attention based on its comprehensive application potential. The presented study focuses on the mode of cellular response underlying the BP interaction with Chlamydomonas reinhardtii as an algal model organism. We observed noticeable ROS formation and changes in outer cellular topology after 72 h of incubation at 5 mg/L BP. Transcriptome profiling was employed to examine C. reinhardtii response after exposure to 25 mg/L BP for a deeper understanding of the associated processes. The RNA sequencing has revealed a comprehensive response with abundant transcript downregulation. The mode of action was attributed to cell wall disruption, ROS elevation, and chloroplast disturbance. Besides many other dysregulated genes, the cell response involved the downregulation of GH9 and gametolysin within a cell wall, pointing to a shift to discrete manipulation with resources. The response also included altered expression of the PRDA1 gene associated with redox governance in chloroplasts implying ROS disharmony. Altered expression of the Cre-miR906-3p, Cre-miR910, and Cre-miR914 pointed to those as potential markers in stress response studies.
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Affiliation(s)
- Pavel Chaloupsky
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Martina Kolackova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Marketa Dobesova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Ondrej Pencik
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Vladimira Tarbajova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Petr Capal
- Institute of Experimental Botany, Centre of the Region Hana for Biotechnological and Agricultural Research, Slechtitelu 241/27, 783 71 Olomouc, Czech Republic
| | - Pavel Svec
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Andrea Ridoskova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Zuzana Bytesnikova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Pavlina Pelcova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Dalibor Huska
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic.
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9
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Yurdakul E, Barlas Y, Ulgen KO. Circadian clock crosstalks with autism. Brain Behav 2023; 13:e3273. [PMID: 37807632 PMCID: PMC10726833 DOI: 10.1002/brb3.3273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/10/2023] [Accepted: 09/24/2023] [Indexed: 10/10/2023] Open
Abstract
BACKGROUND The mechanism underlying autism spectrum disorder (ASD) remains incompletely understood, but researchers have identified over a thousand genes involved in complex interactions within the brain, nervous, and immune systems, particularly during the mechanism of brain development. Various contributory environmental effects including circadian rhythm have also been studied in ASD. Thus, capturing the global picture of the ASD-clock network in combined form is critical. METHODS We reconstructed the protein-protein interaction network of ASD and circadian rhythm to understand the connection between autism and the circadian clock. A graph theoretical study is undertaken to evaluate whether the network attributes are biologically realistic. The gene ontology enrichment analyses provide information about the most important biological processes. RESULTS This study takes a fresh look at metabolic mechanisms and the identification of potential key proteins/pathways (ribosome biogenesis, oxidative stress, insulin/IGF pathway, Wnt pathway, and mTOR pathway), as well as the effects of specific conditions (such as maternal stress or disruption of circadian rhythm) on the development of ASD due to environmental factors. CONCLUSION Understanding the relationship between circadian rhythm and ASD provides insight into the involvement of these essential pathways in the pathogenesis/etiology of ASD, as well as potential early intervention options and chronotherapeutic strategies for treating or preventing the neurodevelopmental disorder.
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Affiliation(s)
- Ekin Yurdakul
- Department of Chemical EngineeringBogazici University, Biosystems Engineering LaboratoryIstanbulTurkey
| | - Yaman Barlas
- Department of Industrial EngineeringBogazici University, Socio‐Economic System Dynamics Research Group (SESDYN)IstanbulTurkey
| | - Kutlu O. Ulgen
- Department of Chemical EngineeringBogazici University, Biosystems Engineering LaboratoryIstanbulTurkey
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10
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Saba JA, Huang Z, Schole KL, Ye X, Bhatt SD, Li Y, Timp W, Cheng J, Green R. LARP1 senses free ribosomes to coordinate supply and demand of ribosomal proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.01.565189. [PMID: 37961604 PMCID: PMC10635049 DOI: 10.1101/2023.11.01.565189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Terminal oligopyrimidine motif-containing mRNAs (TOPs) encode all ribosomal proteins in mammals and are regulated to tune ribosome synthesis to cell state. Previous studies implicate LARP1 in 40S- or 80S-ribosome complexes that repress and stabilize TOPs. However, a mechanistic understanding of how LARP1 and TOPs interact with these complexes to coordinate TOP outcomes is lacking. Here, we show that LARP1 senses the cellular supply of ribosomes by directly binding non-translating ribosomal subunits. Cryo-EM structures reveal a previously uncharacterized domain of LARP1 bound to and occluding the 40S mRNA channel. Free cytosolic ribosomes induce sequestration of TOPs in repressed 80S-LARP1-TOP complexes independent of alterations in mTOR signaling. Together, this work demonstrates a general ribosome-sensing function of LARP1 that allows it to tune ribosome protein synthesis to cellular demand.
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Affiliation(s)
- James A. Saba
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- These authors contributed equally
| | - Zixuan Huang
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
- These authors contributed equally
| | - Kate L. Schole
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xianwen Ye
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
| | - Shrey D. Bhatt
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yi Li
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jingdong Cheng
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Dong’an Road 131, 200032, Shanghai, China
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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11
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Smith JG, Molendijk J, Blazev R, Chen WH, Zhang Q, Litwin C, Zinna VM, Welz PS, Benitah SA, Greco CM, Sassone-Corsi P, Muñoz-Cánoves P, Parker BL, Koronowski KB. Impact of Bmal1 Rescue and Time-Restricted Feeding on Liver and Muscle Proteomes During the Active Phase in Mice. Mol Cell Proteomics 2023; 22:100655. [PMID: 37793502 PMCID: PMC10651687 DOI: 10.1016/j.mcpro.2023.100655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/01/2023] [Accepted: 09/28/2023] [Indexed: 10/06/2023] Open
Abstract
Molecular clocks and daily feeding cycles support metabolism in peripheral tissues. Although the roles of local clocks and feeding are well defined at the transcriptional level, their impact on governing protein abundance in peripheral tissues is unclear. Here, we determine the relative contributions of local molecular clocks and daily feeding cycles on liver and muscle proteomes during the active phase in mice. LC-MS/MS was performed on liver and gastrocnemius muscle harvested 4 h into the dark phase from WT, Bmal1 KO, and dual liver- and muscle-Bmal1-rescued mice under either ad libitum feeding or time-restricted feeding during the dark phase. Feeding-fasting cycles had only minimal effects on levels of liver proteins and few, if any, on the muscle proteome. In contrast, Bmal1 KO altered the abundance of 674 proteins in liver and 80 proteins in muscle. Local rescue of liver and muscle Bmal1 restored ∼50% of proteins in liver and ∼25% in muscle. These included proteins involved in fatty acid oxidation in liver and carbohydrate metabolism in muscle. For liver, proteins involved in de novo lipogenesis were largely dependent on Bmal1 function in other tissues (i.e., the wider clock system). Proteins regulated by BMAL1 in liver and muscle were enriched for secreted proteins. We found that the abundance of fibroblast growth factor 1, a liver secreted protein, requires BMAL1 and that autocrine fibroblast growth factor 1 signaling modulates mitochondrial respiration in hepatocytes. In liver and muscle, BMAL1 is a more potent regulator of dark phase proteomes than daily feeding cycles, highlighting the need to assess protein levels in addition to mRNA when investigating clock mechanisms. The proteome is more extensively regulated by BMAL1 in liver than in muscle, and many metabolic pathways in peripheral tissues are reliant on the function of the clock system as a whole.
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Affiliation(s)
- Jacob G Smith
- Department of Medical and Life Sciences (MELIS), Pompeu Fabra University (UPF), Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain
| | - Jeffrey Molendijk
- Department of Anatomy and Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ronnie Blazev
- Department of Anatomy and Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Wan Hsi Chen
- Department of Radiation Oncology, Mays Cancer Center at UT Health San Antonio MD Anderson, Joe R. and Teresa Lozano Long School of Medicine, San Antonio, Texas, USA; Barshop Institute for Longevity and Aging Studies at UT Health San Antonio, San Antonio, Texas, USA
| | - Qing Zhang
- Department of Biochemistry & Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Christopher Litwin
- Department of Biochemistry & Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Valentina M Zinna
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Patrick-Simon Welz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Hospital del Mar Research Institute Barcelona, Cancer Research Program, Barcelona Biomedical Research Park (PRBB), Barcelona, Spain
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Carolina M Greco
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, University of California, Irvine, California, USA
| | - Pura Muñoz-Cánoves
- Department of Medical and Life Sciences (MELIS), Pompeu Fabra University (UPF), Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain; Altos Labs, Inc, San Diego Institute of Science, San Diego, California, USA
| | - Benjamin L Parker
- Department of Anatomy and Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Kevin B Koronowski
- Barshop Institute for Longevity and Aging Studies at UT Health San Antonio, San Antonio, Texas, USA; Department of Biochemistry & Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA.
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12
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Millius A, Yamada RG, Fujishima H, Maeda K, Standley DM, Sumiyama K, Perrin D, Ueda HR. Circadian ribosome profiling reveals a role for the Period2 upstream open reading frame in sleep. Proc Natl Acad Sci U S A 2023; 120:e2214636120. [PMID: 37769257 PMCID: PMC10556633 DOI: 10.1073/pnas.2214636120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 08/29/2023] [Indexed: 09/30/2023] Open
Abstract
Many mammalian proteins have circadian cycles of production and degradation, and many of these rhythms are altered posttranscriptionally. We used ribosome profiling to examine posttranscriptional control of circadian rhythms by quantifying RNA translation in the liver over a 24-h period from circadian-entrained mice transferred to constant darkness conditions and by comparing ribosome binding levels to protein levels for 16 circadian proteins. We observed large differences in ribosome binding levels compared to protein levels, and we observed delays between peak ribosome binding and peak protein abundance. We found extensive binding of ribosomes to upstream open reading frames (uORFs) in circadian mRNAs, including the core clock gene Period2 (Per2). An increase in the number of uORFs in the 5'UTR was associated with a decrease in ribosome binding in the main coding sequence and a reduction in expression of synthetic reporter constructs. Mutation of the Per2 uORF increased luciferase and fluorescence reporter expression in 3T3 cells and increased luciferase expression in PER2:LUC MEF cells. Mutation of the Per2 uORF in mice increased Per2 mRNA expression, enhanced ribosome binding on Per2, and reduced total sleep time compared to that in wild-type mice. These results suggest that uORFs affect mRNA posttranscriptionally, which can impact physiological rhythms and sleep.
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Affiliation(s)
- Arthur Millius
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
- Laboratory for Host Defense, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
- Laboratory for Systems Immunology, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
| | - Rikuhiro G. Yamada
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
| | - Hiroshi Fujishima
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
| | - Kazuhiko Maeda
- Laboratory for Host Defense, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
| | - Daron M. Standley
- Laboratory for Systems Immunology, Immunology Frontier Research Center, Suita, Osaka565-0871, Japan
| | - Kenta Sumiyama
- Laboratory of Animal Genetics and Breeding, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya464-8601, Japan
| | - Dimitri Perrin
- School of Computer Science, Queensland University of Technology, BrisbaneQLD 4000, Australia
- Centre for Data Science, Queensland University of Technology, BrisbaneQLD 4000, Australia
| | - Hiroki R. Ueda
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka565-0871, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
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13
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Lakin-Thomas P. The Case for the Target of Rapamycin Pathway as a Candidate Circadian Oscillator. Int J Mol Sci 2023; 24:13307. [PMID: 37686112 PMCID: PMC10488232 DOI: 10.3390/ijms241713307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
The molecular mechanisms that drive circadian (24 h) rhythmicity have been investigated for many decades, but we still do not have a complete picture of eukaryotic circadian systems. Although the transcription/translation feedback loop (TTFL) model has been the primary focus of research, there are many examples of circadian rhythms that persist when TTFLs are not functioning, and we lack any good candidates for the non-TTFL oscillators driving these rhythms. In this hypothesis-driven review, the author brings together several lines of evidence pointing towards the Target of Rapamycin (TOR) signalling pathway as a good candidate for a non-TTFL oscillator. TOR is a ubiquitous regulator of metabolism in eukaryotes and recent focus in circadian research on connections between metabolism and rhythms makes TOR an attractive candidate oscillator. In this paper, the evidence for a role for TOR in regulating rhythmicity is reviewed, and the advantages of TOR as a potential oscillator are discussed. Evidence for extensive feedback regulation of TOR provides potential mechanisms for a TOR-driven oscillator. Comparison with ultradian yeast metabolic cycles provides an example of a potential TOR-driven self-sustained oscillation. Unanswered questions and problems to be addressed by future research are discussed.
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14
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van den Berg L, Kokki K, Wowro SJ, Petricek KM, Deniz O, Stegmann CA, Robciuc M, Teesalu M, Melvin RG, Nieminen AI, Schupp M, Hietakangas V. Sugar-responsive inhibition of Myc-dependent ribosome biogenesis by Clockwork orange. Cell Rep 2023; 42:112739. [PMID: 37405919 DOI: 10.1016/j.celrep.2023.112739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 05/25/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
The ability to feed on a sugar-containing diet depends on a gene regulatory network controlled by the intracellular sugar sensor Mondo/ChREBP-Mlx, which remains insufficiently characterized. Here, we present a genome-wide temporal clustering of sugar-responsive gene expression in Drosophila larvae. We identify gene expression programs responding to sugar feeding, including downregulation of ribosome biogenesis genes, known targets of Myc. Clockwork orange (CWO), a component of the circadian clock, is found to be a mediator of this repressive response and to be necessary for survival on a high-sugar diet. CWO expression is directly activated by Mondo-Mlx, and it counteracts Myc through repression of its gene expression and through binding to overlapping genomic regions. CWO mouse ortholog BHLHE41 has a conserved role in repressing ribosome biogenesis genes in primary hepatocytes. Collectively, our data uncover a cross-talk between conserved gene regulatory circuits balancing the activities of anabolic pathways to maintain homeostasis during sugar feeding.
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Affiliation(s)
- Linda van den Berg
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Krista Kokki
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Sylvia J Wowro
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pharmacology, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, 10117 Berlin, Germany
| | - Konstantin M Petricek
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pharmacology, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, 10117 Berlin, Germany
| | - Onur Deniz
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Catrin A Stegmann
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pharmacology, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, 10117 Berlin, Germany
| | - Marius Robciuc
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Mari Teesalu
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Richard G Melvin
- School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3083, Australia
| | - Anni I Nieminen
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland
| | - Michael Schupp
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pharmacology, Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, 10117 Berlin, Germany
| | - Ville Hietakangas
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00790 Helsinki, Finland.
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15
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Fame RM, Kalugin PN, Petrova B, Xu H, Soden PA, Shipley FB, Dani N, Grant B, Pragana A, Head JP, Gupta S, Shannon ML, Chifamba FF, Hawks-Mayer H, Vernon A, Gao F, Zhang Y, Holtzman MJ, Heiman M, Andermann ML, Kanarek N, Lipton JO, Lehtinen MK. Defining diurnal fluctuations in mouse choroid plexus and CSF at high molecular, spatial, and temporal resolution. Nat Commun 2023; 14:3720. [PMID: 37349305 PMCID: PMC10287727 DOI: 10.1038/s41467-023-39326-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 06/07/2023] [Indexed: 06/24/2023] Open
Abstract
Transmission and secretion of signals via the choroid plexus (ChP) brain barrier can modulate brain states via regulation of cerebrospinal fluid (CSF) composition. Here, we developed a platform to analyze diurnal variations in male mouse ChP and CSF. Ribosome profiling of ChP epithelial cells revealed diurnal translatome differences in metabolic machinery, secreted proteins, and barrier components. Using ChP and CSF metabolomics and blood-CSF barrier analyses, we observed diurnal changes in metabolites and cellular junctions. We then focused on transthyretin (TTR), a diurnally regulated thyroid hormone chaperone secreted by the ChP. Diurnal variation in ChP TTR depended on Bmal1 clock gene expression. We achieved real-time tracking of CSF-TTR in awake TtrmNeonGreen mice via multi-day intracerebroventricular fiber photometry. Diurnal changes in ChP and CSF TTR levels correlated with CSF thyroid hormone levels. These datasets highlight an integrated platform for investigating diurnal control of brain states by the ChP and CSF.
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Affiliation(s)
- Ryann M Fame
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Neurosurgery, Stanford University, Stanford, CA, 94305, USA
| | - Peter N Kalugin
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Graduate Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
- Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA, 02115, USA
| | - Boryana Petrova
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Huixin Xu
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Paul A Soden
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Frederick B Shipley
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Graduate Program in Biophysics, Harvard University, Cambridge, MA, 02138, USA
| | - Neil Dani
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Bradford Grant
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Aja Pragana
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Joshua P Head
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Suhasini Gupta
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Morgan L Shannon
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Fortunate F Chifamba
- Department of Neurology and the F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, 02115, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Hannah Hawks-Mayer
- Department of Neurology and the F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, 02115, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Amanda Vernon
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Fan Gao
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Lyterian Therapeutics, South San Francisco, 94080, CA, USA
| | - Yong Zhang
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University, St. Louis, MO, 63110, USA
| | - Michael J Holtzman
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University, St. Louis, MO, 63110, USA
| | - Myriam Heiman
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mark L Andermann
- Graduate Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
- Graduate Program in Biophysics, Harvard University, Cambridge, MA, 02138, USA
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Naama Kanarek
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan O Lipton
- Department of Neurology and the F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, 02115, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Maria K Lehtinen
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Graduate Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA.
- Graduate Program in Biophysics, Harvard University, Cambridge, MA, 02138, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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16
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Weger M, Weger BD, Gachon F. Understanding circadian dynamics: current progress and future directions for chronobiology in drug discovery. Expert Opin Drug Discov 2023. [PMID: 37300813 DOI: 10.1080/17460441.2023.2224554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/08/2023] [Indexed: 06/12/2023]
Abstract
INTRODUCTION Most mammalian physiology is orchestrated by the circadian clock, including drug transport and metabolism. As a result, efficacy and toxicity of many drugs are influenced by the timing of their administration, which has led to the establishment of the field of chronopharmacology. AREAS COVERED In this review, the authors provide an overview of the current knowledge about the time-of-day dependent aspects of drug metabolism and the importance of chronopharmacological strategies for drug development. They also discuss the factors influencing rhythmic drug pharmacokinetic including sex, metabolic diseases, feeding rhythms, and microbiota, that are often overlooked in the context of chronopharmacology. This article summarizes the involved molecular mechanisms and functions and explains why these parameters should be considered in the process of drug discovery. EXPERT OPINION Although chronomodulated treatments have shown promising results, particularly for cancer, the practice is still underdeveloped due to the associated high cost and time investments. However, implementing this strategy at the preclinical stage could offer a new opportunity to translate preclinical discoveries into successful clinical treatments.
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Affiliation(s)
- Meltem Weger
- Institute for Molecular Bioscience, The University of Queensland, QLD, Australia
| | - Benjamin D Weger
- Institute for Molecular Bioscience, The University of Queensland, QLD, Australia
| | - Frédéric Gachon
- Institute for Molecular Bioscience, The University of Queensland, QLD, Australia
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17
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Wong KC, Jayapalan JJ, Subramanian P, Ismail MN, Abdul-Rahman PS. Label-free quantitative mass spectrometry analysis of the circadian proteome of Drosophila melanogaster lethal giant larvae mutants reveals potential therapeutic effects of melatonin. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 113:e22008. [PMID: 36915983 DOI: 10.1002/arch.22008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/10/2023] [Accepted: 02/22/2023] [Indexed: 05/16/2023]
Abstract
Mutation in the Drosophila melanogaster lethal giant larvae (lgl), a tumor suppressor gene with a well-established role in cellular polarity, is known to results in massive cellular proliferation and neoplastic outgrowths. Although the tumorigenic properties of lgl mutant have been previously studied, however, little is known about its consequences on the proteome. In this study, mass spectrometry-based label-free quantitative proteomics was employed to investigate the changes in the head and intestinal tissues proteins of Drosophila melanogaster, due to lgl mutation and following treatment with melatonin. Additionally, to uncover the time-influenced variations in the proteome during tumorigenesis and melatonin treatment, the rhythmic expression of proteins was also investigated at 6-h intervals within 24-h clock. Together, the present study has identified 434 proteins of altered expressions (p < 0.05 and fold change ±1.5) in the tissues of flies in response to lgl mutation as well as posttreatment with melatonin. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially expressed proteins revealed that lgl mutation had significantly affected the biological functions, including metabolism, and protein synthesis and degradation, in flies' tissues. Besides, melatonin had beneficially mitigated the deleterious effects of lgl mutation by reversing the alterations in protein expression closer to baseline levels. Further, changes in protein expression in the tissues due to lgl mutation and melatonin treatment were found rhythmically orchestrated. Together, these findings provide novel insight into the pathways involved in lgl-induced tumorigenesis as well as demonstrated the efficacy of melatonin as a potential anticancer agent. Data are available via ProteomeXchange with identifier PXD033191.
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Affiliation(s)
- Kar-Cheng Wong
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Jaime J Jayapalan
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
- Universiti Malaya Centre for Proteomics Research (UMCPR), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Perumal Subramanian
- Department of Biochemistry and Biotechnology, Annamalai University, Chidambaram, Tamil Nadu, India
| | - Mohd Nazri Ismail
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| | - Puteri S Abdul-Rahman
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
- Universiti Malaya Centre for Proteomics Research (UMCPR), Universiti Malaya, Kuala Lumpur, Malaysia
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18
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Bowazolo C, Morse D. Insights into daily metabolic changes of the dinoflagellate Lingulodinium from ribosome profiling. Cell Cycle 2023; 22:1343-1352. [PMID: 37125841 PMCID: PMC10228409 DOI: 10.1080/15384101.2023.2206771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 05/02/2023] Open
Abstract
The dinoflagellate Lingulodinium specializes its metabolism to perform different tasks better at specific times of day. For example, cells are specialized for photosynthesis during the day and bioluminescence and cell division at night. These rhythms are circadian as they are controlled by an endogenous circadian clock whose mechanism is currently unknown. Despite this, the metabolic rhythms follow coordinated changes in gene expression that occur at a translational level. These changes are revealed by ribosome profiling, a surrogate measure of protein synthesis rates in vivo. Lingulodinium regulates the synthesis rate of over three thousand transcripts. Peak synthesis rates for the different transcripts are clustered around three different times over a light/dark cycle. Furthermore, transcripts involved in the same metabolic process are coordinately regulated. We review the basic principles underlying the correlation of coordinated translation of cell metabolic pathway enzymes with known circadian rhythms, and offer examples where previously unsuspected rhythms are suggested by synchronized changes in gene expression.
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Affiliation(s)
- Carl Bowazolo
- Institut de Recherche en biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
| | - David Morse
- Institut de Recherche en biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
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19
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Delbès AS, Quiñones M, Gobet C, Castel J, Denis RGP, Berthelet J, Weger BD, Challet E, Charpagne A, Metairon S, Piccand J, Kraus M, Rohde BH, Bial J, Wilson EM, Vedin LL, Minniti ME, Pedrelli M, Parini P, Gachon F, Luquet S. Mice with humanized livers reveal the role of hepatocyte clocks in rhythmic behavior. SCIENCE ADVANCES 2023; 9:eadf2982. [PMID: 37196091 DOI: 10.1126/sciadv.adf2982] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 04/13/2023] [Indexed: 05/19/2023]
Abstract
The synchronization of circadian clock depends on a central pacemaker located in the suprachiasmatic nuclei. However, the potential feedback of peripheral signals on the central clock remains poorly characterized. To explore whether peripheral organ circadian clocks may affect the central pacemaker, we used a chimeric model in which mouse hepatocytes were replaced by human hepatocytes. Liver humanization led to reprogrammed diurnal gene expression and advanced the phase of the liver circadian clock that extended to muscle and the entire rhythmic physiology. Similar to clock-deficient mice, liver-humanized mice shifted their rhythmic physiology more rapidly to the light phase under day feeding. Our results indicate that hepatocyte clocks can affect the central pacemaker and offer potential perspectives to apprehend pathologies associated with altered circadian physiology.
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Affiliation(s)
- Anne-Sophie Delbès
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, Paris, France
| | - Mar Quiñones
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, Paris, France
- Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS/SERGAS), Travesía da Choupana s/n, 15706, Santiago de Compostela, Spain
- CIBER de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Cédric Gobet
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Julien Castel
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, Paris, France
| | - Raphaël G P Denis
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, Paris, France
- Institut Cochin, Université Paris Cité, INSERM U1016, CNRS UMR 8104, Paris 75014, France
| | - Jérémy Berthelet
- Université Paris Cité, CNRS, Unité Epigenetique et Destin Cellulaire, Paris F-75013, France
| | - Benjamin D Weger
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Etienne Challet
- Institute for Cellular and Integrative Neurosciences, CNRS and University of Strasbourg, Strasbourg, France
| | - Aline Charpagne
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
| | - Sylviane Metairon
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
| | - Julie Piccand
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
| | - Marine Kraus
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
| | - Bettina H Rohde
- Eurofins Genomics Europe Sequencing GmbH, European Genome and Diagnostics Centre, Konstanz, Germany
| | | | | | - Lise-Lotte Vedin
- Cardio Metabolic Unit, Department of Medicine and department of Laboratory Medicine, Karolinska Institute, Huddinge, Sweden
| | - Mirko E Minniti
- Cardio Metabolic Unit, Department of Medicine and department of Laboratory Medicine, Karolinska Institute, Huddinge, Sweden
| | - Matteo Pedrelli
- Cardio Metabolic Unit, Department of Medicine and department of Laboratory Medicine, Karolinska Institute, Huddinge, Sweden
- Medical Unit Endocrinology, Theme Inflammation and Ageing, Karolinska University Hospital, Stockholm, Sweden
| | - Paolo Parini
- Cardio Metabolic Unit, Department of Medicine and department of Laboratory Medicine, Karolinska Institute, Huddinge, Sweden
- Medical Unit Endocrinology, Theme Inflammation and Ageing, Karolinska University Hospital, Stockholm, Sweden
| | - Frédéric Gachon
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Serge Luquet
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, Paris, France
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20
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McKee CA, Polino AJ, King MW, Musiek ES. Circadian clock protein BMAL1 broadly influences autophagy and endolysosomal function in astrocytes. Proc Natl Acad Sci U S A 2023; 120:e2220551120. [PMID: 37155839 PMCID: PMC10194014 DOI: 10.1073/pnas.2220551120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 04/12/2023] [Indexed: 05/10/2023] Open
Abstract
An emerging role for the circadian clock in autophagy and lysosome function has opened new avenues for exploration in the field of neurodegeneration. The daily rhythms of circadian clock proteins may coordinate gene expression programs involved not only in daily rhythms but in many cellular processes. In the brain, astrocytes are critical for sensing and responding to extracellular cues to support neurons. The core clock protein BMAL1 serves as the primary positive circadian transcriptional regulator and its depletion in astrocytes not only disrupts circadian function but also leads to a unique cell-autonomous activation phenotype. We report here that astrocyte-specific deletion of Bmal1 influences endolysosome function, autophagy, and protein degradation dynamics. In vitro, Bmal1-deficient astrocytes exhibit increased endocytosis, lysosome-dependent protein cleavage, and accumulation of LAMP1- and RAB7-positive organelles. In vivo, astrocyte-specific Bmal1 knockout (aKO) brains show accumulation of autophagosome-like structures within astrocytes by electron microscopy. Transcriptional analysis of isolated astrocytes from young and aged Bmal1 aKO mice indicates broad dysregulation of pathways involved in lysosome function which occur independently of TFEB activation. Since a clear link has been established between neurodegeneration and endolysosome dysfunction over the course of aging, this work implicates BMAL1 as a key regulator of these crucial astrocyte functions in health and disease.
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Affiliation(s)
- Celia A. McKee
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO63110
- Center on Biological Rhythms and Sleep, Washington University School of Medicine in St. Louis, St. Louis, MO63110
| | - Alexander J. Polino
- Department of Cell Biology and Physiology, Washington University School of Medicine in St. Louis, St. Louis, MO63110
| | - Melvin W. King
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO63110
- Center on Biological Rhythms and Sleep, Washington University School of Medicine in St. Louis, St. Louis, MO63110
| | - Erik S. Musiek
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO63110
- Center on Biological Rhythms and Sleep, Washington University School of Medicine in St. Louis, St. Louis, MO63110
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21
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Escalante-Covarrubias Q, Mendoza-Viveros L, González-Suárez M, Sitten-Olea R, Velázquez-Villegas LA, Becerril-Pérez F, Pacheco-Bernal I, Carreño-Vázquez E, Mass-Sánchez P, Bustamante-Zepeda M, Orozco-Solís R, Aguilar-Arnal L. Time-of-day defines NAD + efficacy to treat diet-induced metabolic disease by synchronizing the hepatic clock in mice. Nat Commun 2023; 14:1685. [PMID: 36973248 PMCID: PMC10043291 DOI: 10.1038/s41467-023-37286-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
The circadian clock is an endogenous time-tracking system that anticipates daily environmental changes. Misalignment of the clock can cause obesity, which is accompanied by reduced levels of the clock-controlled, rhythmic metabolite NAD+. Increasing NAD+ is becoming a therapy for metabolic dysfunction; however, the impact of daily NAD+ fluctuations remains unknown. Here, we demonstrate that time-of-day determines the efficacy of NAD+ treatment for diet-induced metabolic disease in mice. Increasing NAD+ prior to the active phase in obese male mice ameliorated metabolic markers including body weight, glucose and insulin tolerance, hepatic inflammation and nutrient sensing pathways. However, raising NAD+ immediately before the rest phase selectively compromised these responses. Remarkably, timed NAD+ adjusted circadian oscillations of the liver clock until completely inverting its oscillatory phase when increased just before the rest period, resulting in misaligned molecular and behavioral rhythms in male and female mice. Our findings unveil the time-of-day dependence of NAD+-based therapies and support a chronobiology-based approach.
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Affiliation(s)
- Quetzalcoatl Escalante-Covarrubias
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Lucía Mendoza-Viveros
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- Laboratorio de Cronobiología y Metabolismo, Instituto Nacional de Medicina Genómica, 14610, Mexico City, Mexico
| | - Mirna González-Suárez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Román Sitten-Olea
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Laura A Velázquez-Villegas
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, 14080, Mexico City, Mexico
| | - Fernando Becerril-Pérez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Ignacio Pacheco-Bernal
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Erick Carreño-Vázquez
- Laboratorio de Cronobiología y Metabolismo, Instituto Nacional de Medicina Genómica, 14610, Mexico City, Mexico
| | - Paola Mass-Sánchez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Marcia Bustamante-Zepeda
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Ricardo Orozco-Solís
- Laboratorio de Cronobiología y Metabolismo, Instituto Nacional de Medicina Genómica, 14610, Mexico City, Mexico
- Centro de Investigación sobre el Envejecimiento, Centro de Investigación y de Estudios Avanzados, 14330, Mexico City, Mexico
| | - Lorena Aguilar-Arnal
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
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22
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S SH, G K, Dey H, Sangoji RV, Thirumal Kumar D, Zayed H, Vasudevan K, George Priya Doss C. Identification of potential circadian genes and associated pathways in colorectal cancer progression and prognosis using microarray gene expression analysis. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 137:181-203. [PMID: 37709376 DOI: 10.1016/bs.apcsb.2023.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Colorectal cancer (CRC) is third cancer causing death in the world. CRC is associated with disrupting the circadian rhythm (CR), closely associating the CRC progression and the dysregulation of genes involved in the biological clock. In this study, we aimed to understand the circadian rhythm changes in patients diagnosed with CRC. We used the GEO database with the ID GSE46549 for our analysis, which consists of 32 patients with CRC and one as normal control. Our study has identified five essential genes involved in CRC, HAPLN1, CDH12, IGFBP5, DCHS2, and DOK5, and had different enriched pathways, such as the Wnt-signaling pathway, at different time points of study. As a part of our study, we also identified various related circadian genes, such as CXCL12, C1QTNF2, MRC2, and GLUL, from the Circadian Gene Expression database, that played a role in circadian rhythm and CRC development. As circadian timing can influence the host tissue's ability to tolerate anticancer medications, the genes reported can serve as a potential drug target for treating CRC and become beneficial to translational settings.
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Affiliation(s)
- Sri Hari S
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, Karnataka, India
| | - Keerthana G
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, Karnataka, India
| | - Hrituraj Dey
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, Karnataka, India
| | - Rahul V Sangoji
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - D Thirumal Kumar
- Faculty of Allied Health Sciences, Meenakshi Academy of Higher Education and Research (MAHER), Chennai, Tamil Nadu, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, QU Health, Doha, Qatar
| | - Karthick Vasudevan
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, Karnataka, India.
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India.
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23
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Richardson RB, Mailloux RJ. Mitochondria Need Their Sleep: Redox, Bioenergetics, and Temperature Regulation of Circadian Rhythms and the Role of Cysteine-Mediated Redox Signaling, Uncoupling Proteins, and Substrate Cycles. Antioxidants (Basel) 2023; 12:antiox12030674. [PMID: 36978924 PMCID: PMC10045244 DOI: 10.3390/antiox12030674] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/12/2023] Open
Abstract
Although circadian biorhythms of mitochondria and cells are highly conserved and crucial for the well-being of complex animals, there is a paucity of studies on the reciprocal interactions between oxidative stress, redox modifications, metabolism, thermoregulation, and other major oscillatory physiological processes. To address this limitation, we hypothesize that circadian/ultradian interaction of the redoxome, bioenergetics, and temperature signaling strongly determine the differential activities of the sleep–wake cycling of mammalians and birds. Posttranslational modifications of proteins by reversible cysteine oxoforms, S-glutathionylation and S-nitrosylation are shown to play a major role in regulating mitochondrial reactive oxygen species production, protein activity, respiration, and metabolomics. Nuclear DNA repair and cellular protein synthesis are maximized during the wake phase, whereas the redoxome is restored and mitochondrial remodeling is maximized during sleep. Hence, our analysis reveals that wakefulness is more protective and restorative to the nucleus (nucleorestorative), whereas sleep is more protective and restorative to mitochondria (mitorestorative). The “redox–bioenergetics–temperature and differential mitochondrial–nuclear regulatory hypothesis” adds to the understanding of mitochondrial respiratory uncoupling, substrate cycling control and hibernation. Similarly, this hypothesis explains how the oscillatory redox–bioenergetics–temperature–regulated sleep–wake states, when perturbed by mitochondrial interactome disturbances, influence the pathogenesis of aging, cancer, spaceflight health effects, sudden infant death syndrome, and diseases of the metabolism and nervous system.
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Affiliation(s)
- Richard B. Richardson
- Radiobiology and Health, Canadian Nuclear Laboratories (CNL), Chalk River, ON K0J 1J0, Canada
- McGill Medical Physics Unit, Cedars Cancer Centre—Glen Site, McGill University, Montreal, QC H4A 3J1, Canada
- Correspondence: or
| | - Ryan J. Mailloux
- School of Human Nutrition, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada;
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24
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Obodo D, Outland EH, Hughey JJ. Sex Inclusion in Transcriptome Studies of Daily Rhythms. J Biol Rhythms 2023; 38:3-14. [PMID: 36419398 PMCID: PMC9903005 DOI: 10.1177/07487304221134160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Biomedical research on mammals has traditionally neglected females, raising the concern that some scientific findings may generalize poorly to half the population. Although this lack of sex inclusion has been broadly documented, its extent within circadian genomics remains undescribed. To address this gap, we examined sex inclusion practices in a comprehensive collection of publicly available transcriptome studies on daily rhythms. Among 148 studies having samples from mammals in vivo, we found strong underrepresentation of females across organisms and tissues. Overall, only 23 of 123 studies in mice, 0 of 10 studies in rats, and 9 of 15 studies in humans included samples from females. In addition, studies having samples from both sexes tended to have more samples from males than from females. These trends appear to have changed little over time, including since 2016, when the US National Institutes of Health began requiring investigators to consider sex as a biological variable. Our findings highlight an opportunity to dramatically improve representation of females in circadian research and to explore sex differences in daily rhythms at the genome level.
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Affiliation(s)
- Dora Obodo
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee,Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Elliot H. Outland
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jacob J. Hughey
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee,Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee,Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee,Jacob J. Hughey, Department of Biomedical Informatics, Vanderbilt University Medical Center, 2525 West End Ave., Suite 1475, Nashville, TN 37232, USA; e-mail:
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25
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Lodovichi C, Ratto GM. Control of circadian rhythm on cortical excitability and synaptic plasticity. Front Neural Circuits 2023; 17:1099598. [PMID: 37063387 PMCID: PMC10098176 DOI: 10.3389/fncir.2023.1099598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/09/2023] [Indexed: 04/18/2023] Open
Abstract
Living organisms navigate through a cyclic world: activity, feeding, social interactions are all organized along the periodic succession of night and day. At the cellular level, periodic activity is controlled by the molecular machinery driving the circadian regulation of cellular homeostasis. This mechanism adapts cell function to the external environment and its crucial importance is underlined by its robustness and redundancy. The cell autonomous clock regulates cell function by the circadian modulation of mTOR, a master controller of protein synthesis. Importantly, mTOR integrates the circadian modulation with synaptic activity and extracellular signals through a complex signaling network that includes the RAS-ERK pathway. The relationship between mTOR and the circadian clock is bidirectional, since mTOR can feedback on the cellular clock to shift the cycle to maintain the alignment with the environmental conditions. The mTOR and ERK pathways are crucial determinants of synaptic plasticity and function and thus it is not surprising that alterations of the circadian clock cause defective responses to environmental challenges, as witnessed by the bi-directional relationship between brain disorders and impaired circadian regulation. In physiological conditions, the feedback between the intrinsic clock and the mTOR pathway suggests that also synaptic plasticity should undergo circadian regulation.
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Affiliation(s)
- Claudia Lodovichi
- Institute of Neuroscience, Consiglio Nazionale delle Ricerche (CNR), Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
- Padova Neuroscience Center, Universitá degli Studi di Padova, Padova, Italy
- *Correspondence: Claudia Lodovichi,
| | - Gian Michele Ratto
- Institute of Neuroscience, Consiglio Nazionale delle Ricerche (CNR), Padova, Italy
- Padova Neuroscience Center, Universitá degli Studi di Padova, Padova, Italy
- National Enterprise for NanoScience and NanoTechnology (NEST), Istituto Nanoscienze, Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore, Pisa, Italy
- Gian Michele Ratto,
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26
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Castillo KD, Wu C, Ding Z, Lopez-Garcia OK, Rowlinson E, Sachs MS, Bell-Pedersen D. A circadian clock translational control mechanism targets specific mRNAs to cytoplasmic messenger ribonucleoprotein granules. Cell Rep 2022; 41:111879. [PMID: 36577368 PMCID: PMC10241597 DOI: 10.1016/j.celrep.2022.111879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 09/13/2022] [Accepted: 12/04/2022] [Indexed: 12/29/2022] Open
Abstract
Phosphorylation of Neurospora crassa eukaryotic initiation factor 2 α (eIF2α), a conserved translation initiation factor, is clock controlled. To determine the impact of rhythmic eIF2α phosphorylation on translation, we performed temporal ribosome profiling and RNA sequencing (RNA-seq) in wild-type (WT), clock mutant Δfrq, eIF2α kinase mutant Δcpc-3, and constitutively active cpc-3c cells. About 14% of mRNAs are rhythmically translated in WT cells, and translation rhythms for ∼30% of these mRNAs, which we named circadian translation-initiation-controlled genes (cTICs), are dependent on the clock and CPC-3. Most cTICs are expressed from arrhythmic mRNAs and contain a P-body (PB) localization motif in their 5' leader sequence. Deletion of SNR-1, a component of cytoplasmic messenger ribonucleoprotein granules (cmRNPgs) that include PBs and stress granules (SGs), and the PB motif on one of the cTIC mRNAs, zip-1, significantly alters zip-1 rhythmic translation. These results reveal that the clock regulates rhythmic translation of specific mRNAs through rhythmic eIF2α activity and cmRNPg metabolism.
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Affiliation(s)
- Kathrina D Castillo
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Cheng Wu
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Zhaolan Ding
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | | | - Emma Rowlinson
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Deborah Bell-Pedersen
- Center for Biological Clocks Research, Texas A&M University, College Station, TX 77843, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA.
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27
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Regulation of RNA Polymerase I Stability and Function. Cancers (Basel) 2022; 14:cancers14235776. [PMID: 36497261 PMCID: PMC9737084 DOI: 10.3390/cancers14235776] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
RNA polymerase I is a highly processive enzyme with fast initiation and elongation rates. The structure of Pol I, with its in-built RNA cleavage ability and incorporation of subunits homologous to transcription factors, enables it to quickly and efficiently synthesize the enormous amount of rRNA required for ribosome biogenesis. Each step of Pol I transcription is carefully controlled. However, cancers have highjacked these control points to switch the enzyme, and its transcription, on permanently. While this provides an exceptional benefit to cancer cells, it also creates a potential cancer therapeutic vulnerability. We review the current research on the regulation of Pol I transcription, and we discuss chemical biology efforts to develop new targeted agents against this process. Lastly, we highlight challenges that have arisen from the introduction of agents with promiscuous mechanisms of action and provide examples of agents with specificity and selectivity against Pol I.
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28
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Meng Y, Zhang N, Li J, Shen X, Sheen J, Xiong Y. TOR kinase, a GPS in the complex nutrient and hormonal signaling networks to guide plant growth and development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7041-7054. [PMID: 35781569 PMCID: PMC9664236 DOI: 10.1093/jxb/erac282] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/24/2022] [Indexed: 06/01/2023]
Abstract
To survive and sustain growth, sessile plants have developed sophisticated internal signalling networks that respond to various external and internal cues. Despite the central roles of nutrient and hormone signaling in plant growth and development, how hormone-driven processes coordinate with metabolic status remains largely enigmatic. Target of rapamycin (TOR) kinase is an evolutionarily conserved master regulator that integrates energy, nutrients, growth factors, hormones, and stress signals to promote growth in all eukaryotes. Inspired by recent comprehensive systems, chemical, genetic, and genomic studies on TOR in plants, this review discusses a potential role of TOR as a 'global positioning system' that directs plant growth and developmental programs both temporally and spatially by integrating dynamic information in the complex nutrient and hormonal signaling networks. We further evaluate and depict the possible functional and mechanistic models for how a single protein kinase, TOR, is able to recognize, integrate, and even distinguish a plethora of positive and negative input signals to execute appropriate and distinct downstream biological processes via multiple partners and effectors.
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Affiliation(s)
| | | | - Jiatian Li
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Haixia Institute of Science and Technology, Plant Synthetic Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuehong Shen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Haixia Institute of Science and Technology, Plant Synthetic Biology Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jen Sheen
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA, USA
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29
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Cavalcante LTDF, da Fonseca GC, Amado Leon LA, Salvio AL, Brustolini OJ, Gerber AL, Guimarães APDC, Marques CAB, Fernandes RA, Ramos Filho CHF, Kader RL, Pimentel Amaro M, da Costa Gonçalves JP, Vieira Alves-Leon S, Vasconcelos ATR. Buffy Coat Transcriptomic Analysis Reveals Alterations in Host Cell Protein Synthesis and Cell Cycle in Severe COVID-19 Patients. Int J Mol Sci 2022; 23:13588. [PMID: 36362378 PMCID: PMC9659271 DOI: 10.3390/ijms232113588] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/25/2023] Open
Abstract
Transcriptome studies have reported the dysregulation of cell cycle-related genes and the global inhibition of host mRNA translation in COVID-19 cases. However, the key genes and cellular mechanisms that are most affected by the severe outcome of this disease remain unclear. For this work, the RNA-seq approach was used to study the differential expression in buffy coat cells of two groups of people infected with SARS-CoV-2: (a) Mild, with mild symptoms; and (b) SARS (Severe Acute Respiratory Syndrome), who were admitted to the intensive care unit with the severe COVID-19 outcome. Transcriptomic analysis revealed 1009 up-regulated and 501 down-regulated genes in the SARS group, with 10% of both being composed of long non-coding RNA. Ribosome and cell cycle pathways were enriched among down-regulated genes. The most connected proteins among the differentially expressed genes involved transport dysregulation, proteasome degradation, interferon response, cytokinesis failure, and host translation inhibition. Furthermore, interactome analysis showed Fibrillarin to be one of the key genes affected by SARS-CoV-2. This protein interacts directly with the N protein and long non-coding RNAs affecting transcription, translation, and ribosomal processes. This work reveals a group of dysregulated processes, including translation and cell cycle, as key pathways altered in severe COVID-19 outcomes.
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Affiliation(s)
| | | | - Luciane Almeida Amado Leon
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro 21040-360, Brazil
| | - Andreza Lemos Salvio
- Laboratório de Neurociências Translacional, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro 20211-040, Brazil
| | - Otávio José Brustolini
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro 25651-076, Brazil
| | - Alexandra Lehmkuhl Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro 25651-076, Brazil
| | - Ana Paula de Campos Guimarães
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro 25651-076, Brazil
| | - Carla Augusta Barreto Marques
- Laboratório de Neurociências Translacional, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro 20211-040, Brazil
- Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
| | - Renan Amphilophio Fernandes
- Laboratório de Neurociências Translacional, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro 20211-040, Brazil
| | | | - Rafael Lopes Kader
- Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
| | - Marisa Pimentel Amaro
- Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
| | - João Paulo da Costa Gonçalves
- Laboratório de Neurociências Translacional, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro 20211-040, Brazil
- Yale New Haven Hospital, New Haven, CT 06510, USA
| | - Soniza Vieira Alves-Leon
- Laboratório de Neurociências Translacional, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro 20211-040, Brazil
- Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
| | - Ana Tereza Ribeiro Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro 25651-076, Brazil
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30
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Rees H, Rusholme-Pilcher R, Bailey P, Colmer J, White B, Reynolds C, Ward SJ, Coombes B, Graham CA, de Barros Dantas LL, Dodd AN, Hall A. Circadian regulation of the transcriptome in a complex polyploid crop. PLoS Biol 2022; 20:e3001802. [PMID: 36227835 PMCID: PMC9560141 DOI: 10.1371/journal.pbio.3001802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/18/2022] [Indexed: 11/07/2022] Open
Abstract
The circadian clock is a finely balanced timekeeping mechanism that coordinates programmes of gene expression. It is currently unknown how the clock regulates expression of homoeologous genes in polyploids. Here, we generate a high-resolution time-course dataset to investigate the circadian balance between sets of 3 homoeologous genes (triads) from hexaploid bread wheat. We find a large proportion of circadian triads exhibit imbalanced rhythmic expression patterns, with no specific subgenome favoured. In wheat, period lengths of rhythmic transcripts are found to be longer and have a higher level of variance than in other plant species. Expression of transcripts associated with circadian controlled biological processes is largely conserved between wheat and Arabidopsis; however, striking differences are seen in agriculturally critical processes such as starch metabolism. Together, this work highlights the ongoing selection for balance versus diversification in circadian homoeologs and identifies clock-controlled pathways that might provide important targets for future wheat breeding.
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Affiliation(s)
- Hannah Rees
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Paul Bailey
- Royal Botanic Gardens Kew, Richmond, Surrey, United Kingdom
| | - Joshua Colmer
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Benjamen White
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Connor Reynolds
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Benedict Coombes
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Calum A. Graham
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | | | - Antony N. Dodd
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
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31
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Laloum D, Robinson-Rechavi M. Rhythmicity is linked to expression cost at the protein level but to expression precision at the mRNA level. PLoS Comput Biol 2022; 18:e1010399. [PMID: 36095022 PMCID: PMC9518874 DOI: 10.1371/journal.pcbi.1010399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 09/28/2022] [Accepted: 07/17/2022] [Indexed: 11/18/2022] Open
Abstract
Many genes have nycthemeral rhythms of expression, i.e. a 24-hours periodic variation, at either mRNA or protein level or both, and most rhythmic genes are tissue-specific. Here, we investigate and discuss the evolutionary origins of rhythms in gene expression. Our results suggest that rhythmicity of protein expression could have been favored by selection to minimize costs. Trends are consistent in bacteria, plants and animals, and are also supported by tissue-specific patterns in mouse. Unlike for protein level, cost cannot explain rhythm at the RNA level. We suggest that instead it allows to periodically reduce expression noise. Noise control had the strongest support in mouse, with limited evidence in other species. We have also found that genes under stronger purifying selection are rhythmically expressed at the mRNA level, and we propose that this is because they are noise sensitive genes. Finally, the adaptive role of rhythmic expression is supported by rhythmic genes being highly expressed yet tissue-specific. This provides a good evolutionary explanation for the observation that nycthemeral rhythms are often tissue-specific. For many genes, their expression, i.e. the production of RNA and proteins, is rhythmic with a 24-hour period. Here, we study and discuss the evolutionary origins of these rhythms. Our analyses of data from different species suggest that the rhythmicity of protein level may have been favored by selection for cost minimization. Furthermore, we have shown that cost cannot explain the rhythmic variations in RNA levels. Instead, we suggest that it periodically reduces the stochasticity of gene expression. We also found that genes under stronger purifying selection are rhythmically expressed at the mRNA level, and propose that this is because they are noise-sensitive genes. Finally, rhythmic expression involves genes that are often highly expressed and tissue-specific. This provides a good evolutionary explanation for the tissue-specificity of these rhythms.
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Affiliation(s)
- David Laloum
- Department of Ecology and Evolution, Batiment Biophore, Quartier UNIL-Sorge, Université de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Batiment Génopode, Quartier UNIL-Sorge, Université de Lausanne, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, Batiment Biophore, Quartier UNIL-Sorge, Université de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Batiment Génopode, Quartier UNIL-Sorge, Université de Lausanne, Lausanne, Switzerland
- * E-mail:
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32
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Liu X, Chiu JC. Nutrient-sensitive protein O-GlcNAcylation shapes daily biological rhythms. Open Biol 2022; 12:220215. [PMID: 36099933 PMCID: PMC9470261 DOI: 10.1098/rsob.220215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/17/2022] [Indexed: 11/12/2022] Open
Abstract
O-linked-N-acetylglucosaminylation (O-GlcNAcylation) is a nutrient-sensitive protein modification that alters the structure and function of a wide range of proteins involved in diverse cellular processes. Similar to phosphorylation, another protein modification that targets serine and threonine residues, O-GlcNAcylation occupancy on cellular proteins exhibits daily rhythmicity and has been shown to play critical roles in regulating daily rhythms in biology by modifying circadian clock proteins and downstream effectors. We recently reported that daily rhythm in global O-GlcNAcylation observed in Drosophila tissues is regulated via the integration of circadian and metabolic signals. Significantly, mistimed feeding, which disrupts coordination of these signals, is sufficient to dampen daily O-GlcNAcylation rhythm and is predicted to negatively impact animal biological rhythms and health span. In this review, we provide an overview of published and potential mechanisms by which metabolic and circadian signals regulate hexosamine biosynthetic pathway metabolites and enzymes, as well as O-GlcNAc processing enzymes to shape daily O-GlcNAcylation rhythms. We also discuss the significance of functional interactions between O-GlcNAcylation and other post-translational modifications in regulating biological rhythms. Finally, we highlight organ/tissue-specific cellular processes and molecular pathways that could be modulated by rhythmic O-GlcNAcylation to regulate time-of-day-specific biology.
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Affiliation(s)
- Xianhui Liu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, CA, USA
- Department of Pharmacology, School of Medicine, University of California Davis, Davis, CA, USA
| | - Joanna C. Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, Davis, CA, USA
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33
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Singla R, Mishra A, Cao R. The trilateral interactions between mammalian target of rapamycin (mTOR) signaling, the circadian clock, and psychiatric disorders: an emerging model. Transl Psychiatry 2022; 12:355. [PMID: 36045116 PMCID: PMC9433414 DOI: 10.1038/s41398-022-02120-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 08/08/2022] [Accepted: 08/12/2022] [Indexed: 02/07/2023] Open
Abstract
Circadian (~24 h) rhythms in physiology and behavior are evolutionarily conserved and found in almost all living organisms. The rhythms are endogenously driven by daily oscillatory activities of so-called "clock genes/proteins", which are widely distributed throughout the mammalian brain. Mammalian (mechanistic) target of rapamycin (mTOR) signaling is a fundamental intracellular signal transduction cascade that controls important neuronal processes including neurodevelopment, synaptic plasticity, metabolism, and aging. Dysregulation of the mTOR pathway is associated with psychiatric disorders including autism spectrum disorders (ASD) and mood disorders (MD), in which patients often exhibit disrupted daily physiological rhythms and abnormal circadian gene expression in the brain. Recent work has found that the activities of mTOR signaling are temporally controlled by the circadian clock and exhibit robust circadian oscillations in multiple systems. In the meantime, mTOR signaling regulates fundamental properties of the central and peripheral circadian clocks, including period length, entrainment, and synchronization. Whereas the underlying mechanisms remain to be fully elucidated, increasing clinical and preclinical evidence support significant crosstalk between mTOR signaling, the circadian clock, and psychiatric disorders. Here, we review recent progress in understanding the trilateral interactions and propose an "interaction triangle" model between mTOR signaling, the circadian clock, and psychiatric disorders (focusing on ASD and MD).
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Affiliation(s)
- Rubal Singla
- grid.17635.360000000419368657Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812 USA
| | - Abhishek Mishra
- grid.17635.360000000419368657Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812 USA
| | - Ruifeng Cao
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, 55812, USA. .,Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
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34
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Ogata S, Ito S, Masuda T, Ohtsuki S. Diurnal Changes in Protein Expression at the Blood-Brain Barrier in Mice. Biol Pharm Bull 2022; 45:751-756. [PMID: 35650102 DOI: 10.1248/bpb.b22-00016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Circadian rhythms influence the transport function of the blood-brain barrier (BBB) and peripheral organs. However, the influence of circadian rhythms on protein expression in the BBB remains to be completely elucidated. Therefore, we aimed to investigate diurnal changes in protein expression in the mouse BBB using quantitative proteomics. Quantitative proteomics showed that the expression of 67, 10, and 20 proteins in the isolated mouse brain capillary fraction changed significantly at zeitgeber time (ZT) 6, 12, and 18, respectively, compared to ZT0. Among them, the levels of 44 proteins were significantly increased at ZT6 and then returned to the same level as ZT0 at ZT12 and ZT18. Gene ontology analysis indicated that the proteins significantly increased at ZT6 were majorly related to translation. The brain capillary endothelial cell-selective proteins sepiapterin reductase and vascular endothelial growth factor receptor 2 showed diurnal variation. In contrast, the expression of ABC transporters, SLC transporters, and receptors associated with receptor-mediated transcytosis, and tight junction proteins did not change within a day. The present findings demonstrated that protein expression related to transport function and physical barrier at the BBB was maintained throughout the day, although the proteins involved in some biological processes exhibited diurnal variation at the BBB.
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Affiliation(s)
- Seiryo Ogata
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University
| | - Shingo Ito
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University.,Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University.,Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University.,Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University
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35
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Fougeray T, Polizzi A, Régnier M, Fougerat A, Ellero-Simatos S, Lippi Y, Smati S, Lasserre F, Tramunt B, Huillet M, Dopavogui L, Salvi J, Nédélec E, Gigot V, Smith L, Naylies C, Sommer C, Haas JT, Wahli W, Duez H, Gourdy P, Gamet-Payrastre L, Benani A, Burnol AF, Loiseau N, Postic C, Montagner A, Guillou H. The hepatocyte insulin receptor is required to program the liver clock and rhythmic gene expression. Cell Rep 2022; 39:110674. [PMID: 35417722 DOI: 10.1016/j.celrep.2022.110674] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/03/2022] [Accepted: 03/23/2022] [Indexed: 12/30/2022] Open
Abstract
Liver physiology is circadian and sensitive to feeding and insulin. Food intake regulates insulin secretion and is a dominant signal for the liver clock. However, how much insulin contributes to the effect of feeding on the liver clock and rhythmic gene expression remains to be investigated. Insulin action partly depends on changes in insulin receptor (IR)-dependent gene expression. Here, we use hepatocyte-restricted gene deletion of IR to evaluate its role in the regulation and oscillation of gene expression as well as in the programming of the circadian clock in the adult mouse liver. We find that, in the absence of IR, the rhythmicity of core-clock gene expression is altered in response to day-restricted feeding. This change in core-clock gene expression is associated with defective reprogramming of liver gene expression. Our data show that an intact hepatocyte insulin receptor is required to program the liver clock and associated rhythmic gene expression.
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Affiliation(s)
- Tiffany Fougeray
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France; Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), UMR1297, INSERM/UPS, Université de Toulouse, 1 Avenue Jean Poulhès, BP 84225, 31432 Toulouse, France
| | - Arnaud Polizzi
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Marion Régnier
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Anne Fougerat
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Sandrine Ellero-Simatos
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Yannick Lippi
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Sarra Smati
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France; Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), UMR1297, INSERM/UPS, Université de Toulouse, 1 Avenue Jean Poulhès, BP 84225, 31432 Toulouse, France; Université de Nantes, INSERM, CNRS, CHU Nantes, Institut du Thorax, 44000 Nantes, France
| | - Frédéric Lasserre
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Blandine Tramunt
- Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), UMR1297, INSERM/UPS, Université de Toulouse, 1 Avenue Jean Poulhès, BP 84225, 31432 Toulouse, France; Service de Diabétologie, Maladies Métaboliques et Nutrition, CHU de Toulouse, Université de Toulouse, Toulouse, France
| | - Marine Huillet
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Léonie Dopavogui
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Juliette Salvi
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Université Bourgogne Franche-Comté, Institut Agro Dijon, 21000 Dijon, France
| | - Emmanuelle Nédélec
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Université Bourgogne Franche-Comté, Institut Agro Dijon, 21000 Dijon, France
| | - Vincent Gigot
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Université Bourgogne Franche-Comté, Institut Agro Dijon, 21000 Dijon, France
| | - Lorraine Smith
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Claire Naylies
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Caroline Sommer
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Joel T Haas
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Walter Wahli
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France; Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore 308232, Singapore; Center for Integrative Genomics, University of Lausanne, Le Génopode, 1015 Lausanne, Switzerland
| | - Hélène Duez
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Pierre Gourdy
- Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), UMR1297, INSERM/UPS, Université de Toulouse, 1 Avenue Jean Poulhès, BP 84225, 31432 Toulouse, France; Service de Diabétologie, Maladies Métaboliques et Nutrition, CHU de Toulouse, Université de Toulouse, Toulouse, France
| | - Laurence Gamet-Payrastre
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Alexandre Benani
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Université Bourgogne Franche-Comté, Institut Agro Dijon, 21000 Dijon, France
| | | | - Nicolas Loiseau
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France
| | - Catherine Postic
- Université de Paris, Institut Cochin, CNRS, INSERM, 75014 Paris, France
| | - Alexandra Montagner
- Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), UMR1297, INSERM/UPS, Université de Toulouse, 1 Avenue Jean Poulhès, BP 84225, 31432 Toulouse, France.
| | - Hervé Guillou
- Toxalim (Research Center in Food Toxicology), INRAE, ENVT, INP- PURPAN, UMR 1331, UPS, Université de Toulouse, 180 Chemin de Tournefeuille, 31027 Toulouse, France.
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36
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Zhang G, Chu Y, Jiang T, Li J, Feng L, Wu H, Wang H, Feng J. Comparative analysis of the daily brain transcriptomes of Asian particolored bat. Sci Rep 2022; 12:3876. [PMID: 35264653 PMCID: PMC8907190 DOI: 10.1038/s41598-022-07787-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/24/2022] [Indexed: 11/21/2022] Open
Abstract
Daily rhythms are found in almost all organisms, and they comprise one of the most basic characteristics of living things. Daily rhythms are generated and mainly regulated by circadian clock. Bats have attracted interest from researchers because of their unique biological characteristics. However, little is known about the molecular underpinnings of daily rhythms in bats. In this study, we used RNA-Seq to uncover the daily rhythms of gene expression in the brains of Asian particolored bats over the 24-h day. Accordingly, four collected time points corresponding to four biological states, rest, sleep, wakefulness, and active, were selected. Several groups of genes with different expression levels in these four states were obtained suggested that different physiological processes were active at various biological states, including drug metabolism, signaling pathways, and the circadian rhythm. Furthermore, downstream analysis of all differentially expressed genes in these four states suggested that groups of genes showed daily rhythms in the bat brain. Especially for Per1, an important circadian clock gene was identified with rhythmic expression in the brain of Asian particolored bat. In summary, our study provides an overview of the brain transcriptomic differences in different physiological states over a 24-h cycle.
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Affiliation(s)
- Guoting Zhang
- College of Life Science, Jilin Agricultural University, Changchun, 130118, China
| | - Yujia Chu
- College of Life Science, Jilin Agricultural University, Changchun, 130118, China
| | - Tinglei Jiang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China
| | - Jingjing Li
- College of Life Science, Jilin Agricultural University, Changchun, 130118, China
| | - Lei Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China
| | - Hui Wu
- College of Life Science, Jilin Agricultural University, Changchun, 130118, China
| | - Hui Wang
- College of Life Science, Jilin Agricultural University, Changchun, 130118, China.
| | - Jiang Feng
- College of Life Science, Jilin Agricultural University, Changchun, 130118, China. .,Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China.
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37
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Manoogian ENC, Chow LS, Taub PR, Laferrère B, Panda S. Time-restricted Eating for the Prevention and Management of Metabolic Diseases. Endocr Rev 2022; 43:405-436. [PMID: 34550357 PMCID: PMC8905332 DOI: 10.1210/endrev/bnab027] [Citation(s) in RCA: 109] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Indexed: 02/08/2023]
Abstract
Time-restricted feeding (TRF, animal-based studies) and time-restricted eating (TRE, humans) are an emerging behavioral intervention approach based on the understanding of the role of circadian rhythms in physiology and metabolism. In this approach, all calorie intake is restricted within a consistent interval of less than 12 hours without overtly attempting to reduce calories. This article will summarize the origin of TRF/TRE starting with concept of circadian rhythms and the role of chronic circadian rhythm disruption in increasing the risk for chronic metabolic diseases. Circadian rhythms are usually perceived as the sleep-wake cycle and dependent rhythms arising from the central nervous system. However, the recent discovery of circadian rhythms in peripheral organs and the plasticity of these rhythms in response to changes in nutrition availability raised the possibility that adopting a consistent daily short window of feeding can sustain robust circadian rhythm. Preclinical animal studies have demonstrated proof of concept and identified potential mechanisms driving TRF-related benefits. Pilot human intervention studies have reported promising results in reducing the risk for obesity, diabetes, and cardiovascular diseases. Epidemiological studies have indicated that maintaining a consistent long overnight fast, which is similar to TRE, can significantly reduce risks for chronic diseases. Despite these early successes, more clinical and mechanistic studies are needed to implement TRE alone or as adjuvant lifestyle intervention for the prevention and management of chronic metabolic diseases.
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Affiliation(s)
| | - Lisa S Chow
- University of Minnesota, Division of Diabetes, Endocrinology and Metabolism, Minneapolis, Minnesota 55455, USA
| | - Pam R Taub
- University of California, San Diego, Division of Cardiovascular Diseases, Department of Medicine, 9434 Medical Center Drive, La Jolla, California 92037, USA
| | - Blandine Laferrère
- New York Nutrition Obesity Research Center, Division of Endocrinology, Department of Medicine, Columbia University Irving Medical Center; New York, New York 10032, USA
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38
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Jouffe C, Weger BD, Martin E, Atger F, Weger M, Gobet C, Ramnath D, Charpagne A, Morin-Rivron D, Powell EE, Sweet MJ, Masoodi M, Uhlenhaut NH, Gachon F. Disruption of the circadian clock component BMAL1 elicits an endocrine adaption impacting on insulin sensitivity and liver disease. Proc Natl Acad Sci U S A 2022; 119:e2200083119. [PMID: 35238641 PMCID: PMC8916004 DOI: 10.1073/pnas.2200083119] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/25/2022] [Indexed: 02/06/2023] Open
Abstract
SignificanceWhile increasing evidence associates the disruption of circadian rhythms with pathologic conditions, including obesity, type 2 diabetes, and nonalcoholic fatty liver diseases (NAFLD), the involved mechanisms are still poorly described. Here, we show that, in both humans and mice, the pathogenesis of NAFLD is associated with the disruption of the circadian clock combined with perturbations of the growth hormone and sex hormone pathways. However, while this condition protects mice from the development of fibrosis and insulin resistance, it correlates with increased fibrosis in humans. This suggests that the perturbation of the circadian clock and its associated disruption of the growth hormone and sex hormone pathways are critical for the pathogenesis of metabolic and liver diseases.
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Affiliation(s)
- Céline Jouffe
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
- Department of Pharmacology and Toxicology, University of Lausanne, CH-1011 Lausanne, Switzerland
- Helmholtz Diabetes Center, Helmholtz Zentrum München, DE-85764 Neuherberg, Germany
| | - Benjamin D. Weger
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia
| | - Eva Martin
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
| | - Florian Atger
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
- Department of Pharmacology and Toxicology, University of Lausanne, CH-1011 Lausanne, Switzerland
| | - Meltem Weger
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia
| | - Cédric Gobet
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Divya Ramnath
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia
| | - Aline Charpagne
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
| | | | - Elizabeth E. Powell
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane QLD 4102, Australia
- Faculty of Medicine, Center for Liver Disease Research, Translational Research Institute, The University of Queensland, Brisbane QLD 4102, Australia
| | - Matthew J. Sweet
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia
| | - Mojgan Masoodi
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
- Institute of Clinical Chemistry, Bern University Hospital, Bern 3010, Switzerland
| | - N. Henriette Uhlenhaut
- Helmholtz Diabetes Center, Helmholtz Zentrum München, DE-85764 Neuherberg, Germany
- Metabolic Programming, Technical University of Munich School of Life Sciences, DE-85354 Freising, Germany
| | - Frédéric Gachon
- Nestlé Research, Société des Produits Nestlé, CH-1015 Lausanne, Switzerland
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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39
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Wong DCS, Seinkmane E, Zeng A, Stangherlin A, Rzechorzek NM, Beale AD, Day J, Reed M, Peak‐Chew SY, Styles CT, Edgar RS, Putker M, O’Neill JS. CRYPTOCHROMES promote daily protein homeostasis. EMBO J 2022; 41:e108883. [PMID: 34842284 PMCID: PMC8724739 DOI: 10.15252/embj.2021108883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 11/29/2022] Open
Abstract
The daily organisation of most mammalian cellular functions is attributed to circadian regulation of clock-controlled protein expression, driven by daily cycles of CRYPTOCHROME-dependent transcriptional feedback repression. To test this, we used quantitative mass spectrometry to compare wild-type and CRY-deficient fibroblasts under constant conditions. In CRY-deficient cells, we found that temporal variation in protein, phosphopeptide, and K+ abundance was at least as great as wild-type controls. Most strikingly, the extent of temporal variation within either genotype was much smaller than overall differences in proteome composition between WT and CRY-deficient cells. This proteome imbalance in CRY-deficient cells and tissues was associated with increased susceptibility to proteotoxic stress, which impairs circadian robustness, and may contribute to the wide-ranging phenotypes of CRY-deficient mice. Rather than generating large-scale daily variation in proteome composition, we suggest it is plausible that the various transcriptional and post-translational functions of CRY proteins ultimately act to maintain protein and osmotic homeostasis against daily perturbation.
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Affiliation(s)
| | | | - Aiwei Zeng
- MRC Laboratory of Molecular BiologyCambridgeUK
| | | | | | | | - Jason Day
- Department of Earth SciencesUniversity of CambridgeCambridgeUK
| | - Martin Reed
- MRC Laboratory of Molecular BiologyCambridgeUK
| | | | | | - Rachel S Edgar
- Department of Infectious DiseasesImperial CollegeLondonUK
| | - Marrit Putker
- MRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
Crown BioscienceUtrechtthe Netherlands
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40
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Aviram R, Dandavate V, Manella G, Golik M, Asher G. Ultradian rhythms of AKT phosphorylation and gene expression emerge in the absence of the circadian clock components Per1 and Per2. PLoS Biol 2021; 19:e3001492. [PMID: 34968386 PMCID: PMC8718012 DOI: 10.1371/journal.pbio.3001492] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 11/23/2021] [Indexed: 12/26/2022] Open
Abstract
Rhythmicity of biological processes can be elicited either in response to environmental cycles or driven by endogenous oscillators. In mammals, the circadian clock drives about 24-hour rhythms of multitude metabolic and physiological processes in anticipation to environmental daily oscillations. Also at the intersection of environment and metabolism is the protein kinase—AKT. It conveys extracellular signals, primarily feeding-related signals, to regulate various key cellular functions. Previous studies in mice identified rhythmicity in AKT activation (pAKT) with elevated levels in the fed state. However, it is still unknown whether rhythmic AKT activation can be driven through intrinsic mechanisms. Here, we inspected temporal changes in pAKT levels both in cultured cells and animal models. In cultured cells, pAKT levels showed circadian oscillations similar to those observed in livers of wild-type mice under free-running conditions. Unexpectedly, in livers of Per1,2−/− but not of Bmal1−/− mice we detected ultradian (about 16 hours) oscillations of pAKT levels. Importantly, the liver transcriptome of Per1,2−/− mice also showed ultradian rhythms, corresponding to pAKT rhythmicity and consisting of AKT-related genes and regulators. Overall, our findings reveal ultradian rhythms in liver gene expression and AKT phosphorylation that emerge in the absence of environmental rhythms and Per1,2−/− genes. This study reveals ultradian (16-hour) rhythms in the activation of the protein kinase AKT in the livers of mice, accompanied by corresponding downstream changes in gene expression. Intriguingly, these oscillations emerge in the absence of rhythmic environmental cues and in mice lacking the circadian clock proteins Per1 and Per2.
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Affiliation(s)
- Rona Aviram
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Vaishnavi Dandavate
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gal Manella
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Marina Golik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gad Asher
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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41
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Crislip GR, Johnston JG, Douma LG, Costello HM, Juffre A, Boyd K, Li W, Maugans CC, Gutierrez-Monreal M, Esser KA, Bryant AJ, Liu AC, Gumz ML. Circadian Rhythm Effects on the Molecular Regulation of Physiological Systems. Compr Physiol 2021; 12:2769-2798. [PMID: 34964116 DOI: 10.1002/cphy.c210011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Nearly every system within the body contains an intrinsic cellular circadian clock. The circadian clock contributes to the regulation of a variety of homeostatic processes in mammals through the regulation of gene expression. Circadian disruption of physiological systems is associated with pathophysiological disorders. Here, we review the current understanding of the molecular mechanisms contributing to the known circadian rhythms in physiological function. This article focuses on what is known in humans, along with discoveries made with cell and rodent models. In particular, the impact of circadian clock components in metabolic, cardiovascular, endocrine, musculoskeletal, immune, and central nervous systems are discussed. © 2021 American Physiological Society. Compr Physiol 11:1-30, 2021.
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Affiliation(s)
- G Ryan Crislip
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida, USA
| | - Jermaine G Johnston
- Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, University of Florida, Gainesville, Florida, USA
| | - Lauren G Douma
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Hannah M Costello
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida, USA
| | - Alexandria Juffre
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Kyla Boyd
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Wendy Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Cheoting C Maugans
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Miguel Gutierrez-Monreal
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida, USA
| | - Karyn A Esser
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida, USA.,Myology Institute, University of Florida, Gainesville, Florida, USA
| | - Andrew J Bryant
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, University of Florida, Gainesville, Florida, USA
| | - Andrew C Liu
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida, USA.,Myology Institute, University of Florida, Gainesville, Florida, USA
| | - Michelle L Gumz
- Department of Medicine, Division of Nephrology, Hypertension, and Renal Transplantation, University of Florida, Gainesville, Florida, USA.,Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA.,Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida, USA.,Center for Integrative Cardiovascular and Metabolic Disease, University of Florida, Gainesville, Florida, USA
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Stangherlin A, Seinkmane E, O'Neill JS. Understanding circadian regulation of mammalian cell function, protein homeostasis, and metabolism. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 28:None. [PMID: 34950808 PMCID: PMC8660647 DOI: 10.1016/j.coisb.2021.100391] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Circadian rhythms are ∼24 h cycles of organismal and cellular activity ubiquitous to mammalian physiology. A prevailing paradigm suggests that timing information flows linearly from rhythmic transcription via protein abundance changes to drive circadian regulation of cellular function. Challenging this view, recent evidence indicates daily variation in many cellular functions arises through rhythmic post-translational regulation of protein activity. We suggest cellular circadian timing primarily functions to maintain proteome homeostasis rather than perturb it. Indeed, although relevant to timekeeping mechanism, daily rhythms of clock protein abundance may be the exception, not the rule. Informed by insights from yeast and mammalian models, we propose that optimal bioenergetic efficiency results from coupled rhythms in mammalian target of rapamycin complex activity, protein synthesis/turnover, ion transport and protein sequestration, which drive facilitatory rhythms in metabolic flux and substrate utilisation. Such daily consolidation of proteome renewal would account for many aspects of circadian cell biology whilst maintaining osmotic homeostasis.
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Compensatory ion transport buffers daily protein rhythms to regulate osmotic balance and cellular physiology. Nat Commun 2021; 12:6035. [PMID: 34654800 PMCID: PMC8520019 DOI: 10.1038/s41467-021-25942-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/04/2021] [Indexed: 01/15/2023] Open
Abstract
Between 6-20% of the cellular proteome is under circadian control and tunes mammalian cell function with daily environmental cycles. For cell viability, and to maintain volume within narrow limits, the daily variation in osmotic potential exerted by changes in the soluble proteome must be counterbalanced. The mechanisms and consequences of this osmotic compensation have not been investigated before. In cultured cells and in tissue we find that compensation involves electroneutral active transport of Na+, K+, and Cl- through differential activity of SLC12A family cotransporters. In cardiomyocytes ex vivo and in vivo, compensatory ion fluxes confer daily variation in electrical activity. Perturbation of soluble protein abundance has commensurate effects on ion composition and cellular function across the circadian cycle. Thus, circadian regulation of the proteome impacts ion homeostasis with substantial consequences for the physiology of electrically active cells such as cardiomyocytes.
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Bonnot T, Nagel DH. Time of the day prioritizes the pool of translating mRNAs in response to heat stress. THE PLANT CELL 2021; 33:2164-2182. [PMID: 33871647 PMCID: PMC8364243 DOI: 10.1093/plcell/koab113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/07/2021] [Indexed: 05/24/2023]
Abstract
The circadian clock helps organisms to anticipate and coordinate gene regulatory responses to changes in environmental stimuli. Under growth limiting temperatures, the time of the day modulates the accumulation of polyadenylated mRNAs. In response to heat stress, plants will conserve energy and selectively translate mRNAs. How the clock and/or the time of the day regulates polyadenylated mRNAs bound by ribosomes in response to heat stress is unknown. In-depth analysis of Arabidopsis thaliana translating mRNAs found that the time of the day gates the response of approximately one-third of the circadian-regulated heat-responsive translatome. Specifically, the time of the day and heat stress interact to prioritize the pool of mRNAs in cue to be translated. For a subset of mRNAs, we observed a stronger gated response during the day, and preferentially before the peak of expression. We propose previously overlooked transcription factors (TFs) as regulatory nodes and show that the clock plays a role in the temperature response for select TFs. When the stress was removed, the redefined priorities for translation recovered within 1 h, though slower recovery was observed for abiotic stress regulators. Through hierarchical network connections between clock genes and prioritized TFs, our work provides a framework to target key nodes underlying heat stress tolerance throughout the day.
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Affiliation(s)
- Titouan Bonnot
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Dawn H. Nagel
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
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Ghosh S, Lewis KN, Tulsian R, Astafev AA, Buffenstein R, Kondratov RV. It's about time; divergent circadian clocks in livers of mice and naked mole-rats. FASEB J 2021; 35:e21590. [PMID: 33871093 DOI: 10.1096/fj.202100116r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/15/2021] [Accepted: 03/26/2021] [Indexed: 01/07/2023]
Abstract
Light is the key regulator of circadian clock, the time-keeping system synchronizing organism physiology and behavior with environmental day and night conditions. In its natural habitat, the strictly subterranean naked mole-rat (Heterocephalus glaber) has lived in a light-free environment for millennia. We questioned if this species retains a circadian clock and if the patterns of this clock and concomitant rhythms differed in liver tissue from mice and naked mole-rats. As expected, in mice, the various circadian clock genes peaked at different times of the day; the Period gene (Per) group peaked in the evening, whereas Brain and Muscle ARNT-like1 (Bmal1) gene peaked in the morning; this phase shift is considered to be fundamental for circadian clock function. In sharp contrast, in the naked mole-rat both Per1 and Per2, as well as Bmal1, peaked at the same time in the morning-around ZT2-suggesting the organization of the molecular circadian oscillator was different. Moreover, gene expression rhythms associated with glucose metabolism and mTOR signaling also differed between the species. Although the activity of mTORC1 was lower, while that of mTORC2 was higher in naked mole-rat livers compared to mice, unlike that of mice where the expression profiles of glucose metabolism genes were not synchronized, these were highly synchronized in naked mole-rats and likely linked to their use of feeding times at zeitgebers.
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Affiliation(s)
- Soumyaditya Ghosh
- BGES Department, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA
| | - Kaitlyn N Lewis
- Barshop Institute for Aging and Longevity Studies, UTHSCSA, San Antonio, TX, USA
| | - Richa Tulsian
- BGES Department, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA
| | - Artem A Astafev
- BGES Department, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA
| | - Rochelle Buffenstein
- Barshop Institute for Aging and Longevity Studies, UTHSCSA, San Antonio, TX, USA.,Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Roman V Kondratov
- BGES Department, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA
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Mehta D, Krahmer J, Uhrig RG. Closing the protein gap in plant chronobiology. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1509-1522. [PMID: 33783885 DOI: 10.1111/tpj.15254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Our modern understanding of diel cell regulation in plants stems from foundational work in the late 1990s that analysed the dynamics of selected genes and mutants in Arabidopsis thaliana. The subsequent rise of transcriptomics technologies such as microarrays and RNA sequencing has substantially increased our understanding of anticipatory (circadian) and reactive (light- or dark-triggered) diel events in plants. However, it is also becoming clear that gene expression data fail to capture critical events in diel regulation that can only be explained by studying protein-level dynamics. Over the past decade, mass spectrometry technologies and quantitative proteomic workflows have significantly advanced, finally allowing scientists to characterise diel protein regulation at high throughput. Initial proteomic investigations suggest that the diel transcriptome and proteome generally lack synchrony and that the timing of daily regulatory events in plants is impacted by multiple levels of protein regulation (e.g., post-translational modifications [PTMs] and protein-protein interactions [PPIs]). Here, we highlight and summarise how the use of quantitative proteomics to elucidate diel plant cell regulation has advanced our understanding of these processes. We argue that this new understanding, coupled with the extraordinary developments in mass spectrometry technologies, demands greater focus on protein-level regulation of, and by, the circadian clock. This includes hitherto unexplored diel dynamics of protein turnover, PTMs, protein subcellular localisation and PPIs that can be masked by simple transcript- and protein-level changes. Finally, we propose new directions for how the latest advancements in quantitative proteomics can be utilised to answer outstanding questions in plant chronobiology.
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Affiliation(s)
- Devang Mehta
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Johanna Krahmer
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - R Glen Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
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Circadian Clock Control of Translation Initiation Factor eIF2α Activity Requires eIF2γ-Dependent Recruitment of Rhythmic PPP-1 Phosphatase in Neurospora crassa. mBio 2021; 12:mBio.00871-21. [PMID: 34006661 PMCID: PMC8262944 DOI: 10.1128/mbio.00871-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The circadian clock controls the phosphorylation and activity of eukaryotic translation initiation factor 2α (eIF2α). In Neurospora crassa, the clock drives a daytime peak in the activity of the eIF2α kinase CPC-3, the homolog of yeast and mammalian GCN2 kinase. This leads to increased levels of phosphorylated eIF2α (P-eIF2α) and reduced mRNA translation initiation during the day. We hypothesized that rhythmic eIF2α activity also requires dephosphorylation of P-eIF2α at night by phosphatases. In support of this hypothesis, we show that mutation of N. crassa PPP-1, a homolog of the yeast eIF2α phosphatase GLC7, leads to high and arrhythmic P-eIF2α levels, while maintaining core circadian oscillator function. PPP-1 levels are clock-controlled, peaking in the early evening, and rhythmic PPP-1 levels are necessary for rhythmic P-eIF2α accumulation. Deletion of the N terminus of N. crassa eIF2γ, the region necessary for eIF2γ interaction with GLC7 in yeast, led to high and arrhythmic P-eIF2α levels. These data supported that N. crassa eIF2γ functions to recruit PPP-1 to dephosphorylate eIF2α at night. Thus, in addition to the activity of CPC-3 kinase, circadian clock regulation of eIF2α activity requires dephosphorylation by PPP-1 phosphatase at night. These data show how the circadian clock controls the activity a central regulator of translation, critical for cellular metabolism and growth control, through the temporal coordination of phosphorylation and dephosphorylation events.
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48
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de Assis LVM, Oster H. The circadian clock and metabolic homeostasis: entangled networks. Cell Mol Life Sci 2021; 78:4563-4587. [PMID: 33683376 PMCID: PMC8195959 DOI: 10.1007/s00018-021-03800-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/28/2021] [Accepted: 02/23/2021] [Indexed: 12/12/2022]
Abstract
The circadian clock exerts an important role in systemic homeostasis as it acts a keeper of time for the organism. The synchrony between the daily challenges imposed by the environment needs to be aligned with biological processes and with the internal circadian clock. In this review, it is provided an in-depth view of the molecular functioning of the circadian molecular clock, how this system is organized, and how central and peripheral clocks communicate with each other. In this sense, we provide an overview of the neuro-hormonal factors controlled by the central clock and how they affect peripheral tissues. We also evaluate signals released by peripheral organs and their effects in the central clock and other brain areas. Additionally, we evaluate a possible communication between peripheral tissues as a novel layer of circadian organization by reviewing recent studies in the literature. In the last section, we analyze how the circadian clock can modulate intracellular and tissue-dependent processes of metabolic organs. Taken altogether, the goal of this review is to provide a systemic and integrative view of the molecular clock function and organization with an emphasis in metabolic tissues.
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Affiliation(s)
| | - Henrik Oster
- Center of Brain, Behavior and Metabolism, University of Lübeck, Institute of Neurobiology, Marie Curie Street, 23562, Lübeck, Germany.
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Dudek M, Angelucci C, Pathiranage D, Wang P, Mallikarjun V, Lawless C, Swift J, Kadler KE, Boot-Handford RP, Hoyland JA, Lamande SR, Bateman JF, Meng QJ. Circadian time series proteomics reveals daily dynamics in cartilage physiology. Osteoarthritis Cartilage 2021; 29:739-749. [PMID: 33610821 PMCID: PMC8113022 DOI: 10.1016/j.joca.2021.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 01/28/2021] [Accepted: 02/08/2021] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Cartilage in joints such as the hip and knee experiences repeated phases of heavy loading and low load recovery during the 24-h day/night cycle. Our previous work has shown 24 h rhythmic changes in gene expression at transcript level between night and day in wild type mouse cartilage which is lost in a circadian clock knock-out mouse model. However, it remains unknown to what extent circadian rhythms also regulate protein level gene expression in this matrix rich tissue. METHODS We investigated daily changes of protein abundance in mouse femoral head articular cartilage by performing a 48-h time-series LC-MS/MS analysis. RESULTS Out of the 1,177 proteins we identified across all time points, 145 proteins showed rhythmic changes in their abundance within the femoral head cartilage. Among these were molecules that have been implicated in key cartilage functions, including CTGF, MATN1, PAI-1 and PLOD1 & 2. Pathway analysis revealed that protein synthesis, cytoskeleton and glucose metabolism exhibited time-of-day dependent functions. Analysis of published cartilage proteomics datasets revealed that a significant portion of rhythmic proteins were dysregulated in osteoarthritis and/or ageing. CONCLUSIONS Our circadian proteomics study reveals that articular cartilage is a much more dynamic tissue than previously thought, with chondrocytes driving circadian rhythms not only in gene transcription but also in protein abundance. Our results clearly call for the consideration of circadian timing mechanisms not only in cartilage biology, but also in the pathogenesis, treatment strategies and biomarker detection in osteoarthritis.
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Affiliation(s)
- M Dudek
- Wellcome Centre for Cell Matrix Research, Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, UK
| | - C Angelucci
- Murdoch Children's Research Institute and University of Melbourne, Parkville, Victoria, Australia
| | - D Pathiranage
- Wellcome Centre for Cell Matrix Research, Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, UK
| | - P Wang
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - V Mallikarjun
- Wellcome Centre for Cell Matrix Research, Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, UK
| | - C Lawless
- Wellcome Centre for Cell Matrix Research, Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, UK
| | - J Swift
- Wellcome Centre for Cell Matrix Research, Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, UK
| | - K E Kadler
- Wellcome Centre for Cell Matrix Research, Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, UK
| | - R P Boot-Handford
- Wellcome Centre for Cell Matrix Research, Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, UK
| | - J A Hoyland
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK; NIHR Manchester Biomedical Research Centre, Central Manchester Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - S R Lamande
- Murdoch Children's Research Institute and University of Melbourne, Parkville, Victoria, Australia
| | - J F Bateman
- Murdoch Children's Research Institute and University of Melbourne, Parkville, Victoria, Australia
| | - Q-J Meng
- Wellcome Centre for Cell Matrix Research, Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, UK.
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Maury E, Navez B, Brichard SM. Circadian clock dysfunction in human omental fat links obesity to metabolic inflammation. Nat Commun 2021; 12:2388. [PMID: 33888702 PMCID: PMC8062496 DOI: 10.1038/s41467-021-22571-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 03/12/2021] [Indexed: 01/01/2023] Open
Abstract
To unravel the pathogenesis of obesity and its complications, we investigate the interplay between circadian clocks and NF-κB pathway in human adipose tissue. The circadian clock function is impaired in omental fat from obese patients. ChIP-seq analyses reveal that the core clock activator, BMAL1 binds to several thousand target genes. NF-κB competes with BMAL1 for transcriptional control of some targets and overall, BMAL1 chromatin binding occurs in close proximity to NF-κB consensus motifs. Obesity relocalizes BMAL1 occupancy genome-wide in human omental fat, thereby altering the transcription of numerous target genes involved in metabolic inflammation and adipose tissue remodeling. Eventually, clock dysfunction appears at early stages of obesity in mice and is corrected, together with impaired metabolism, by NF-κB inhibition. Collectively, our results reveal a relationship between NF-κB and the molecular clock in adipose tissue, which may contribute to obesity-related complications.
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Affiliation(s)
- Eleonore Maury
- Endocrinology, Diabetes and Nutrition Unit, Institute of Experimental and Clinical Research, UCLouvain, Brussels, Belgium.
| | - Benoit Navez
- Digestive Surgery Unit, Saint-Luc University Hospital, UCLouvain, Brussels, Belgium
| | - Sonia M Brichard
- Endocrinology, Diabetes and Nutrition Unit, Institute of Experimental and Clinical Research, UCLouvain, Brussels, Belgium
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