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Mauri S, Favaro M, Bernardo G, Mazzotta GM, Ziviani E. Mitochondrial autophagy in the sleeping brain. Front Cell Dev Biol 2022; 10:956394. [PMID: 36092697 PMCID: PMC9449320 DOI: 10.3389/fcell.2022.956394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
A significant percentage of the mitochondrial mass is replaced on a daily basis via mechanisms of mitochondrial quality control. Through mitophagy (a selective type of autophagy that promotes mitochondrial proteostasis) cells keep a healthy pool of mitochondria, and prevent oxidative stress and inflammation. Furthermore, mitophagy helps adapting to the metabolic demand of the cells, which changes on a daily basis.Core components of the mitophagy process are PINK1 and Parkin, which mutations are linked to Parkinson’s Disease. The crucial role of PINK1/Parkin pathway during stress-induced mitophagy has been extensively studied in vitro in different cell types. However, recent advances in the field allowed discovering that mitophagy seems to be only slightly affected in PINK1 KO mice and flies, putting into question the physiological relevance of this pathway in vivo in the whole organism. Indeed, several cell-specific PINK1/Parkin-independent mitophagy pathways have been recently discovered, which appear to be activated under physiological conditions such as those that promote mitochondrial proteome remodeling during differentiation or in response to specific physiological stimuli.In this Mini Review we want to summarize the recent advances in the field, and add another level of complexity by focusing attention on a potentially important aspect of mitophagy regulation: the implication of the circadian clock. Recent works showed that the circadian clock controls many aspects of mitochondrial physiology, including mitochondrial morphology and dynamic, respiratory activity, and ATP synthesis. Furthermore, one of the essential functions of sleep, which is controlled by the clock, is the clearance of toxic metabolic compounds from the brain, including ROS, via mechanisms of proteostasis. Very little is known about a potential role of the clock in the quality control mechanisms that maintain the mitochondrial repertoire healthy during sleep/wake cycles. More importantly, it remains completely unexplored whether (dys)function of mitochondrial proteostasis feedbacks to the circadian clockwork.
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Affiliation(s)
| | | | | | | | - Elena Ziviani
- *Correspondence: Gabriella M. Mazzotta, Elena Ziviani,
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2
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Ukita Y, Okumura M, Chihara T. Ubiquitin proteasome system in circadian rhythm and sleep homeostasis: Lessons from Drosophila. Genes Cells 2022; 27:381-391. [PMID: 35438236 PMCID: PMC9322287 DOI: 10.1111/gtc.12935] [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] [Received: 02/15/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 11/30/2022]
Abstract
Sleep is regulated by two main processes: the circadian clock and sleep homeostasis. Circadian rhythms have been well studied at the molecular level. In the Drosophila circadian clock neurons, the core clock proteins are precisely regulated by post-translational modifications and degraded via the ubiquitin-proteasome system (UPS). Sleep homeostasis, however, is less understood; nevertheless, recent reports suggest that proteasome-mediated degradation of core clock proteins or synaptic proteins contributes to the regulation of sleep amount. Here, we review the molecular mechanism of the UPS and summarize the role of protein degradation in the regulation of circadian clock and homeostatic sleep in Drosophila. Moreover, we discuss the potential interaction between circadian clock and homeostatic sleep regulation with a prime focus on E3 ubiquitin ligases.
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Affiliation(s)
- Yumiko Ukita
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Misako Okumura
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan.,Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Takahiro Chihara
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan.,Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
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3
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de Sousa Nogueira Freitas L, da Silva FR, Andrade HDA, Guerreiro RC, Paulo FV, de Mello MT, Silva A. Sleep debt induces skeletal muscle injuries in athletes: A promising hypothesis. Med Hypotheses 2020; 142:109836. [PMID: 32422497 DOI: 10.1016/j.mehy.2020.109836] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/23/2020] [Accepted: 05/11/2020] [Indexed: 01/18/2023]
Abstract
Sleep is a physiological state and it is fundamental for physical and cognitive recovery of athletes. Due to strenuous training and competitions, athletes may present sleep complaints compromising good quality and quantity of sleep. Studies have related sleep debt to the occurrence of musculoskeletal injuries in athletes, but the mechanisms that can lead to this are not entirely clear. Studies involving animals and humans have shown that poor sleep quality can cause significant changes in hormones and cytokines. Demonstrating that this hormones changes lead to a decrease of testosterone and growth hormone levels and increased cortisol levels, important hormones in the process of protein synthesis and degradation. In athletes, the sport itself is a risk factor of injuries, and sleep debt may result in overtraining syndrome associated with inflammatory markers and ultimately to immune system dysfunction. Thus, we hypothesize that athletes who have sleep debt are more susceptible to musculoskeletal injuries due to increased catabolic pathway signaling, i.e. protein degradation and decreased anabolic pathway signaling, compromising muscle integrity. In this sense, we indicate the relationship between musculoskeletal injuries and sleep debt involving new targets for immunological signaling pathways that start the reduction of the muscle recovery process.
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Affiliation(s)
| | - Flavia Rodrigues da Silva
- Departamento de Esportes, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Renato Carvalho Guerreiro
- Departamento de Esportes, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fernanda Viegas Paulo
- Departamento de Esportes, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marco Túlio de Mello
- Departamento de Esportes, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Andressa Silva
- Departamento de Esportes, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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4
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Abstract
Alzheimer's amyloid beta can perform a wide variety of actions that are highly concentration dependent. This viewpoint aims to provide a framework for basic considerations on what might be considered brain-relevant concentrations of the peptide. Some implications for the therapeutic implementation of the recently emerged oligomer-to-fibril strategy are discussed.
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Affiliation(s)
- Jevgenij A. Raskatov
- Department of Chemistry and Biochemistry, Physical Science Building 356, 1156 High Street, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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5
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On the cause of sleep: Protein fragments, the concept of sentinels, and links to epilepsy. Proc Natl Acad Sci U S A 2019; 116:10773-10782. [PMID: 31085645 DOI: 10.1073/pnas.1904709116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The molecular-level cause of sleep is unknown. In 2012, we suggested that the cause of sleep stems from cumulative effects of numerous intracellular and extracellular protein fragments. According to the fragment generation (FG) hypothesis, protein fragments (which are continually produced through nonprocessive cleavages by intracellular, intramembrane, and extracellular proteases) can be beneficial but toxic as well, and some fragments are eliminated slowly during wakefulness. We consider the FG hypothesis and propose that, during wakefulness, the degradation of accumulating fragments is delayed within natural protein aggregates such as postsynaptic densities (PSDs) in excitatory synapses and in other dense protein meshworks, owing to an impeded diffusion of the ∼3,000-kDa 26S proteasome. We also propose that a major function of sleep involves a partial and reversible expansion of PSDs, allowing an accelerated destruction of PSD-localized fragments by the ubiquitin/proteasome system. Expansion of PSDs would alter electrochemistry of synapses, thereby contributing to a decreased neuronal firing during sleep. If so, the loss of consciousness, a feature of sleep, would be the consequence of molecular processes (expansions of protein meshworks) that are required for degradation of protein fragments. We consider the concept of FG sentinels, which signal to sleep-regulating circuits that the levels of fragments are going up. Also discussed is the possibility that protein fragments, which are known to be overproduced during an epileptic seizure, may contribute to postictal sleep and termination of seizures. These and related suggestions, described in the paper, are compatible with current evidence about sleep and lead to testable predictions.
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N-terminal arginylation generates a bimodal degron that modulates autophagic proteolysis. Proc Natl Acad Sci U S A 2018; 115:E2716-E2724. [PMID: 29507222 DOI: 10.1073/pnas.1719110115] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The conjugation of amino acids to the protein N termini is universally observed in eukaryotes and prokaryotes, yet its functions remain poorly understood. In eukaryotes, the amino acid l-arginine (l-Arg) is conjugated to N-terminal Asp (Nt-Asp), Glu, Gln, Asn, and Cys, directly or associated with posttranslational modifications. Following Nt-arginylation, the Nt-Arg is recognized by UBR boxes of N-recognins such as UBR1, UBR2, UBR4/p600, and UBR5/EDD, leading to substrate ubiquitination and proteasomal degradation via the N-end rule pathway. It has been a mystery, however, why studies for the past five decades identified only a handful of Nt-arginylated substrates in mammals, although five of 20 principal amino acids are eligible for arginylation. Here, we show that the Nt-Arg functions as a bimodal degron that directs substrates to either the ubiquitin (Ub)-proteasome system (UPS) or macroautophagy depending on physiological states. In normal conditions, the arginylated forms of proteolytic cleavage products, D101-CDC6 and D1156-BRCA1, are targeted to UBR box-containing N-recognins and degraded by the proteasome. However, when proteostasis by the UPS is perturbed, their Nt-Arg redirects these otherwise cellular wastes to macroautophagy through its binding to the ZZ domain of the autophagic adaptor p62/STQSM/Sequestosome-1. Upon binding to the Nt-Arg, p62 acts as an autophagic N-recognin that undergoes self-polymerization, facilitating cargo collection and lysosomal degradation of p62-cargo complexes. A chemical mimic of Nt-Arg redirects Ub-conjugated substrates from the UPS to macroautophagy and promotes their lysosomal degradation. Our results suggest that the Nt-Arg proteome of arginylated proteins contributes to reprogramming global proteolytic flux under stresses.
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Sanders J, Scholz M, Merutka I, Biron D. Distinct unfolded protein responses mitigate or mediate effects of nonlethal deprivation of C. elegans sleep in different tissues. BMC Biol 2017; 15:67. [PMID: 28844202 PMCID: PMC5572162 DOI: 10.1186/s12915-017-0407-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 07/24/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Disrupting sleep during development leads to lasting deficits in chordates and arthropods. To address lasting impacts of sleep deprivation in Caenorhabditis elegans, we established a nonlethal deprivation protocol. RESULTS Deprivation triggered protective insulin-like signaling and two unfolded protein responses (UPRs): the mitochondrial (UPRmt) and the endoplasmic reticulum (UPRER) responses. While the latter is known to be triggered by sleep deprivation in rodent and insect brains, the former was not strongly associated with sleep deprivation previously. We show that deprivation results in a feeding defect when the UPRmt is deficient and in UPRER-dependent germ cell apoptosis. In addition, when the UPRER is deficient, deprivation causes excess twitching in vulval muscles, mirroring a trend caused by loss of egg-laying command neurons. CONCLUSIONS These data show that nonlethal deprivation of C. elegans sleep causes proteotoxic stress. Unless mitigated, distinct types of deprivation-induced proteotoxicity can lead to anatomically and genetically separable lasting defects. The relative importance of different UPRs post-deprivation likely reflects functional, developmental, and genetic differences between the respective tissues and circuits.
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Affiliation(s)
- Jarred Sanders
- Genetics, Genomics, and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA.
| | - Monika Scholz
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - Ilaria Merutka
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - David Biron
- Genetics, Genomics, and Systems Biology, The University of Chicago, Chicago, IL, 60637, USA.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA.,Department of Physics, The University of Chicago, Chicago, IL, 60637, USA
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8
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Sleep and Development in Genetically Tractable Model Organisms. Genetics 2017; 203:21-33. [PMID: 27183564 DOI: 10.1534/genetics.116.189589] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/21/2016] [Indexed: 12/21/2022] Open
Abstract
Sleep is widely recognized as essential, but without a clear singular function. Inadequate sleep impairs cognition, metabolism, immune function, and many other processes. Work in genetic model systems has greatly expanded our understanding of basic sleep neurobiology as well as introduced new concepts for why we sleep. Among these is an idea with its roots in human work nearly 50 years old: sleep in early life is crucial for normal brain maturation. Nearly all known species that sleep do so more while immature, and this increased sleep coincides with a period of exuberant synaptogenesis and massive neural circuit remodeling. Adequate sleep also appears critical for normal neurodevelopmental progression. This article describes recent findings regarding molecular and circuit mechanisms of sleep, with a focus on development and the insights garnered from models amenable to detailed genetic analyses.
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Wadas B, Piatkov KI, Brower CS, Varshavsky A. Analyzing N-terminal Arginylation through the Use of Peptide Arrays and Degradation Assays. J Biol Chem 2016; 291:20976-20992. [PMID: 27510035 DOI: 10.1074/jbc.m116.747956] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Indexed: 01/29/2023] Open
Abstract
Nα-terminal arginylation (Nt-arginylation) of proteins is mediated by the Ate1 arginyltransferase (R-transferase), a component of the Arg/N-end rule pathway. This proteolytic system recognizes proteins containing N-terminal degradation signals called N-degrons, polyubiquitylates these proteins, and thereby causes their degradation by the proteasome. The definitively identified ("canonical") residues that are Nt-arginylated by R-transferase are N-terminal Asp, Glu, and (oxidized) Cys. Over the last decade, several publications have suggested (i) that Ate1 can also arginylate non-canonical N-terminal residues; (ii) that Ate1 is capable of arginylating not only α-amino groups of N-terminal residues but also γ-carboxyl groups of internal (non-N-terminal) Asp and Glu; and (iii) that some isoforms of Ate1 are specific for substrates bearing N-terminal Cys residues. In the present study, we employed arrays of immobilized 11-residue peptides and pulse-chase assays to examine the substrate specificity of mouse R-transferase. We show that amino acid sequences immediately downstream of a substrate's canonical (Nt-arginylatable) N-terminal residue, particularly a residue at position 2, can affect the rate of Nt-arginylation by R-transferase and thereby the rate of degradation of a substrate protein. We also show that the four major isoforms of mouse R-transferase have similar Nt-arginylation specificities in vitro, contrary to the claim about the specificity of some Ate1 isoforms for N-terminal Cys. In addition, we found no evidence for a significant activity of the Ate1 R-transferase toward previously invoked non-canonical N-terminal or internal amino acid residues. Together, our results raise technical concerns about earlier studies that invoked non-canonical arginylation specificities of Ate1.
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Affiliation(s)
- Brandon Wadas
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Konstantin I Piatkov
- the Center for Biotechnology and Biomedicine, Skolkovo Institute of Science and Technology, Moscow 143026, Russia, and
| | | | - Alexander Varshavsky
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125,
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10
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Mader EC, Mader ACL. Sleep as spatiotemporal integration of biological processes that evolved to periodically reinforce neurodynamic and metabolic homeostasis: The 2m3d paradigm of sleep. J Neurol Sci 2016; 367:63-80. [PMID: 27423566 DOI: 10.1016/j.jns.2016.05.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 05/12/2016] [Accepted: 05/13/2016] [Indexed: 11/19/2022]
Abstract
Sleep continues to perplex scientists and researchers. Despite decades of sleep research, we still lack a clear understanding of the biological functions and evolution of sleep. In this review, we will examine sleep from a functional and phylogenetic perspective and describe some important conceptual gaps in understanding sleep. Classical theories of the biology and evolution of sleep emphasize sensory activation, energy balance, and metabolic homeostasis. Advances in electrophysiology, functional neuroimaging, and neuroplasticity allow us to view sleep within the framework of neural dynamics. With this paradigm shift, we have come to realize the importance of neurodynamic homeostasis in shaping the biology of sleep. Evidently, animals sleep to achieve neurodynamic and metabolic homeostasis. We are not aware of any framework for understanding sleep where neurodynamic, metabolic, homeostatic, chronophasic, and afferent variables are all taken into account. This motivated us to propose the two-mode three-drive (2m3d) paradigm of sleep. In the 2m3d paradigm, local neurodynamic/metabolic (N/M) processes switch between two modes-m0 and m1-in response to three drives-afferent, chronophasic, and homeostatic. The spatiotemporal integration of local m0/m1 operations gives rise to the global states of sleep and wakefulness. As a framework of evolution, the 2m3d paradigm allows us to view sleep as a robust adaptive strategy that evolved so animals can periodically reinforce neurodynamic and metabolic homeostasis while remaining sensitive to their internal and external environment.
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Affiliation(s)
- Edward Claro Mader
- Louisiana State University Health Sciences Center, Department of Neurology, New Orleans, LA 70112, USA.
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11
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Liu YJ, Liu C, Chang Z, Wadas B, Brower CS, Song ZH, Xu ZL, Shang YL, Liu WX, Wang LN, Dong W, Varshavsky A, Hu RG, Li W. Degradation of the Separase-cleaved Rec8, a Meiotic Cohesin Subunit, by the N-end Rule Pathway. J Biol Chem 2016; 291:7426-38. [PMID: 26858254 DOI: 10.1074/jbc.m116.714964] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Indexed: 02/05/2023] Open
Abstract
The Ate1 arginyltransferase (R-transferase) is a component of the N-end rule pathway, which recognizes proteins containing N-terminal degradation signals called N-degrons, polyubiquitylates these proteins, and thereby causes their degradation by the proteasome. Ate1 arginylates N-terminal Asp, Glu, or (oxidized) Cys. The resulting N-terminal Arg is recognized by ubiquitin ligases of the N-end rule pathway. In the yeastSaccharomyces cerevisiae, the separase-mediated cleavage of the Scc1/Rad21/Mcd1 cohesin subunit generates a C-terminal fragment that bears N-terminal Arg and is destroyed by the N-end rule pathway without a requirement for arginylation. In contrast, the separase-mediated cleavage of Rec8, the mammalian meiotic cohesin subunit, yields a fragment bearing N-terminal Glu, a substrate of the Ate1 R-transferase. Here we constructed and used a germ cell-confinedAte1(-/-)mouse strain to analyze the separase-generated C-terminal fragment of Rec8. We show that this fragment is a short-lived N-end rule substrate, that its degradation requires N-terminal arginylation, and that maleAte1(-/-)mice are nearly infertile, due to massive apoptotic death ofAte1(-/-)spermatocytes during the metaphase of meiosis I. These effects ofAte1ablation are inferred to be caused, at least in part, by the failure to destroy the C-terminal fragment of Rec8 in the absence of N-terminal arginylation.
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Affiliation(s)
- Yu-Jiao Liu
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China, the College of Marine Life, Ocean University of China, Qingdao 266003, China, and
| | - Chao Liu
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China, the University of the Chinese Academy of Sciences, Beijing 100049, China
| | - ZeNan Chang
- the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Brandon Wadas
- the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Christopher S Brower
- the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, the Department of Biology, Texas Woman's University, Denton, Texas 76204
| | - Zhen-Hua Song
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China, the University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi-Liang Xu
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China, the University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Liang Shang
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China, the University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wei-Xiao Liu
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Li-Na Wang
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China, the University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wen Dong
- the College of Marine Life, Ocean University of China, Qingdao 266003, China, and
| | - Alexander Varshavsky
- the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125,
| | - Rong-Gui Hu
- the State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wei Li
- From the State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China,
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Eldeeb MA, Fahlman RP. The anti-apoptotic form of tyrosine kinase Lyn that is generated by proteolysis is degraded by the N-end rule pathway. Oncotarget 2015; 5:2714-22. [PMID: 24798867 PMCID: PMC4058039 DOI: 10.18632/oncotarget.1931] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The activation of apoptotic pathways results in the caspase cleavage of the Lyn tyrosine kinase to generate the N-terminal truncated LynΔN. This LynΔN fragment has been demonstrated to exert negative feedback on imatinib induced apoptosis in chronic myelogenous leukemia (CML) K562 cells. Our investigations focus on LynΔN stability and how reduced stability reduces imatinib resistance. As the proteolytical generated LynΔN has a leucine as an N-terminal amino acid, we hypothesized that LynΔN would be degraded by the N-end rule pathway. We demonstrated that LynΔN is unstable and that its stability is dependent on the identity of its N-terminus. Additionally we established that LynΔN degradation could be inhibited by either inhibiting the proteasome or knocking down the UBR1 and UBR2 ubiquitin E3 ligases. Importantly, we also demonstrate that LynΔN degradation by the N-end rule counters the imatinib resistance of K562 cells provided by LynΔN expression. Together our data suggest a possible mechanism for the N-end rule pathway having a link to imatinib resistance in CML. With LynΔN being an N-end rule substrate, it provides the first example that this pathway can also provide a pro-apoptotic function as previous reports have currently only demonstrated anti-apoptotic roles for the N-end rule pathway.
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Affiliation(s)
- Mohamed A Eldeeb
- Department of Biochemistry, University of Alberta, Edmonton Alberta Canada
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13
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Abstract
A commonly held view is that extended wakefulness is causal for a broad spectrum of deleterious effects at molecular, cellular, network, physiological, psychological, and behavioral levels. Consequently, it is often presumed that sleep plays an active role in providing renormalization of the changes incurred during preceding waking. Not surprisingly, unequivocal empirical evidence supporting such a simple bi-directional interaction between waking and sleep is often limited or controversial. One difficulty is that, invariably, a constellation of many intricately interrelated factors, including the time of day, specific activities or behaviors during preceding waking, metabolic status and stress are present at the time of measurement, shaping the overall effect observed. In addition to this, although insufficient or disrupted sleep is thought to prevent efficient recovery of specific physiological variables, it is also often difficult to attribute specific changes to the lack of sleep proper. Furthermore, sleep is a complex phenomenon characterized by a multitude of processes, whose unique and distinct contributions to the purported functions of sleep are difficult to determine, because they are interrelated. Intensive research effort over the last decades has greatly progressed current understanding of the cellular and physiological processes underlying the regulation of vigilance states. Notably, it also highlighted the infinite complexity within both waking and sleep, and revealed a number of fundamental conceptual and technical obstacles that need to be overcome in order to fully understand these processes. A promising approach could be to view sleep not as an entity, which has specific function(s) and is subject to direct regulation, but as a manifestation of the process of metaregulation, which enables efficient moment-to-moment integration between internal and external factors, preceding history and current homeostatic needs.
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14
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Liat1, an arginyltransferase-binding protein whose evolution among primates involved changes in the numbers of its 10-residue repeats. Proc Natl Acad Sci U S A 2014; 111:E4936-45. [PMID: 25369936 DOI: 10.1073/pnas.1419587111] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The arginyltransferase Ate1 is a component of the N-end rule pathway, which recognizes proteins containing N-terminal degradation signals called N-degrons, polyubiquitylates these proteins, and thereby causes their degradation by the proteasome. At least six isoforms of mouse Ate1 are produced through alternative splicing of Ate1 pre-mRNA. We identified a previously uncharacterized mouse protein, termed Liat1 (ligand of Ate1), that interacts with Ate1 but does not appear to be its arginylation substrate. Liat1 has a higher affinity for the isoforms Ate1(1A7A) and Ate1(1B7A). Liat1 stimulated the in vitro N-terminal arginylation of a model substrate by Ate1. All examined vertebrate and some invertebrate genomes encode proteins sequelogous (similar in sequence) to mouse Liat1. Sequelogs of Liat1 share a highly conserved ∼30-residue region that is shown here to be required for the binding of Liat1 to Ate1. We also identified non-Ate1 proteins that interact with Liat1. In contrast to Liat1 genes of nonprimate mammals, Liat1 genes of primates are subtelomeric, a location that tends to confer evolutionary instability on a gene. Remarkably, Liat1 proteins of some primates, from macaques to humans, contain tandem repeats of a 10-residue sequence, whereas Liat1 proteins of other mammals contain a single copy of this motif. Quantities of these repeats are, in general, different in Liat1 of different primates. For example, there are 1, 4, 13, 13, 17, and 17 repeats in the gibbon, gorilla, orangutan, bonobo, neanderthal, and human Liat1, respectively, suggesting that repeat number changes in this previously uncharacterized protein may contribute to evolution of primates.
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15
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The energy allocation function of sleep: A unifying theory of sleep, torpor, and continuous wakefulness. Neurosci Biobehav Rev 2014; 47:122-53. [DOI: 10.1016/j.neubiorev.2014.08.001] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 06/27/2014] [Accepted: 08/02/2014] [Indexed: 12/14/2022]
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16
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Role of cardiorespiratory synchronization and sleep physiology: effects on membrane potential in the restorative functions of sleep. Sleep Med 2014; 15:279-88. [DOI: 10.1016/j.sleep.2013.10.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 10/18/2013] [Accepted: 10/19/2013] [Indexed: 01/26/2023]
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Calpain-generated natural protein fragments as short-lived substrates of the N-end rule pathway. Proc Natl Acad Sci U S A 2014; 111:E817-26. [PMID: 24550490 DOI: 10.1073/pnas.1401639111] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Calpains are Ca(2+)-dependent intracellular proteases. We show here that calpain-generated natural C-terminal fragments of proteins that include G protein-coupled receptors, transmembrane ion channels, transcriptional regulators, apoptosis controllers, kinases, and phosphatases (Phe-GluN2a, Lys-Ica512, Arg-Ankrd2, Tyr-Grm1, Arg-Atp2b2, Glu-Bak, Arg-Igfbp2, Glu-IκBα, and Arg-c-Fos), are short-lived substrates of the Arg/N-end rule pathway, which targets destabilizing N-terminal residues. We also found that the identity of a fragment's N-terminal residue can change during evolution, but the residue's destabilizing activity is virtually always retained, suggesting selection pressures that favor a short half-life of the calpain-generated fragment. It is also shown that a self-cleavage of a calpain can result in an N-end rule substrate. Thus, the autoprocessing of calpains can control them by making active calpains short-lived. These and related results indicate that the Arg/N-end rule pathway mediates the remodeling of oligomeric complexes by eliminating protein fragments that are produced in these complexes through cleavages by calpains or other nonprocessive proteases. We suggest that this capability of the Arg/N-end rule pathway underlies a multitude of its previously known but mechanistically unclear functions.
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Abstract
In the last decades a substantial knowledge about sleep mechanisms has been accumulated. However, the function of sleep still remains elusive. The difficulty with unraveling sleep's function may arise from the lack of understanding of how the multitude of processes associated with waking and sleep-from gene expression and single neuron activity to the whole brain dynamics and behavior-functionally and mechanistically relate to each other. Therefore, novel conceptual frameworks, which integrate and take into account the variety of phenomena occurring during waking and sleep at different levels, will likely lead to advances in our understanding of the function of sleep, above and beyond what merely descriptive or correlative approaches can provide. One such framework, the synaptic homeostasis hypothesis, focuses on wake- and sleep-dependent changes in synaptic strength. The core claim of this hypothesis is that learning and experience during wakefulness are associated with a net increase in synaptic strength. In turn, the proposed function of sleep is to provide synaptic renormalization, which has important implications with respect to energy needs, intracranial space, metabolic supplies, and, importantly, enables further plastic changes. In this article we review the empirical evidence for this hypothesis, which was obtained at several levels-from gene expression and cellular excitability to structural synaptic modifications and behavioral outcomes. We conclude that although the mechanisms behind the proposed role of sleep in synaptic homeostasis are undoubtedly complex, this conceptual framework offers a unique opportunity to provide mechanistic and functional explanation for many previously disparate observations, and define future research strategies.
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Witek MA, Fung LWM. Quantitative studies of caspase-3 catalyzed αII-spectrin breakdown. Brain Res 2013; 1533:1-15. [PMID: 23948103 PMCID: PMC3786445 DOI: 10.1016/j.brainres.2013.08.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/27/2013] [Accepted: 08/02/2013] [Indexed: 11/29/2022]
Abstract
Under various physiological and patho-physiological conditions, spectrin breakdown reactions generate several spectrin breakdown products (SBDPs)-in particular SBDPs of 150 kDa (SBDP150) and 120 kDa (SBDP120). Recently, numerous studies have shown that reactions leading to SBDPs are physiologically relevant, well regulated, and complex. Yet molecular studies on the mechanism of the SBDP formation are comparatively scarce. We have designed basic systems to allow us to follow the breakdown of αII-spectrin model proteins by caspase-3 in detail with gel electrophoresis, fluorescence and mass spectrometry methods. Amongst the predicted and reported sites, our results show that caspase-3 cleaves after residues D1185 and D1478, but not after residues D888, D1340 and D1475. We also found that the cleavage at these two sites is independent of each other. It may be possible to inhibit one site without affecting the other site. Cleavage after residue D1185 in intact αII-spectrin leads to SBDP150, and cleavage after D1478 site leads to SBDP120. Our results also show that the cleavage after the D1185 residue is unusually efficient, with a kcat/KM value of 40,000 M(-1) s(-1), and the cleavage after the D1478 site is more similar to most of the other reported caspase-3 substrates, with a kcat/KM value of 3000 M(-1) s(-1). We believe that this study lays out a methodology and foundation to study caspase-3 catalyzed spectrin breakdown to provide quantitative information. Molecular understanding may lead to better understanding of brain injuries and more precise and specific biomarker development.
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Affiliation(s)
- Marta A. Witek
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, MC 111, Chicago, IL 60607
| | - L. W.-M. Fung
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, MC 111, Chicago, IL 60607
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Brower CS, Piatkov KI, Varshavsky A. Neurodegeneration-associated protein fragments as short-lived substrates of the N-end rule pathway. Mol Cell 2013; 50:161-71. [PMID: 23499006 DOI: 10.1016/j.molcel.2013.02.009] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 01/18/2013] [Accepted: 02/06/2013] [Indexed: 10/27/2022]
Abstract
Protein aggregates are a common feature of neurodegenerative syndromes. Specific protein fragments were found to be aggregated in disorders including Alzheimer's disease, amyotrophic lateral sclerosis, and Parkinson's disease. Here, we show that the natural C-terminal fragments of Tau, TDP43, and α-synuclein are short-lived substrates of the Arg/N-end rule pathway, a processive proteolytic system that targets proteins bearing "destabilizing" N-terminal residues. Furthermore, a natural TDP43 fragment is shown to be metabolically stabilized in Ate1(-/-) fibroblasts that lack the arginylation branch of the Arg/N-end rule pathway, leading to accumulation and aggregation of this fragment. We also found that a fraction of Aβ42, the Alzheimer's disease-associated fragment of APP, is N-terminally arginylated in the brains of 5xFAD mice and is degraded by the Arg/N-end rule pathway. The discovery that neurodegeneration-associated natural fragments of TDP43, Tau, α-synuclein, and APP can be selectively destroyed by the Arg/N-end rule pathway suggests that this pathway counteracts neurodegeneration.
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Affiliation(s)
- Christopher S Brower
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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