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Vodičková A, Müller-Eigner A, Okoye CN, Bischer AP, Horn J, Koren SA, Selim NA, Wojtovich AP. Mitochondrial energy state controls AMPK-mediated foraging behavior in C. elegans. SCIENCE ADVANCES 2024; 10:eadm8815. [PMID: 38630817 PMCID: PMC11023558 DOI: 10.1126/sciadv.adm8815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/14/2024] [Indexed: 04/19/2024]
Abstract
Organisms surveil and respond to their environment using behaviors entrained by metabolic cues that reflect food availability. Mitochondria act as metabolic hubs and at the center of mitochondrial energy production is the protonmotive force (PMF), an electrochemical gradient generated by metabolite consumption. The PMF serves as a central integrator of mitochondrial status, but its role in governing metabolic signaling is poorly understood. We used optogenetics to dissipate the PMF in Caenorhabditis elegans tissues to test its role in food-related behaviors. Our data demonstrate that PMF reduction in the intestine is sufficient to initiate locomotor responses to acute food deprivation. This behavioral adaptation requires the cellular energy regulator AMP-activated protein kinase (AMPK) in neurons, not in the intestine, and relies on mitochondrial dynamics and axonal trafficking. Our results highlight a role for intestinal PMF as an internal metabolic cue, and we identify a bottom-up signaling axis through which changes in the PMF trigger AMPK activity in neurons to promote foraging behavior.
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Affiliation(s)
- Anežka Vodičková
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Annika Müller-Eigner
- Research Group Epigenetics, Metabolism and Longevity, Research Institute for Farm Animal Biology (FBN), Dummerstorf 18196, Germany
| | - Chidozie N. Okoye
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Andrew P. Bischer
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Jacob Horn
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Shon A. Koren
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Nada Ahmed Selim
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, USA
| | - Andrew P. Wojtovich
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester, NY, USA
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2
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Vlasova AD, Bukhalovich SM, Bagaeva DF, Polyakova AP, Ilyinsky NS, Nesterov SV, Tsybrov FM, Bogorodskiy AO, Zinovev EV, Mikhailov AE, Vlasov AV, Kuklin AI, Borshchevskiy VI, Bamberg E, Uversky VN, Gordeliy VI. Intracellular microbial rhodopsin-based optogenetics to control metabolism and cell signaling. Chem Soc Rev 2024; 53:3327-3349. [PMID: 38391026 DOI: 10.1039/d3cs00699a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Microbial rhodopsin (MRs) ion channels and pumps have become invaluable optogenetic tools for neuroscience as well as biomedical applications. Recently, MR-optogenetics expanded towards subcellular organelles opening principally new opportunities in optogenetic control of intracellular metabolism and signaling via precise manipulations of organelle ion gradients using light. This new optogenetic field expands the opportunities for basic and medical studies of cancer, cardiovascular, and metabolic disorders, providing more detailed and accurate control of cell physiology. This review summarizes recent advances in studies of the cellular metabolic processes and signaling mediated by optogenetic tools targeting mitochondria, endoplasmic reticulum (ER), lysosomes, and synaptic vesicles. Finally, we discuss perspectives of such an optogenetic approach in both fundamental and applied research.
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Affiliation(s)
- Anastasiia D Vlasova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Siarhei M Bukhalovich
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Diana F Bagaeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Aleksandra P Polyakova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Nikolay S Ilyinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Semen V Nesterov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Fedor M Tsybrov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Andrey O Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Egor V Zinovev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anatolii E Mikhailov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexey V Vlasov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Alexander I Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Valentin I Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Valentin I Gordeliy
- Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, 38027 Grenoble, France.
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Peterson A, Baskett C, Ratcliff WC, Burnetti A. Transforming yeast into a facultative photoheterotroph via expression of vacuolar rhodopsin. Curr Biol 2024; 34:648-654.e3. [PMID: 38218181 DOI: 10.1016/j.cub.2023.12.044] [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: 04/20/2023] [Revised: 11/03/2023] [Accepted: 12/13/2023] [Indexed: 01/15/2024]
Abstract
Phototrophic metabolism, the capture of light for energy, was a pivotal biological innovation that greatly increased the total energy available to the biosphere. Chlorophyll-based photosynthesis is the most familiar phototrophic metabolism, but retinal-based microbial rhodopsins transduce nearly as much light energy as chlorophyll does,1 via a simpler mechanism, and are found in far more taxonomic groups. Although this system has apparently spread widely via horizontal gene transfer,2,3,4 little is known about how rhodopsin genes (with phylogenetic origins within prokaryotes5,6) are horizontally acquired by eukaryotic cells with complex internal membrane architectures or the conditions under which they provide a fitness advantage. To address this knowledge gap, we sought to determine whether Saccharomyces cerevisiae, a heterotrophic yeast with no known evolutionary history of phototrophy, can function as a facultative photoheterotroph after acquiring a single rhodopsin gene. We inserted a rhodopsin gene from Ustilago maydis,7 which encodes a proton pump localized to the vacuole, an organelle normally acidified via a V-type rotary ATPase, allowing the rhodopsin to supplement heterotrophic metabolism. Probes of the physiology of modified cells show that they can deacidify the cytoplasm using light energy, demonstrating the ability of rhodopsins to ameliorate the effects of starvation and quiescence. Further, we show that yeast-bearing rhodopsins gain a selective advantage when illuminated, proliferating more rapidly than their non-phototrophic ancestor or rhodopsin-bearing yeast cultured in the dark. These results underscore the ease with which rhodopsins may be horizontally transferred even in eukaryotes, providing novel biological function without first requiring evolutionary optimization.
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Affiliation(s)
- Autumn Peterson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA
| | - Carina Baskett
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA.
| | - Anthony Burnetti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA.
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Daicho KM, Hirono-Hara Y, Kikukawa H, Tamura K, Hara KY. Engineering yeast with a light-driven proton pump system in the vacuolar membrane. Microb Cell Fact 2024; 23:4. [PMID: 38172917 PMCID: PMC10763269 DOI: 10.1186/s12934-023-02273-1] [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: 09/28/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The supply of ATP is a limiting factor for cellular metabolism. Therefore, cell factories require a sufficient ATP supply to drive metabolism for efficient bioproduction. In the current study, a light-driven proton pump in the vacuolar membrane was constructed in yeast to reduce the ATP consumption required by V-ATPase to maintain the acidification of the vacuoles and increase the intracellular ATP supply for bioproduction. RESULTS Delta rhodopsin (dR), a microbial light-driven proton-pumping rhodopsin from Haloterrigena turkmenica, was expressed and localized in the vacuolar membrane of Saccharomyces cerevisiae by conjugation with a vacuolar membrane-localized protein. Vacuoles with dR were isolated from S. cerevisiae, and the light-driven proton pumping activity was evaluated based on the pH change outside the vacuoles. A light-induced increase in the intracellular ATP content was observed in yeast harboring vacuoles with dR. CONCLUSIONS Yeast harboring the light-driven proton pump in the vacuolar membrane developed in this study are a potential optoenergetic cell factory suitable for various bioproduction applications.
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Affiliation(s)
- Kaoru M Daicho
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-Ku, Shizuoka, 422-8526, Japan
| | - Yoko Hirono-Hara
- 396Bio, Inc., University of Shizuoka, 52-1 Yada, Suruga-Ku, Shizuoka, 422-8526, Japan
| | - Hiroshi Kikukawa
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-Ku, Shizuoka, 422-8526, Japan
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-Ku, Shizuoka, 422-8526, Japan
| | - Kentaro Tamura
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-Ku, Shizuoka, 422-8526, Japan
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-Ku, Shizuoka, 422-8526, Japan
| | - Kiyotaka Y Hara
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-Ku, Shizuoka, 422-8526, Japan.
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-Ku, Shizuoka, 422-8526, Japan.
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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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6
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Chen K, Ernst P, Liu XM, Zhou L. Optogenetic Studies of Mitochondria. Methods Mol Biol 2022; 2501:311-324. [PMID: 35857235 DOI: 10.1007/978-1-0716-2329-9_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
While optogenetic approaches have been widely used for remote control of cell membrane excitability and intracellular signaling pathways, their application in mitochondrial study has been limited, largely due to the challenge of effectively and specifically expressing heterologous light-gated rhodopsin channels in the mitochondria. Here, we describe the methods for expressing functional channelrhodopsin 2 (ChR2) proteins in the mitochondrial inner membrane with an unusually long mitochondrial leading sequence and characterizing optogenetic-mediated mitochondrial membrane potential (ΔΨm) depolarization. We then illustrate how this next-generation optogenetic approach can be used to study the effect of ΔΨm on mitochondrial functions such as mitophagy, programed cell death, and preconditioning-mediated cytoprotection. We anticipate that this innovative technology will enable new insights into the mechanisms by which changes in ΔΨm differentially impacts mitochondrial and cellular functions.
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Affiliation(s)
- Kai Chen
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, USA
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Patrick Ernst
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, USA
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Xiaoguang Margaret Liu
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Lufang Zhou
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, USA.
- Division of Cardiovascular Disease, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
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Tsunoda SP, Sugiura M, Kandori H. Molecular Properties and Optogenetic Applications of Enzymerhodopsins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:153-165. [PMID: 33398812 DOI: 10.1007/978-981-15-8763-4_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The cyclic nucleotides cAMP and cGMP are ubiquitous secondary messengers that regulate multiple biological functions including gene expression, differentiation, proliferation, and cell survival. In sensory neurons, cyclic nucleotides are responsible for signal modulation, amplification, and encoding. For spatial and temporal manipulation of cyclic nucleotide dynamics, optogenetics have a great advantage over pharmacological approaches. Enzymerhodopsins are a unique family of microbial rhodopsins. These molecules are made up of a membrane-embedded rhodopsin domain, which binds an all trans-retinal to form a chromophore, and a cytoplasmic water-soluble catalytic domain. To date, three kinds of molecules have been identified from lower eukaryotes such as fungi, algae, and flagellates. Among these, histidine kinase rhodopsin (HKR) is a light-inhibited guanylyl cyclase. Rhodopsin GC (Rh-GC) functions as a light-activated guanylyl cyclase, while rhodopsin PDE (Rh-PDE) functions as a light-activated phosphodiesterase that degrades cAMP and cGMP. These enzymerhodopsins have great potential in optogenetic applications for manipulating the intracellular cyclic nucleotide dynamics of living cells. Here we introduce the molecular function and applicability of these molecules.
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Affiliation(s)
- Satoshi P Tsunoda
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan. .,JST PRESTO, Saitama, Japan.
| | - Masahiro Sugiura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
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Berry BJ, Wojtovich AP. Mitochondrial light switches: optogenetic approaches to control metabolism. FEBS J 2020; 287:4544-4556. [PMID: 32459870 DOI: 10.1111/febs.15424] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/11/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023]
Abstract
Developing new technologies to study metabolism is increasingly important as metabolic disease prevalence increases. Mitochondria control cellular metabolism and dynamic changes in mitochondrial function are associated with metabolic abnormalities in cardiovascular disease, cancer, and obesity. However, a lack of precise and reversible methods to control mitochondrial function has prevented moving from association to causation. Recent advances in optogenetics have addressed this challenge, and mitochondrial function can now be precisely controlled in vivo using light. A class of genetically encoded, light-activated membrane channels and pumps has addressed mechanistic questions that promise to provide new insights into how cellular metabolism downstream of mitochondrial function contributes to disease. Here, we highlight emerging reagents-mitochondria-targeted light-activated cation channels or proton pumps-to decrease or increase mitochondrial activity upon light exposure, a technique we refer to as mitochondrial light switches, or mtSWITCH . The mtSWITCH technique is broadly applicable, as energy availability and metabolic signaling are conserved aspects of cellular function and health. Here, we outline the use of these tools in diverse cellular models of disease. We review the molecular details of each optogenetic tool, summarize the results obtained with each, and outline best practices for using optogenetic approaches to control mitochondrial function and downstream metabolism.
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Affiliation(s)
- Brandon J Berry
- Department of Pharmacology and Physiology, University of Rochester Medical Center, NY, USA
| | - Andrew P Wojtovich
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, NY, USA
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9
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Berry BJ, Trewin AJ, Milliken AS, Baldzizhar A, Amitrano AM, Lim Y, Kim M, Wojtovich AP. Optogenetic control of mitochondrial protonmotive force to impact cellular stress resistance. EMBO Rep 2020; 21:e49113. [PMID: 32043300 PMCID: PMC7132214 DOI: 10.15252/embr.201949113] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/26/2019] [Accepted: 01/15/2020] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial respiration generates an electrochemical proton gradient across the mitochondrial inner membrane called protonmotive force (PMF) to drive diverse functions and synthesize ATP. Current techniques to manipulate the PMF are limited to its dissipation; yet, there is no precise and reversible method to increase the PMF. To address this issue, we aimed to use an optogenetic approach and engineered a mitochondria-targeted light-activated proton pump that we name mitochondria-ON (mtON) to selectively increase the PMF in Caenorhabditis elegans. Here we show that mtON photoactivation increases the PMF in a dose-dependent manner, supports ATP synthesis, increases resistance to mitochondrial toxins, and modulates energy-sensing behavior. Moreover, transient mtON activation during hypoxic preconditioning prevents the well-characterized adaptive response of hypoxia resistance. Our results show that optogenetic manipulation of the PMF is a powerful tool to modulate metabolism and cell signaling.
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Affiliation(s)
- Brandon J Berry
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNYUSA
| | - Adam J Trewin
- Department of Anesthesiology and Perioperative MedicineUniversity of Rochester Medical CenterRochesterNYUSA
| | - Alexander S Milliken
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNYUSA
| | - Aksana Baldzizhar
- Department of Anesthesiology and Perioperative MedicineUniversity of Rochester Medical CenterRochesterNYUSA
| | - Andrea M Amitrano
- Department of PathologyUniversity of Rochester Medical CenterRochesterNYUSA
- Department of Microbiology and ImmunologyUniversity of Rochester Medical CenterRochesterNYUSA
| | - Yunki Lim
- Nephrology DivisionDepartment of MedicineSchool of Medicine and DentistryUniversity of Rochester Medical CenterRochesterNYUSA
| | - Minsoo Kim
- Department of PathologyUniversity of Rochester Medical CenterRochesterNYUSA
- Department of Microbiology and ImmunologyUniversity of Rochester Medical CenterRochesterNYUSA
| | - Andrew P Wojtovich
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNYUSA
- Department of Anesthesiology and Perioperative MedicineUniversity of Rochester Medical CenterRochesterNYUSA
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Kurihara T, Asahi T, Sawamura N. Cereblon-mediated degradation of the amyloid precursor protein via the ubiquitin-proteasome pathway. Biochem Biophys Res Commun 2020; 524:236-241. [DOI: 10.1016/j.bbrc.2020.01.078] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/15/2020] [Indexed: 11/30/2022]
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11
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Imai Y, Inoshita T, Meng H, Shiba-Fukushima K, Hara KY, Sawamura N, Hattori N. Light-driven activation of mitochondrial proton-motive force improves motor behaviors in a Drosophila model of Parkinson's disease. Commun Biol 2019; 2:424. [PMID: 31799427 PMCID: PMC6874642 DOI: 10.1038/s42003-019-0674-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 11/01/2019] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial degeneration is considered one of the major causes of Parkinson's disease (PD). Improved mitochondrial functions are expected to be a promising therapeutic strategy for PD. In this study, we introduced a light-driven proton transporter, Delta-rhodopsin (dR), to Drosophila mitochondria, where the mitochondrial proton-motive force (Δp) and mitochondrial membrane potential are maintained in a light-dependent manner. The loss of the PD-associated mitochondrial gene CHCHD2 resulted in reduced ATP production, enhanced mitochondrial peroxide production and lower Ca2+-buffering activity in dopaminergic (DA) terminals in flies. These cellular defects were improved by the light-dependent activation of mitochondrion-targeted dR (mito-dR). Moreover, mito-dR reversed the pathology caused by the CHCHD2 deficiency to suppress α-synuclein aggregation, DA neuronal loss, and elevated lipid peroxidation in brain tissue, improving motor behaviors. This study suggests the enhancement of Δp by mito-dR as a therapeutic mechanism that ameliorates neurodegeneration by protecting mitochondrial functions.
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Affiliation(s)
- Yuzuru Imai
- Department of Research for Parkinson’s Disease, Juntendo University Graduate School of Medicine, Tokyo, 113-8421 Japan
- Department of Neurology, Juntendo University Graduate School of Medicine, Tokyo, 113-8421 Japan
| | - Tsuyoshi Inoshita
- Department of Treatment and Research in Multiple Sclerosis and Neuro-intractable Disease, Juntendo University Graduate School of Medicine, Tokyo, 113-8421 Japan
| | - Hongrui Meng
- Department of Neurodegenerative and Demented Disorders, Juntendo University Graduate School of Medicine, Tokyo, 113-8421 Japan
| | - Kahori Shiba-Fukushima
- Department of Treatment and Research in Multiple Sclerosis and Neuro-intractable Disease, Juntendo University Graduate School of Medicine, Tokyo, 113-8421 Japan
| | - Kiyotaka Y. Hara
- Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka, 422-8526 Japan
| | - Naoya Sawamura
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, 162-8480 Japan
- Faculty of Science and Engineering, Waseda University, Tokyo, 162-8480 Japan
| | - Nobutaka Hattori
- Department of Research for Parkinson’s Disease, Juntendo University Graduate School of Medicine, Tokyo, 113-8421 Japan
- Department of Neurology, Juntendo University Graduate School of Medicine, Tokyo, 113-8421 Japan
- Department of Treatment and Research in Multiple Sclerosis and Neuro-intractable Disease, Juntendo University Graduate School of Medicine, Tokyo, 113-8421 Japan
- Department of Neurodegenerative and Demented Disorders, Juntendo University Graduate School of Medicine, Tokyo, 113-8421 Japan
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12
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Onodera W, Asahi T, Sawamura N. Positive selection of cereblon modified function including its E3 ubiquitin ligase activity and binding efficiency with AMPK. Mol Phylogenet Evol 2019; 135:78-85. [PMID: 30836149 DOI: 10.1016/j.ympev.2019.03.001] [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] [Received: 10/24/2018] [Revised: 02/06/2019] [Accepted: 03/01/2019] [Indexed: 12/20/2022]
Abstract
Cereblon (CRBN) is a substrate receptor for an E3 ubiquitin ligase that directly binds to target proteins resulting in cellular activities, such as energy metabolism, membrane potential regulation, and transcription factor degradation. Genetic mutations in human CRBN lead to intellectual disabilities. In addition, it draws pathological attention because direct binding with immunomodulatory drugs can cure multiple myeloma (MM) and lymphocytic leukemia. To further explore the function of CRBN, we focused on its molecular evolution. Since CRBN interacts directly with its substrates and is widely conserved in vertebrates, evolutionary study to identify the selective pressure on CRBN that occur during CRBN-substrate interaction is an effective approach to search for a novel active site. Using mammalian CRBN sequences, dN/dS analysis was conducted to detect positive selection. By multiple sequence alignment we found that the residue at position 366 was under positive selection. This residue is present in the substrate-binding domain of CRBN. Most mammals harbor cysteine at position 366, whereas rodents and chiroptera have serine at this site. Subsequently, we constructed a C366S human CRBN to confirm the potential of positive selection. Auto-ubiquitination activity occurs in E3 ubiquitin ligases, including CRBN, and increased in C366S CRBN, which lead to the conclusion that E3 ubiquitin ligase activity may have changed over the course of mammalian evolution. Furthermore, binding with AMP-activated protein kinase was augmented when the substitution was present, which is supported by coevolution analysis. These results suggest that the molecular evolution of CRBN occurred through codon-based positive selection, providing a new approach to investigate CRBN function.
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Affiliation(s)
- Wataru Onodera
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan
| | - Toru Asahi
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan; Research Organization for Nano & Life Innovation, Waseda University, Japan
| | - Naoya Sawamura
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan; Research Organization for Nano & Life Innovation, Waseda University, Japan.
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Mansouri M, Strittmatter T, Fussenegger M. Light-Controlled Mammalian Cells and Their Therapeutic Applications in Synthetic Biology. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1800952. [PMID: 30643713 PMCID: PMC6325585 DOI: 10.1002/advs.201800952] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/21/2018] [Indexed: 05/12/2023]
Abstract
The ability to remote control the expression of therapeutic genes in mammalian cells in order to treat disease is a central goal of synthetic biology-inspired therapeutic strategies. Furthermore, optogenetics, a combination of light and genetic sciences, provides an unprecedented ability to use light for precise control of various cellular activities with high spatiotemporal resolution. Recent work to combine optogenetics and therapeutic synthetic biology has led to the engineering of light-controllable designer cells, whose behavior can be regulated precisely and noninvasively. This Review focuses mainly on non-neural optogenetic systems, which are often used in synthetic biology, and their applications in genetic programing of mammalian cells. Here, a brief overview of the optogenetic tool kit that is available to build light-sensitive mammalian cells is provided. Then, recently developed strategies for the control of designer cells with specific biological functions are summarized. Recent translational applications of optogenetically engineered cells are also highlighted, ranging from in vitro basic research to in vivo light-controlled gene therapy. Finally, current bottlenecks, possible solutions, and future prospects for optogenetics in synthetic biology are discussed.
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Affiliation(s)
- Maysam Mansouri
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH‐4058BaselSwitzerland
| | - Tobias Strittmatter
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH‐4058BaselSwitzerland
| | - Martin Fussenegger
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH‐4058BaselSwitzerland
- Faculty of ScienceUniversity of BaselMattenstrasse 26CH‐4058BaselSwitzerland
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Wada T, Hanyu T, Nozaki K, Kataoka K, Kawatani T, Asahi T, Sawamura N. Antioxidant Activity of Ge-132, a Synthetic Organic Germanium, on Cultured Mammalian Cells. Biol Pharm Bull 2018; 41:749-753. [PMID: 29503400 DOI: 10.1248/bpb.b17-00949] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ge-132 is a synthetic organic germanium that is used as a dietary supplement. The antioxidant activity of Ge-132 on cultured mammalian cells was investigated in this study. First, Ge-132 cytotoxicity on mammalian cultured cells was determined by measuring lactate dehydrogenase (LDH) levels. Ge-132 had no cytotoxic effect on three different cell lines. Second, the cell proliferative effect of Ge-132 was determined by measuring ATP content of whole cells and counting them. Ge-132 treatment of Chinese hamster ovary (CHO-K1) and SH-SY5Y cells promoted cell proliferation in a dose-dependent manner. Finally, antioxidant activity of Ge-132 against hydrogen peroxide-induced oxidative stress was determined by measuring the levels of intracellular reactive oxygen species (ROS) and carbonylated proteins. Pre-incubation of CHO-K1 and SH-SY5Y cells with Ge-132 suppressed intracellular ROS production and carbonylated protein levels induced by hydrogen peroxide. Our results suggest that Ge-132 has antioxidant activity against hydrogen peroxide-induced oxidative stress.
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Affiliation(s)
| | - Takashi Hanyu
- Faculty of Science and Engineering, Waseda University
| | - Kota Nozaki
- Faculty of Science and Engineering, Waseda University
| | | | | | - Toru Asahi
- Faculty of Science and Engineering, Waseda University.,Research Organization for Nano & Life Innovation, Waseda University
| | - Naoya Sawamura
- Faculty of Science and Engineering, Waseda University.,Research Organization for Nano & Life Innovation, Waseda University
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The Neuroprotective Effect of Thalidomide against Ischemia through the Cereblon-mediated Repression of AMPK Activity. Sci Rep 2018; 8:2459. [PMID: 29410497 PMCID: PMC5802741 DOI: 10.1038/s41598-018-20911-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/25/2018] [Indexed: 01/28/2023] Open
Abstract
Thalidomide was originally used as a sedative and found to be a teratogen, but now thalidomide and its derivatives are widely used to treat haematologic malignancies. Accumulated evidence suggests that thalidomide suppresses nerve cell death in neurologic model mice. However, detailed molecular mechanisms are unknown. Here we examined the molecular mechanism of thalidomide’s neuroprotective effects, focusing on its target protein, cereblon (CRBN), and its binding protein, AMP-activated protein kinase (AMPK), which plays an important role in maintaining intracellular energy homeostasis in the brain. We used a cerebral ischemia rat model of middle cerebral artery occlusion/reperfusion (MCAO/R). Thalidomide treatment significantly decreased the infarct volume and neurological deficits of MCAO/R rats. AMPK was the key signalling protein in this mechanism. Furthermore, we considered that the AMPK–CRBN interaction was altered when neuroprotective action by thalidomide occurred in cells under ischemic conditions. Binding was strong between AMPK and CRBN in normal SH-SY5Y cells, but was weakened by the addition of H2O2. However, when thalidomide was administered at the same time as H2O2, the binding of AMPK and CRBN was partly restored. These results suggest that thalidomide inhibits the activity of AMPK via CRBN under oxidative stress and suppresses nerve cell death.
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Ju Y, Asahi T, Sawamura N. Arctic Aβ40 blocks the nicotine-induced neuroprotective effect of CHRNA7 by inhibiting the ERK1/2 pathway in human neuroblastoma cells. Neurochem Int 2017; 110:49-56. [PMID: 28890319 DOI: 10.1016/j.neuint.2017.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/01/2017] [Accepted: 09/06/2017] [Indexed: 12/23/2022]
Abstract
Amyloid β protein (Aβ) plays a central role in Alzheimer's disease (AD) pathogenesis. Point mutations in the Aβ sequence, which cluster around the central hydrophobic core of the peptide, are associated with familial AD (FAD). Several mutations have been identified, with the Arctic mutation exhibiting a purely cognitive phenotype that is typical of AD. Our previous findings suggest that Arctic Aβ40 binds to and aggregates with CHRNA7, thereby inhibiting the calcium response and signaling pathways downstream of the receptor. Activation of CHRNA7 is neuroprotective both in vitro and in vivo. Therefore, in the present study, we investigated whether Arctic Aβ40 affects neuronal survival and/or death via CHRNA7. Using human neuroblastoma SH-SY5Y cells, we found that the neuroprotective function of CHRNA7 is blocked by CHRNA7 knockdown using RNA interference. Furthermore, Arctic Aβ40 blocked the neuroprotective effect of nicotine by inhibiting the ERK1/2 pathway downstream of CHRNA7. Moreover, we show that ERK1/2 activation mediates the neuroprotective effect of nicotine against oxidative stress. Collectively, our findings further our understanding of the molecular pathogenesis of Arctic FAD.
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Affiliation(s)
- Ye Ju
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan
| | - Toru Asahi
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan; Research Organization for Nano & Life Innovation, Waseda University #03C309, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan
| | - Naoya Sawamura
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan; Research Organization for Nano & Life Innovation, Waseda University #03C309, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan.
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Wada T, Asahi T, Sawamura N. Nuclear cereblon modulates transcriptional activity of Ikaros and regulates its downstream target, enkephalin, in human neuroblastoma cells. Biochem Biophys Res Commun 2016; 477:388-94. [DOI: 10.1016/j.bbrc.2016.06.091] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 06/17/2016] [Indexed: 11/16/2022]
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18
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Mitochondrial cereblon functions as a Lon-type protease. Sci Rep 2016; 6:29986. [PMID: 27417535 PMCID: PMC4945938 DOI: 10.1038/srep29986] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/28/2016] [Indexed: 12/13/2022] Open
Abstract
Lon protease plays a major role in the protein quality control system in mammalian cell mitochondria. It is present in the mitochondrial matrix, and degrades oxidized and misfolded proteins, thereby protecting the cell from various extracellular stresses, including oxidative stress. The intellectual disability-associated and thalidomide-binding protein cereblon (CRBN) contains a large, highly conserved Lon domain. However, whether CRBN has Lon protease-like function remains unknown. Here, we determined if CRBN has a protective function against oxidative stress, similar to Lon protease. We report that CRBN partially distributes in mitochondria, suggesting it has a mitochondrial function. To specify the mitochondrial role of CRBN, we mitochondrially expressed CRBN in human neuroblastoma SH-SY5Y cells. The resulting stable SH-SY5Y cell line showed no apparent effect on the mitochondrial functions of fusion, fission, and membrane potential. However, mitochondrially expressed CRBN exhibited protease activity, and was induced by oxidative stress. In addition, stably expressed cells exhibited suppressed neuronal cell death induced by hydrogen peroxide. These results suggest that CRBN functions specifically as a Lon-type protease in mitochondria.
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Min WJ, Hao H, Wang XL, Zheng XH, Zeng Z. Chemical substitution assisted ion sensing with organic molecules: a case study of naphthalene. RSC Adv 2016. [DOI: 10.1039/c5ra24047f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Using first-principles calculations, we predict that a naphthalene molecule with N substitutions for the –CH groups is a good system for H+ sensing.
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Affiliation(s)
- Wei-Jie Min
- Key Laboratory of Materials Physics
- Institute of Solid State Physics
- Chinese Academy of Sciences
- Hefei 230031
- China
| | - Hua Hao
- Key Laboratory of Materials Physics
- Institute of Solid State Physics
- Chinese Academy of Sciences
- Hefei 230031
- China
| | - Xian-Long Wang
- Key Laboratory of Materials Physics
- Institute of Solid State Physics
- Chinese Academy of Sciences
- Hefei 230031
- China
| | - Xiao-Hong Zheng
- Key Laboratory of Materials Physics
- Institute of Solid State Physics
- Chinese Academy of Sciences
- Hefei 230031
- China
| | - Zhi Zeng
- Key Laboratory of Materials Physics
- Institute of Solid State Physics
- Chinese Academy of Sciences
- Hefei 230031
- China
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Sawamura N, Wakabayashi S, Matsumoto K, Yamada H, Asahi T. Cereblon is recruited to aggresome and shows cytoprotective effect against ubiquitin-proteasome system dysfunction. Biochem Biophys Res Commun 2015; 464:1054-1059. [PMID: 26188093 DOI: 10.1016/j.bbrc.2015.07.068] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 07/14/2015] [Indexed: 12/01/2022]
Abstract
Cereblon (CRBN) is encoded by a candidate gene for autosomal recessive nonsyndromic intellectual disability (ID). The nonsense mutation, R419X, causes deletion of 24 amino acids at the C-terminus of CRBN, leading to mild ID. Although abnormal CRBN function may be associated with ID disease onset, its cellular mechanism is still unclear. Here, we examine the role of CRBN in aggresome formation and cytoprotection. In the presence of a proteasome inhibitor, exogenous CRBN formed perinuclear inclusions and co-localized with aggresome markers. Endogenous CRBN also formed perinuclear inclusions under the same condition. Treatment with a microtubule destabilizer or an inhibitor of the E3 ubiquitin ligase activity of CRBN blocked formation of CRBN inclusions. Biochemical analysis showed CRBN containing inclusions were high-molecular weight, ubiquitin-positive. CRBN overexpression in cultured cells suppressed cell death induced by proteasome inhibitor. Furthermore, knockdown of endogenous CRBN in cultured cells increased cell death induced by proteasome inhibitor, compared with control cells. Our results show CRBN is recruited to aggresome and has functional roles in cytoprotection against ubiquitin-proteasome system impaired condition.
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Affiliation(s)
- Naoya Sawamura
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan; Research Organization for Nano-life Innovation, Waseda University, Japan.
| | - Satoru Wakabayashi
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan
| | - Kodai Matsumoto
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan
| | - Haruka Yamada
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan
| | - Toru Asahi
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan; Research Organization for Nano-life Innovation, Waseda University, Japan
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Allen BD, Singer AC, Boyden ES. Principles of designing interpretable optogenetic behavior experiments. ACTA ACUST UNITED AC 2015; 22:232-8. [PMID: 25787711 PMCID: PMC4371169 DOI: 10.1101/lm.038026.114] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Over the last decade, there has been much excitement about the use of optogenetic tools to test whether specific cells, regions, and projection pathways are necessary or sufficient for initiating, sustaining, or altering behavior. However, the use of such tools can result in side effects that can complicate experimental design or interpretation. The presence of optogenetic proteins in cells, the effects of heat and light, and the activity of specific ions conducted by optogenetic proteins can result in cellular side effects. At the network level, activation or silencing of defined neural populations can alter the physiology of local or distant circuits, sometimes in undesired ways. We discuss how, in order to design interpretable behavioral experiments using optogenetics, one can understand, and control for, these potential confounds.
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Affiliation(s)
- Brian D Allen
- Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Departments of Biological Engineering and Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Annabelle C Singer
- Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Departments of Biological Engineering and Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Edward S Boyden
- Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Departments of Biological Engineering and Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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