1
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Identification of a modulator of the actin cytoskeleton, mitochondria, nutrient metabolism and lifespan in yeast. Nat Commun 2022; 13:2706. [PMID: 35577788 PMCID: PMC9110415 DOI: 10.1038/s41467-022-30045-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 04/06/2022] [Indexed: 11/26/2022] Open
Abstract
In yeast, actin cables are F-actin bundles that are essential for cell division through their function as tracks for cargo movement from mother to daughter cell. Actin cables also affect yeast lifespan by promoting transport and inheritance of higher-functioning mitochondria to daughter cells. Here, we report that actin cable stability declines with age. Our genome-wide screen for genes that affect actin cable stability identified the open reading frame YKL075C. Deletion of YKL075C results in increases in actin cable stability and abundance, mitochondrial fitness, and replicative lifespan. Transcriptome analysis revealed a role for YKL075C in regulating branched-chain amino acid (BCAA) metabolism. Consistent with this, modulation of BCAA metabolism or decreasing leucine levels promotes actin cable stability and function in mitochondrial quality control. Our studies support a role for actin stability in yeast lifespan, and demonstrate that this process is controlled by BCAA and a previously uncharacterized ORF YKL075C, which we refer to as actin, aging and nutrient modulator protein 1 (AAN1). Actin cables affect lifespan by supporting movement and inheritance of fitter mitochondria to daughter cells in yeast. Here the authors show that branched-chain amino acid (BCAA) levels affect actin cable stability and a role for YKL075C/AAN1 in control of BCAA metabolism and actin cable stability and function.
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2
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A role for cell polarity in lifespan and mitochondrial quality control in the budding yeast Saccharomyces cerevisiae. iScience 2022; 25:103957. [PMID: 35281729 PMCID: PMC8914336 DOI: 10.1016/j.isci.2022.103957] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 12/15/2021] [Accepted: 02/17/2022] [Indexed: 01/03/2023] Open
Abstract
Babies are born young, largely independent of the age of their mothers. Mother-daughter age asymmetry in yeast is achieved, in part, by inheritance of higher-functioning mitochondria by buds and retention of some high-functioning mitochondria in mother cells. The mitochondrial F box protein, Mfb1p, tethers mitochondria at both poles in a cell cycle-regulated manner: it localizes to and anchors mitochondria at the mother cell tip throughout the cell cycle and at the bud tip before cytokinesis. Here, we report that cell polarity and polarized localization of Mfb1p decline with age in Saccharomyces cerevisiae. Moreover, deletion of genes (BUD1, BUD2, and BUD5) that mediate symmetry breaking during establishment of cell polarity and asymmetric yeast cell division cause depolarized Mfb1p localization and defects in mitochondrial distribution and quality control. Our results support a role for the polarity machinery in lifespan through modulating Mfb1 function in asymmetric inheritance of mitochondria during yeast cell division. Budding polarity declines with age Polarization of a mitochondrial tether, Mfb1p, within mother cells declines with age Defects in budding polarity disrupt Mfb1p polarization and mitochondrial distribution Polarity defects affect Mfb1p-mediated mitochondrial quality and lifespan control
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3
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Teixeira RB, Karbasiafshar C, Sabra M, Abid MR. Optimization of mito-roGFP protocol to measure mitochondrial oxidative status in human coronary artery endothelial cells. STAR Protoc 2021; 2:100753. [PMID: 34458871 PMCID: PMC8377591 DOI: 10.1016/j.xpro.2021.100753] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Reactive oxygen species (ROS) are implicated in endothelial dysfunction and cardiovascular disease. Endothelial cells (ECs) produce most ATP through glycolysis rather than oxidative phosphorylation; thus mitochondrial ROS production is lower than in other cell types. This makes quantification of changes in EC mitochondrial oxidative status challenging. Here, we present an optimized protocol using mitochondrial-targeted adenovirus-based redox sensor for ratiometric quantification of specific changes in mitochondrial ROS in live human coronary artery EC. For complete details on the use and execution of this protocol, please refer to Waypa et al. (2010); Liao et al. (2020); Gao et al. (2021). An optimized protocol for measuring mitochondrial oxidative status of primary HCAEC Use of mito-roGFP adenovirus transduction Live imaging using reducing and oxidizing factors Applicable to other types of murine and human cells
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Affiliation(s)
- Rayane Brinck Teixeira
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Catherine Karbasiafshar
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Mohamed Sabra
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - M Ruhul Abid
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA
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4
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Liao PC, Wolken DMA, Serrano E, Srivastava P, Pon LA. Mitochondria-Associated Degradation Pathway (MAD) Function beyond the Outer Membrane. Cell Rep 2021; 32:107902. [PMID: 32668258 PMCID: PMC7391283 DOI: 10.1016/j.celrep.2020.107902] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 01/07/2020] [Accepted: 06/23/2020] [Indexed: 12/01/2022] Open
Abstract
The mitochondria-associated degradation pathway (MAD) mediates ubiquitination and degradation of mitochondrial outer membrane (MOM) proteins by the proteasome. We find that the MAD, but not other quality-control pathways including macroautophagy, mitophagy, or mitochondrial chaperones and proteases, is critical for yeast cellular fitness under conditions of paraquat (PQ)-induced oxidative stress in mitochondria. Specifically, inhibition of the MAD increases PQ-induced defects in growth and mitochondrial quality and decreases chronological lifespan. We use mass spectrometry analysis to identify possible MAD substrates as mitochondrial proteins that exhibit increased ubiquitination in response to PQ treatment and inhibition of the MAD. We identify candidate substrates in the mitochondrial matrix and inner membrane and confirm that two matrix proteins are MAD substrates. Our studies reveal a broader function for the MAD in mitochondrial protein surveillance beyond the MOM and a major role for the MAD in cellular and mitochondrial fitness in response to chronic, low-level oxidative stress in mitochondria.
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Affiliation(s)
- Pin-Chao Liao
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | | | - Edith Serrano
- Department of Chemistry, Barnard College, Columbia University, New York, NY 10027, USA
| | - Pallavi Srivastava
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G1H9, Canada
| | - Liza A Pon
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA.
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5
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Yang Y, Zhang G, Yang T, Gan J, Xu L, Yang H. A flow-cytometry-based protocol for detection of mitochondrial ROS production under hypoxia. STAR Protoc 2021; 2:100466. [PMID: 33997804 PMCID: PMC8086139 DOI: 10.1016/j.xpro.2021.100466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Hypoxia is known to stimulate mitochondrial reactive oxygen species (mROS) in cells. Here, we present a detailed protocol to detect mROS using MitoSOX staining in live cells under normoxia and hypoxia. Flow cytometry allows sensitive and reliable quantification of mROS by FlowJo software. We optimized several aspects of the procedure including hypoxic treatment, working concentrations of the staining buffer, and quantitative analyses. Here, we use HepG2 cells, but the protocol can be applied to other cell lines. For complete details on the use and execution of this protocol, please refer to Yang et al. (2020).
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Affiliation(s)
- Yun Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, NO.17, South of Renmin Road, Chengdu 610041, China
| | - Guimin Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, NO.17, South of Renmin Road, Chengdu 610041, China
| | - Tao Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, NO.17, South of Renmin Road, Chengdu 610041, China
| | - Jia Gan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, NO.17, South of Renmin Road, Chengdu 610041, China
| | - Lin Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, NO.17, South of Renmin Road, Chengdu 610041, China
| | - Hanshuo Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, NO.17, South of Renmin Road, Chengdu 610041, China.,Experimental and Research Animal Institute, Sichuan University, Chengdu, China
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6
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Spurlock B, Mitra K. Mito-SinCe 2 Approach to Analyze Mitochondrial Structure-Function Relationship in Single Cells. Methods Mol Biol 2021; 2275:415-432. [PMID: 34118054 DOI: 10.1007/978-1-0716-1262-0_27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The cross talk between mitochondrial dynamic structure, determined primarily by mitochondrial fission and fusion events, and mitochondrial function of energetics, primarily ATP and ROS production, is widely appreciated. Understanding the mechanistic details of such cross talk between mitochondrial structure and function needs integrated quantitative analyses between mitochondrial dynamics and energetics. Here we describe our recently designed approach of mito-SinCe2 that involves high resolution confocal microscopy of genetically expressed ratiometric fluorescent probes targeted to mitochondria, and its quantitative analyses. Mito-SinCe2 analyses allows for quantitative analyses of mitochondrial structure-function relationship in single cells toward understanding the role of mitochondria and their heterogeneity in various physiological and pathological conditions.
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Affiliation(s)
- B Spurlock
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - K Mitra
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
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7
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Abstract
The redox state of mitochondria is one indicator of the functional state of the organelles. Mitochondria are also the primary endogenous source of reactive oxygen species (ROS). Therefore, the redox state of the organelles also reflects their function in ROS production. Here, we provide step-by-step protocols for live-cell imaging and quantification of mitochondrial redox state using the genetically encoded fluorescent biosensor, mitochondria-targeted redox sensing GFP (mito-roGFP), and mitochondrial ROS using the membrane-permeant small molecule dihydroethidium (DHE) in budding yeast cells. For complete details on the use and execution of this protocol, please refer to Liao et al. (2020c). Protocols for analysis of mitochondrial redox state and ROS in S. cerevisiae Analysis is performed in living cells at the resolution of individual organelles Methods for analysis using commercial and open-source software are provided These protocols can be adapted for use in other cell types
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Affiliation(s)
- Pin-Chao Liao
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Emily J Yang
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Liza A Pon
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
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8
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Mitochondrial Dysfunction Combined with High Calcium Load Leads to Impaired Antioxidant Defense Underlying the Selective Loss of Nigral Dopaminergic Neurons. J Neurosci 2020; 40:1975-1986. [PMID: 32005765 DOI: 10.1523/jneurosci.1345-19.2019] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 10/15/2019] [Accepted: 11/24/2019] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial dysfunction is critically involved in Parkinson's disease, characterized by loss of dopaminergic neurons (DaNs) in the substantia nigra (SNc), whereas DaNs in the neighboring ventral tegmental area (VTA) are much less affected. In contrast to VTA, SNc DaNs engage calcium channels to generate action potentials, which lead to oxidant stress by yet unknown pathways. To determine the molecular mechanisms linking calcium load with selective cell death in the presence of mitochondrial deficiency, we analyzed the mitochondrial redox state and the mitochondrial membrane potential in mice of both sexes with genetically induced, severe mitochondrial dysfunction in DaNs (MitoPark mice), at the same time expressing a redox-sensitive GFP targeted to the mitochondrial matrix. Despite mitochondrial insufficiency in all DaNs, exclusively SNc neurons showed an oxidized redox-system, i.e., a low reduced/oxidized glutathione (GSH-GSSG) ratio. This was mimicked by cyanide, but not by rotenone or antimycin A, making the involvement of reactive oxygen species rather unlikely. Surprisingly, a high mitochondrial inner membrane potential was maintained in MitoPark SNc DaNs. Antagonizing calcium influx into the cell and into mitochondria, respectively, rescued the disturbed redox ratio and induced further hyperpolarization of the inner mitochondrial membrane. Our data therefore show that the constant calcium load in SNc DaNs is counterbalanced by a high mitochondrial inner membrane potential, even under conditions of severe mitochondrial dysfunction, but triggers a detrimental imbalance in the mitochondrial redox system, which will lead to neuron death. Our findings thus reveal a new mechanism, redox imbalance, which underlies the differential vulnerability of DaNs to mitochondrial defects.SIGNIFICANCE STATEMENT Parkinson's disease is characterized by the preferential degeneration of dopaminergic neurons (DaNs) of the substantia nigra pars compacta (SNc), resulting in the characteristic hypokinesia in patients. Ubiquitous pathological triggers cannot be responsible for the selective neuron loss. Here we show that mitochondrial impairment together with elevated calcium burden destabilize the mitochondrial antioxidant defense only in SNc DaNs, and thus promote the increased vulnerability of this neuron population.
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Abstract
With the rapid development of DNA synthesis and next-generation sequencing, synthetic biology that aims to standardize, modularize, and innovate cellular functions, has achieved vast progress. Here we review key advances in synthetic biology of the yeast Saccharomyces cerevisiae, which serves as an important eukaryal model organism and widely applied cell factory. This covers the development of new building blocks, i.e., promoters, terminators and enzymes, pathway engineering, tools developments, and gene circuits utilization. We will also summarize impacts of synthetic biology on both basic and applied biology, and end with further directions for advancing synthetic biology in yeast.
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Affiliation(s)
- Zihe Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing Key Laboratory of Bioprocess , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Yueping Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing Key Laboratory of Bioprocess , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Jens Nielsen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing Key Laboratory of Bioprocess , Beijing University of Chemical Technology , Beijing 100029 , China.,Department of Biology and Biological Engineering , Chalmers University of Technology , Gothenburg SE41296 , Sweden.,Novo Nordisk Foundation Center for Biosustainability , Technical University of Denmark , Kongens Lyngby DK2800 , Denmark
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10
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Isolation of mitochondria from Saccharomyces cerevisiae using magnetic bead affinity purification. PLoS One 2018; 13:e0196632. [PMID: 29698455 PMCID: PMC5919621 DOI: 10.1371/journal.pone.0196632] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/16/2018] [Indexed: 11/30/2022] Open
Abstract
Isolated mitochondria are widely used to study the function of the organelle. Typically, mitochondria are prepared using differential centrifugation alone or in conjunction with density gradient ultracentrifugation. However, mitochondria isolated using differential centrifugation contain membrane or organelle contaminants, and further purification of crude mitochondria by density gradient ultracentrifugation requires large amounts of starting material, and is time-consuming. Mitochondria have also been isolated by irreversible binding to antibody-coated magnetic beads. We developed a method to prepare mitochondria from budding yeast that overcomes many of the limitations of other methods. Mitochondria are tagged by insertion of 6 histidines (6xHis) into the TOM70 (Translocase of outer membrane 70) gene at its chromosomal locus, isolated using Ni-NTA (nickel (II) nitrilotriacetic acid) paramagnetic beads and released from the magnetic beads by washing with imidazole. Mitochondria prepared using this method contain fewer contaminants, and are similar in ultrastructure as well as protein import and cytochrome c oxidase complex activity compared to mitochondria isolated by differential centrifugation. Moreover, this isolation method is amenable to small samples, faster than purification by differential and density gradient centrifugation, and more cost-effective than purification using antibody-coated magnetic beads. Importantly, this method can be applied to any cell type where the genetic modification can be introduced by CRISPR or other methods.
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11
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Garcia EJ, Vevea JD, Pon LA. Lipid droplet autophagy during energy mobilization, lipid homeostasis and protein quality control. Front Biosci (Landmark Ed) 2018; 23:1552-1563. [PMID: 29293450 DOI: 10.2741/4660] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lipid droplets (LDs) have well-established functions as sites for lipid storage and energy mobilization to meet the metabolic demands of cells. However, recent studies have expanded the roles of LDs to protein quality control. Lipophagy, or LD degradation by autophagy, plays a vital role not only in the mobilization of free fatty acids (FFAs) and lipid homeostasis at LDs, but also in the adaptation of cells to certain forms of stress including lipid imbalance. Recent studies have provided new mechanistic insights about the diverse types of lipophagy, in particular microlipophagy. This review summarizes key findings about the mechanisms and functions of lipophagy and highlights a novel function of LD microlipophagy as a mechanism to maintain endoplasmic reticulum (ER) proteostasis under conditions of lipid imbalance.
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Affiliation(s)
- Enrique J Garcia
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032 USA
| | - Jason D Vevea
- HHMI and Dept. of Neuroscience, University of Wisconsin, Madison, WI, 53705 USA
| | - Liza A Pon
- Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032 USA,
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12
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Pelosse M, Cottet-Rousselle C, Grichine A, Berger I, Schlattner U. Genetically Encoded Fluorescent Biosensors to Explore AMPK Signaling and Energy Metabolism. ACTA ACUST UNITED AC 2017; 107:491-523. [PMID: 27812993 DOI: 10.1007/978-3-319-43589-3_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Maintenance of energy homeostasis is a basic requirement for cell survival. Different mechanisms have evolved to cope with spatial and temporal mismatch between energy-providing and -consuming processes. Among these, signaling by AMP-activated protein kinase (AMPK) is one of the key players, regulated by and itself regulating cellular adenylate levels. Further understanding its complex cellular function requires deeper insight into its activation patterns in space and time at a single cell level. This may become possible with an increasing number of genetically encoded fluorescent biosensors, mostly based on fluorescence resonance energy transfer, which have been engineered to monitor metabolic parameters and kinase activities. Here, we review basic principles of biosensor design and function and the advantages and limitations of their use and provide an overview on existing FRET biosensors to monitor AMPK activation, ATP concentration, and ATP/ADP ratios, together with other key metabolites and parameters of energy metabolism.
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Affiliation(s)
- Martin Pelosse
- Laboratory of Fundamental and Applied Bioenergetics (LBFA) and SFR Environmental and Systems Biology (BEeSy), University Grenoble Alpes, Grenoble, France.,Inserm, U1055 and U1209, Grenoble, France
| | - Cécile Cottet-Rousselle
- Laboratory of Fundamental and Applied Bioenergetics (LBFA) and SFR Environmental and Systems Biology (BEeSy), University Grenoble Alpes, Grenoble, France.,Inserm, U1055 and U1209, Grenoble, France
| | - Alexei Grichine
- Inserm, U1055 and U1209, Grenoble, France.,Institute for Advanced Biosciences, University Grenoble Alpes, Grenoble, France
| | | | - Uwe Schlattner
- Laboratory of Fundamental and Applied Bioenergetics (LBFA) and SFR Environmental and Systems Biology (BEeSy), University Grenoble Alpes, Grenoble, France. .,Inserm, U1055 and U1209, Grenoble, France.
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13
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Vevea JD, Garcia EJ, Chan RB, Zhou B, Schultz M, Di Paolo G, McCaffery JM, Pon LA. Role for Lipid Droplet Biogenesis and Microlipophagy in Adaptation to Lipid Imbalance in Yeast. Dev Cell 2016; 35:584-599. [PMID: 26651293 DOI: 10.1016/j.devcel.2015.11.010] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 08/14/2015] [Accepted: 11/09/2015] [Indexed: 12/22/2022]
Abstract
The immediate responses to inhibition of phosphatidylcholine (PC) biosynthesis in yeast are altered phospholipid levels, slow growth, and defects in the morphology and localization of ER and mitochondria. With chronic lipid imbalance, yeast adapt. Lipid droplet (LD) biogenesis and conversion of phospholipids to triacylglycerol are required for restoring some phospholipids to near-wild-type levels. We confirmed that the unfolded protein response is activated by this lipid stress and find that Hsp104p is recruited to ER aggregates. We also find that LDs form at ER aggregates, contain polyubiquitinated proteins and an ER chaperone, and are degraded in the vacuole by a process resembling microautophagy. This process, microlipophagy, is required for restoration of organelle morphology and cell growth during adaptation to lipid stress. Microlipophagy does not require ATG7 but does requires ESCRT components and a newly identified class E VPS protein that localizes to ER and is upregulated by lipid imbalance.
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Affiliation(s)
- Jason D Vevea
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 West 168(th) Street, New York, NY 10032, USA
| | - Enrique J Garcia
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 West 168(th) Street, New York, NY 10032, USA
| | - Robin B Chan
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 West 168(th) Street, New York, NY 10032, USA
| | - Bowen Zhou
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 West 168(th) Street, New York, NY 10032, USA
| | - Mei Schultz
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 West 168(th) Street, New York, NY 10032, USA
| | - Gilbert Di Paolo
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 West 168(th) Street, New York, NY 10032, USA
| | - J Michael McCaffery
- Integrated Imaging Center, Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Liza A Pon
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 West 168(th) Street, New York, NY 10032, USA.
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14
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A role for Mfb1p in region-specific anchorage of high-functioning mitochondria and lifespan in Saccharomyces cerevisiae. Nat Commun 2016; 7:10595. [PMID: 26839174 PMCID: PMC4742906 DOI: 10.1038/ncomms10595] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/04/2016] [Indexed: 01/20/2023] Open
Abstract
Previous studies indicate that replicative lifespan in daughter cells of Sacchraromyces cerevisiae depends on the preferential inheritance of young, high-functioning mitochondria. We report here that mitochondria are functionally segregated even within single mother cells in S. cerevisiae. A high-functioning population of mitochondria accumulates at the tip of the mother cell distal to the bud. We find that the mitochondrial F-box protein (Mfb1p) localizes to mitochondria in the mother tip and is required for mitochondrial anchorage at that site, independent of the previously identified anchorage protein Num1p. Deletion of MFB1 results in loss of the mother-tip-localized mitochondrial population, defects in mitochondrial function and premature replicative ageing. Inhibiting mitochondrial inheritance to buds, by deletion of MMR1, in mfb1Δ cells restores mitochondrial distribution, promotes mitochondrial function and extends replicative lifespan. Our results identify a mechanism that retains a reservoir of high-functioning mitochondria in mother cells and thereby preserves maternal reproductive capacity. Mitochondria are asymmetrically inherited during cell division, a process that can affect cell fate and lifespan. Here the authors describe a mechanism for mitochondrial quality control in yeast that maintains a reservoir of high-functioning mitochondria in mother cells and preserves maternal reproductive capacity.
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15
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Higuchi-Sanabria R, Swayne TC, Boldogh IR, Pon LA. Live-Cell Imaging of Mitochondria and the Actin Cytoskeleton in Budding Yeast. Methods Mol Biol 2016; 1365:25-62. [PMID: 26498778 DOI: 10.1007/978-1-4939-3124-8_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Maintenance and regulation of proper mitochondrial dynamics and functions are necessary for cellular homeostasis. Numerous diseases, including neurodegeneration and muscle myopathies, and overall cellular aging are marked by declining mitochondrial function and subsequent loss of multiple other cellular functions. For these reasons, optimized protocols are needed for visualization and quantification of mitochondria and their function and fitness. In budding yeast, mitochondria are intimately associated with the actin cytoskeleton and utilize actin for their movement and inheritance. This chapter describes optimal approaches for labeling mitochondria and the actin cytoskeleton in living budding yeast cells, for imaging the labeled cells, and for analyzing the resulting images.
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Affiliation(s)
- Ryo Higuchi-Sanabria
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 W. 168th Street, New York, NY, 10032, USA
| | - Theresa C Swayne
- Confocal and Specialized Microscopy Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Istvan R Boldogh
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 W. 168th Street, New York, NY, 10032, USA
| | - Liza A Pon
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 W. 168th Street, New York, NY, 10032, USA. .,Confocal and Specialized Microscopy Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
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16
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Hochreiter B, Garcia AP, Schmid JA. Fluorescent proteins as genetically encoded FRET biosensors in life sciences. SENSORS 2015; 15:26281-314. [PMID: 26501285 PMCID: PMC4634415 DOI: 10.3390/s151026281] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 10/08/2015] [Indexed: 12/11/2022]
Abstract
Fluorescence- or Förster resonance energy transfer (FRET) is a measurable physical energy transfer phenomenon between appropriate chromophores, when they are in sufficient proximity, usually within 10 nm. This feature has made them incredibly useful tools for many biomedical studies on molecular interactions. Furthermore, this principle is increasingly exploited for the design of biosensors, where two chromophores are linked with a sensory domain controlling their distance and thus the degree of FRET. The versatility of these FRET-biosensors made it possible to assess a vast amount of biological variables in a fast and standardized manner, allowing not only high-throughput studies but also sub-cellular measurements of biological processes. In this review, we aim at giving an overview over the recent advances in genetically encoded, fluorescent-protein based FRET-biosensors, as these represent the largest and most vividly growing group of FRET-based sensors. For easy understanding, we are grouping them into four categories, depending on their molecular mechanism. These are based on: (a) cleavage; (b) conformational-change; (c) mechanical force and (d) changes in the micro-environment. We also address the many issues and considerations that come with the development of FRET-based biosensors, as well as the possibilities that are available to measure them.
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Affiliation(s)
- Bernhard Hochreiter
- Institute for Vascular Biology and Thrombosis Research, Medical University Vienna, Schwarzspanierstraße17, Vienna A-1090, Austria.
| | - Alan Pardo Garcia
- Institute for Vascular Biology and Thrombosis Research, Medical University Vienna, Schwarzspanierstraße17, Vienna A-1090, Austria.
| | - Johannes A Schmid
- Institute for Vascular Biology and Thrombosis Research, Medical University Vienna, Schwarzspanierstraße17, Vienna A-1090, Austria.
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Higuchi-Sanabria R, Pernice WMA, Vevea JD, Alessi Wolken DM, Boldogh IR, Pon LA. Role of asymmetric cell division in lifespan control in Saccharomyces cerevisiae. FEMS Yeast Res 2014; 14:1133-46. [PMID: 25263578 PMCID: PMC4270926 DOI: 10.1111/1567-1364.12216] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/22/2014] [Accepted: 09/22/2014] [Indexed: 11/29/2022] Open
Abstract
Aging determinants are asymmetrically distributed during cell division in S. cerevisiae, which leads to production of an immaculate, age-free daughter cell. During this process, damaged components are sequestered and retained in the mother cell, and higher functioning organelles and rejuvenating factors are transported to and/or enriched in the bud. Here, we will describe the key quality control mechanisms in budding yeast that contribute to asymmetric cell division of aging determinants including mitochondria, endoplasmic reticulum (ER), vacuoles, extrachromosomal rDNA circles (ERCs), and protein aggregates.
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Affiliation(s)
- Ryo Higuchi-Sanabria
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
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Van Vranken JG, Bricker DK, Dephoure N, Gygi SP, Cox JE, Thummel CS, Rutter J. SDHAF4 promotes mitochondrial succinate dehydrogenase activity and prevents neurodegeneration. Cell Metab 2014; 20:241-52. [PMID: 24954416 PMCID: PMC4126880 DOI: 10.1016/j.cmet.2014.05.012] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/28/2014] [Accepted: 04/28/2014] [Indexed: 02/05/2023]
Abstract
Succinate dehydrogenase (SDH) occupies a central place in cellular energy production, linking the tricarboxylic cycle with the electron transport chain. As a result, a subset of cancers and neuromuscular disorders result from mutations affecting any of the four SDH structural subunits or either of two known SDH assembly factors. Herein we characterize an evolutionarily conserved SDH assembly factor designated Sdh8/SDHAF4, using yeast, Drosophila, and mammalian cells. Sdh8 interacts specifically with the catalytic Sdh1 subunit in the mitochondrial matrix, facilitating its association with Sdh2 and the subsequent assembly of the SDH holocomplex. These roles for Sdh8 are critical for preventing motility defects and neurodegeneration in Drosophila as well as the excess ROS generated by free Sdh1. These studies provide insights into the mechanisms by which SDH is assembled and raise the possibility that some forms of neuromuscular disease may be associated with mutations that affect this SDH assembly factor.
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Affiliation(s)
- Jonathan G Van Vranken
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Daniel K Bricker
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Noah Dephoure
- Department of Cell Biology, Harvard University Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard University Medical School, Boston, MA 02115, USA
| | - James E Cox
- Metabolomics Core Research Facility, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Carl S Thummel
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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Higuchi R, Vevea JD, Swayne TC, Chojnowski R, Hill V, Boldogh IR, Pon LA. Actin dynamics affect mitochondrial quality control and aging in budding yeast. Curr Biol 2013; 23:2417-22. [PMID: 24268413 DOI: 10.1016/j.cub.2013.10.022] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 09/27/2013] [Accepted: 10/09/2013] [Indexed: 11/24/2022]
Abstract
Actin cables of budding yeast are bundles of F-actin that extend from the bud tip or neck to the mother cell tip, serve as tracks for bidirectional cargo transport, and undergo continuous movement from buds toward mother cells [1]. This movement, retrograde actin cable flow (RACF), is similar to retrograde actin flow in lamellipodia, growth cones, immunological synapses, dendritic spines, and filopodia [2-5]. In all cases, actin flow is driven by the push of actin polymerization and assembly at the cell cortex, and myosin-driven pulling forces deeper within the cell [6-10]. Therefore, for movement and inheritance from mothers to buds, mitochondria must "swim upstream" against the opposing force of RACF [11]. We find that increasing RACF rates results in increased fitness of mitochondria inherited by buds and that the increase in mitochondrial fitness leads to extended replicative lifespan and increased cellular healthspan. The sirtuin SIR2 is required for normal RACF and mitochondrial fitness, and increasing RACF rates in sir2Δ cells increases mitochondrial fitness and cellular healthspan but does not affect replicative lifespan. These studies support the model that RACF serves as a filter for segregation of fit from less-fit mitochondria during inheritance, which controls cellular lifespan and healthspan. They also support a role for Sir2p in these processes.
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Affiliation(s)
- Ryo Higuchi
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 W. 168(th) Street, New York, NY 10032, USA
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