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Liao PC, Yang EJ, Borgman T, Boldogh IR, Sing CN, Swayne TC, Pon LA. Touch and Go: Membrane Contact Sites Between Lipid Droplets and Other Organelles. Front Cell Dev Biol 2022; 10:852021. [PMID: 35281095 PMCID: PMC8908909 DOI: 10.3389/fcell.2022.852021] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/03/2022] [Indexed: 12/26/2022] Open
Abstract
Lipid droplets (LDs) have emerged not just as storage sites for lipids but as central regulators of metabolism and organelle quality control. These critical functions are achieved, in part, at membrane contact sites (MCS) between LDs and other organelles. MCS are sites of transfer of cellular constituents to or from LDs for energy mobilization in response to nutrient limitations, as well as LD biogenesis, expansion and autophagy. Here, we describe recent findings on the mechanisms underlying the formation and function of MCS between LDs and mitochondria, ER and lysosomes/vacuoles and the role of the cytoskeleton in promoting LD MCS through its function in LD movement and distribution in response to environmental cues.
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Affiliation(s)
- Pin-Chao Liao
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, United States
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Emily J. Yang
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, United States
| | - Taylor Borgman
- Institute of Human Nutrition, Columbia University Irving Medical Center, New York, NY, United States
| | - Istvan R. Boldogh
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, United States
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, United States
| | - Cierra N. Sing
- Institute of Human Nutrition, Columbia University Irving Medical Center, New York, NY, United States
| | - Theresa C. Swayne
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, United States
| | - Liza A. Pon
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, United States
- Institute of Human Nutrition, Columbia University Irving Medical Center, New York, NY, United States
- *Correspondence: Liza A. Pon,
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2
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Sing CN, Yang EJ, Swayne TC, Higuchi-Sanabria R, Tsang CA, Boldogh IR, Pon LA. Imaging the Actin Cytoskeleton in Live Budding Yeast Cells. Methods Mol Biol 2022; 2364:53-80. [PMID: 34542848 PMCID: PMC11060504 DOI: 10.1007/978-1-0716-1661-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Although budding yeast, Saccharomyces cerevisiae, is widely used as a model organism in biological research, studying cell biology in yeast was hindered due to its small size, rounded morphology, and cell wall. However, with improved techniques, researchers can acquire high-resolution images and carry out rapid multidimensional analysis of a yeast cell. As a result, imaging in yeast has emerged as an important tool to study cytoskeletal organization, function, and dynamics. This chapter describes techniques and approaches for visualizing the actin cytoskeleton in live yeast cells.
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Affiliation(s)
- Cierra N Sing
- Department of Pathology and Cell Biology, Columbia University, College of Physicians and Surgeons, New York, NY, USA
| | - Emily J Yang
- Department of Pathology and Cell Biology, Columbia University, College of Physicians and Surgeons, New York, NY, USA
| | - Theresa C Swayne
- Confocal and Specialized Microscopy Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Ryo Higuchi-Sanabria
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Catherine A Tsang
- Department of Pathology and Cell Biology, Columbia University, College of Physicians and Surgeons, New York, NY, USA
| | - Istvan R Boldogh
- Department of Pathology and Cell Biology, Columbia University, College of Physicians and Surgeons, New York, NY, USA
- Confocal and Specialized Microscopy Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Liza A Pon
- Department of Pathology and Cell Biology, Columbia University, College of Physicians and Surgeons, New York, NY, USA.
- Confocal and Specialized Microscopy Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
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Garcia EJ, Liao PC, Tan G, Vevea JD, Sing CN, Tsang CA, McCaffery JM, Boldogh IR, Pon LA. Membrane dynamics and protein targets of lipid droplet microautophagy during ER stress-induced proteostasis in the budding yeast, Saccharomyces cerevisiae. Autophagy 2020. [PMID: 33021864 DOI: 10.1080/15548627.2020.1826691.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022] Open
Abstract
Our previous studies reveal a mechanism for lipid droplet (LD)-mediated proteostasis in the endoplasmic reticulum (ER) whereby unfolded proteins that accumulate in the ER in response to lipid imbalance-induced ER stress are removed by LDs and degraded by microlipophagy (µLP), autophagosome-independent LD uptake into the vacuole (the yeast lysosome). Here, we show that dithiothreitol- or tunicamycin-induced ER stress also induces µLP and identify an unexpected role for vacuolar membrane dynamics in this process. All stressors studied induce vacuolar fragmentation prior to µLP. Moreover, during µLP, fragmented vacuoles fuse to form cup-shaped structures that encapsulate and ultimately take up LDs. Our studies also indicate that proteins of the endosome sorting complexes required for transport (ESCRT) are upregulated, required for µLP, and recruited to LDs, vacuolar membranes, and sites of vacuolar membrane scission during µLP. We identify possible target proteins for LD-mediated ER proteostasis. Our live-cell imaging studies reveal that one potential target (Nup159) localizes to punctate structures that colocalizes with LDs 1) during movement from ER membranes to the cytosol, 2) during microautophagic uptake into vacuoles, and 3) within the vacuolar lumen. Finally, we find that mutations that inhibit LD biogenesis, homotypic vacuolar membrane fusion or ESCRT function inhibit stress-induced autophagy of Nup159 and other ER proteins. Thus, we have obtained the first direct evidence that LDs and µLP can mediate ER stress-induced ER proteostasis, and identified direct roles for ESCRT and vacuolar membrane fusion in that process.
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Affiliation(s)
- Enrique J Garcia
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Pin-Chao Liao
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Gary Tan
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Jason D Vevea
- HHMI and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin, USA
| | - Cierra N Sing
- Institute of Human Nutrition, Columbia University, New York, NY, USA
| | - Catherine A Tsang
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - J Michael McCaffery
- Integrated Imaging Center, Department of Biology, The Johns Hopkins University, Baltimore, MD, USA
| | - Istvan R Boldogh
- 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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4
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Garcia EJ, Liao PC, Tan G, Vevea JD, Sing CN, Tsang CA, McCaffery JM, Boldogh IR, Pon LA. Membrane dynamics and protein targets of lipid droplet microautophagy during ER stress-induced proteostasis in the budding yeast, Saccharomyces cerevisiae. Autophagy 2020; 17:2363-2383. [PMID: 33021864 PMCID: PMC8496710 DOI: 10.1080/15548627.2020.1826691] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Our previous studies reveal a mechanism for lipid droplet (LD)-mediated proteostasis in the endoplasmic reticulum (ER) whereby unfolded proteins that accumulate in the ER in response to lipid imbalance-induced ER stress are removed by LDs and degraded by microlipophagy (µLP), autophagosome-independent LD uptake into the vacuole (the yeast lysosome). Here, we show that dithiothreitol- or tunicamycin-induced ER stress also induces µLP and identify an unexpected role for vacuolar membrane dynamics in this process. All stressors studied induce vacuolar fragmentation prior to µLP. Moreover, during µLP, fragmented vacuoles fuse to form cup-shaped structures that encapsulate and ultimately take up LDs. Our studies also indicate that proteins of the endosome sorting complexes required for transport (ESCRT) are upregulated, required for µLP, and recruited to LDs, vacuolar membranes, and sites of vacuolar membrane scission during µLP. We identify possible target proteins for LD-mediated ER proteostasis. Our live-cell imaging studies reveal that one potential target (Nup159) localizes to punctate structures that colocalizes with LDs 1) during movement from ER membranes to the cytosol, 2) during microautophagic uptake into vacuoles, and 3) within the vacuolar lumen. Finally, we find that mutations that inhibit LD biogenesis, homotypic vacuolar membrane fusion or ESCRT function inhibit stress-induced autophagy of Nup159 and other ER proteins. Thus, we have obtained the first direct evidence that LDs and µLP can mediate ER stress-induced ER proteostasis, and identified direct roles for ESCRT and vacuolar membrane fusion in that process.
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Affiliation(s)
- Enrique J Garcia
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Pin-Chao Liao
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Gary Tan
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Jason D Vevea
- HHMI and Department of Neuroscience, University of Wisconsin, Madison, Wisconsin, USA
| | - Cierra N Sing
- Institute of Human Nutrition, Columbia University, New York, NY, USA
| | - Catherine A Tsang
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - J Michael McCaffery
- Integrated Imaging Center, Department of Biology, The Johns Hopkins University, Baltimore, MD, USA
| | - Istvan R Boldogh
- 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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Higuchi-Sanabria R, Shen K, Kelet N, Frankino PA, Durieux J, Bar-Ziv R, Sing CN, Garcia EJ, Homentcovschi S, Sanchez M, Wu R, Tronnes SU, Joe L, Webster B, Ahilon-Jeronimo A, Monshietehadi S, Dallarda S, Pender C, Pon LA, Zoncu R, Dillin A. Lysosomal recycling of amino acids affects ER quality control. Sci Adv 2020; 6:eaaz9805. [PMID: 32637599 PMCID: PMC7319768 DOI: 10.1126/sciadv.aaz9805] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
Recent work has highlighted the fact that lysosomes are a critical signaling hub of metabolic processes, providing fundamental building blocks crucial for anabolic functions. How lysosomal functions affect other cellular compartments is not fully understood. Here, we find that lysosomal recycling of the amino acids lysine and arginine is essential for proper ER quality control through the UPRER. Specifically, loss of the lysine and arginine amino acid transporter LAAT-1 results in increased sensitivity to proteotoxic stress in the ER and decreased animal physiology. We find that these LAAT-1-dependent effects are linked to glycine metabolism and transport and that the loss of function of the glycine transporter SKAT-1 also increases sensitivity to ER stress. Direct lysine and arginine supplementation, or glycine supplementation alone, can ameliorate increased ER stress sensitivity found in laat-1 mutants. These data implicate a crucial role in recycling lysine, arginine, and glycine in communication between the lysosome and ER.
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Affiliation(s)
- Ryo Higuchi-Sanabria
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Koning Shen
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Naame Kelet
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Phillip A. Frankino
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Jenni Durieux
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Raz Bar-Ziv
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Cierra N. Sing
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Enrique J. Garcia
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Stefan Homentcovschi
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Melissa Sanchez
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Rui Wu
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Sarah U. Tronnes
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Larry Joe
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Brant Webster
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Alex Ahilon-Jeronimo
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Samira Monshietehadi
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Sofia Dallarda
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Corinne Pender
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Liza A. Pon
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Roberto Zoncu
- Department of Biochemistry, Biophysics, and Structural Biology, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Andrew Dillin
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
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Abstract
Mitochondria are highly dynamic organelles that undergo directed movement and anchorage, which in turn are critical for calcium buffering and energy mobilization at specific regions within cells or at sites of contact with other organelles. Physical and functional interactions between mitochondria and other organelles also impact processes, including phospholipid biogenesis and calcium homeostasis. Indeed, mitochondrial motility, localization, and interaction with other organelles are compromised in many neurodegenerative diseases. Here, we describe methods to visualize and carry out quantitative analysis of mitochondrial movement in two genetically-manipulatable, widely-used model systems: Drosophila neurons and the budding yeast, Saccharomyces cerevisiae. We also describe approaches for multi-color imaging in living yeast cells that may be used to visualize colocalization of proteins within mitochondria, as well as interactions of mitochondria with other organelles.
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Affiliation(s)
- Pin-Chao Liao
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
| | - Ryo Higuchi-Sanabria
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States; Institute of Human Nutrition, Columbia University, New York, NY, United States
| | - Theresa C Swayne
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, United States
| | - Cierra N Sing
- Institute of Human Nutrition, Columbia University, New York, NY, United States
| | - Liza A Pon
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, United States; Institute of Human Nutrition, Columbia University, New York, NY, United States.
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Garcia EJ, de Jonge JJ, Liao PC, Stivison E, Sing CN, Higuchi-Sanabria R, Boldogh IR, Pon LA. Reciprocal interactions between mtDNA and lifespan control in budding yeast. Mol Biol Cell 2019; 30:2943-2952. [PMID: 31599702 PMCID: PMC6857569 DOI: 10.1091/mbc.e18-06-0356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 01/01/2023] Open
Abstract
Loss of mitochondrial DNA (mtDNA) results in loss of mitochondrial respiratory activity, checkpoint-regulated inhibition of cell cycle progression, defects in growth, and nuclear genome instability. However, after several generations, yeast cells can adapt to the loss of mtDNA. During this adaptation, rho0 cells, which have no mtDNA, exhibit increased growth rates and nuclear genome stabilization. Here, we report that an immediate response to loss of mtDNA is a decrease in replicative lifespan (RLS). Moreover, we find that adapted rho0 cells bypass the mtDNA inheritance checkpoint, exhibit increased mitochondrial function, and undergo an increase in RLS as they adapt to the loss of mtDNA. Transcriptome analysis reveals that metabolic reprogramming to compensate for defects in mitochondrial function is an early event during adaptation and that up-regulation of stress response genes occurs later in the adaptation process. We also find that specific subtelomeric genes are silenced during adaptation to loss of mtDNA. Moreover, we find that deletion of SIR3, a subtelomeric gene silencing protein, inhibits silencing of subtelomeric genes associated with adaptation to loss of mtDNA, as well as adaptation-associated increases in mitochondrial function and RLS extension.
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Affiliation(s)
- Enrique J. Garcia
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Janeska J. de Jonge
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Pin-Chao Liao
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Elizabeth Stivison
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Cierra N. Sing
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Ryo Higuchi-Sanabria
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Istvan R. Boldogh
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Liza A. Pon
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
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8
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Chen X, Wang G, Zhang Y, Dayhoff-Brannigan M, Diny NL, Zhao M, He G, Sing CN, Metz KA, Stolp ZD, Aouacheria A, Cheng WC, Hardwick JM, Teng X. Whi2 is a conserved negative regulator of TORC1 in response to low amino acids. PLoS Genet 2018; 14:e1007592. [PMID: 30142151 PMCID: PMC6126876 DOI: 10.1371/journal.pgen.1007592] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 09/06/2018] [Accepted: 07/26/2018] [Indexed: 01/29/2023] Open
Abstract
Yeast WHI2 was originally identified in a genetic screen for regulators of cell cycle arrest and later suggested to function in general stress responses. However, the function of Whi2 is unknown. Whi2 has predicted structure and sequence similarity to human KCTD family proteins, which have been implicated in several cancers and are causally associated with neurological disorders but are largely uncharacterized. The identification of conserved functions between these yeast and human proteins may provide insight into disease mechanisms. We report that yeast WHI2 is a new negative regulator of TORC1 required to suppress TORC1 activity and cell growth specifically in response to low amino acids. In contrast to current opinion, WHI2 is dispensable for TORC1 inhibition in low glucose. The only widely conserved mechanism that actively suppresses both yeast and mammalian TORC1 specifically in response to low amino acids is the conserved SEACIT/GATOR1 complex that inactivates the TORC1-activating RAG-like GTPases. Unexpectedly, Whi2 acts independently and simultaneously with these established GATOR1-like Npr2-Npr3-Iml1 and RAG-like Gtr1-Gtr2 complexes, and also acts independently of the PKA pathway. Instead, Whi2 inhibits TORC1 activity through its binding partners, protein phosphatases Psr1 and Psr2, which were previously thought to only regulate amino acid levels downstream of TORC1. Furthermore, the ability to suppress TORC1 is conserved in the SKP1/BTB/POZ domain-containing, Whi2-like human protein KCTD11 but not other KCTD family members tested. Yeast and human cells respond to declining levels of available nutrients to prepare ahead for leaner times. The detailed mechanisms of nutrient sensing are not well understood, but defects in these processes have key roles in diseases such as cancer. The evolutionarily conserved protein complex TORC1 is the control hub for responding to both high and low nutrients, particularly amino acids. We identified yeast Whi2 and the human tumor suppressor KCTD11 as novel suppressors of TORC1 activity in low amino acid conditions, and we investigated the detailed mechanisms for Whi2. Unexpectedly, Whi2 works differently from the usual mechanism where TORC1 is controlled by the SEACIT-Gtr complex (mammalian GATOR1-RAG complex). Furthermore, both the Whi2 and the SEACIT-Gtr pathways work independently and together in parallel to suppress TORC1. For this function, Whi2 requires its binding partners, the yeast protein phosphatases Psr1 and Psr2, which were previously thought to function downstream of TORC1 in amino acid signaling. These studies have important implications for human KCTD11 to help advance the understanding of its pathological role.
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Affiliation(s)
- Xianghui Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Guiqin Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Yu Zhang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Margaret Dayhoff-Brannigan
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Nicola L. Diny
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Mingjun Zhao
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Ge He
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Cierra N. Sing
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Kyle A. Metz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Zachary D. Stolp
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Abdel Aouacheria
- ISEM, Institut des Sciences de l’Evolution de Montpellier, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Wen-Chih Cheng
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - J. Marie Hardwick
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- * E-mail: (JMH); (XT)
| | - Xinchen Teng
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States of America
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- * E-mail: (JMH); (XT)
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9
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Higuchi-Sanabria R, Charalel JK, Viana MP, Garcia EJ, Sing CN, Koenigsberg A, Swayne TC, Vevea JD, Boldogh IR, Rafelski SM, Pon LA. Mitochondrial anchorage and fusion contribute to mitochondrial inheritance and quality control in the budding yeast Saccharomyces cerevisiae. Mol Biol Cell 2016; 27:776-87. [PMID: 26764088 PMCID: PMC4803304 DOI: 10.1091/mbc.e15-07-0455] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 01/07/2016] [Indexed: 11/30/2022] Open
Abstract
Fzo1p contributes to mitochondrial inheritance by fusion of mitochondria that enter the bud to mitochondria that are anchored in the bud tip. This promotes retention of mitochondria in the bud tip. However, it also promotes anchorage of lower-functioning mitochondria in the bud tip, which inhibits clearance of those organelles from buds. Higher-functioning mitochondria that are more reduced and have less ROS are anchored in the yeast bud tip by the Dsl1-family protein Mmr1p. Here we report a role for mitochondrial fusion in bud-tip anchorage of mitochondria. Fluorescence loss in photobleaching (FLIP) and network analysis experiments revealed that mitochondria in large buds are a continuous reticulum that is physically distinct from mitochondria in mother cells. FLIP studies also showed that mitochondria that enter the bud can fuse with mitochondria that are anchored in the bud tip. In addition, loss of fusion and mitochondrial DNA (mtDNA) by deletion of mitochondrial outer or inner membrane fusion proteins (Fzo1p or Mgm1p) leads to decreased accumulation of mitochondria at the bud tip and inheritance of fitter mitochondria by buds compared with cells with no mtDNA. Conversely, increasing the accumulation and anchorage of mitochondria in the bud tip by overexpression of MMR1 results in inheritance of less-fit mitochondria by buds and decreased replicative lifespan and healthspan. Thus quantity and quality of mitochondrial inheritance are ensured by two opposing processes: bud-tip anchorage by mitochondrial fusion and Mmr1p, which favors bulk inheritance; and quality control mechanisms that promote segregation of fitter mitochondria to the bud.
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Affiliation(s)
- Ryo Higuchi-Sanabria
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| | - Joseph K Charalel
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| | - Matheus P Viana
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697
| | - Enrique J Garcia
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| | - Cierra N Sing
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| | - Andrea Koenigsberg
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| | - Theresa C Swayne
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032
| | - Jason D Vevea
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| | - Istvan R Boldogh
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032
| | - Susanne M Rafelski
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697
| | - Liza A Pon
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032 Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032
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Teng X, Dayhoff-Brannigan M, Cheng WC, Gilbert CE, Sing CN, Diny NL, Wheelan SJ, Dunham MJ, Boeke JD, Pineda FJ, Hardwick JM. Genome-wide consequences of deleting any single gene. Mol Cell 2013; 52:485-94. [PMID: 24211263 DOI: 10.1016/j.molcel.2013.09.026] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 08/18/2013] [Accepted: 09/19/2013] [Indexed: 11/19/2022]
Abstract
Loss or duplication of chromosome segments can lead to further genomic changes associated with cancer. However, it is not known whether only a select subset of genes is responsible for driving further changes. To determine whether perturbation of any given gene in a genome suffices to drive subsequent genetic changes, we analyzed the yeast knockout collection for secondary mutations of functional consequence. Unlike wild-type, most gene knockout strains were found to have one additional mutant gene affecting nutrient responses and/or heat-stress-induced cell death. Moreover, independent knockouts of the same gene often evolved mutations in the same secondary gene. Genome sequencing identified acquired mutations in several human tumor suppressor homologs. Thus, mutation of any single gene may cause a genomic imbalance, with consequences sufficient to drive adaptive genetic changes. This complicates genetic analyses but is a logical consequence of losing a functional unit originally acquired under pressure during evolution.
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Affiliation(s)
- Xinchen Teng
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
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