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Egebjerg JM, Szomek M, Thaysen K, Juhl AD, Kozakijevic S, Werner S, Pratsch C, Schneider G, Kapishnikov S, Ekman A, Röttger R, Wüstner D. Automated quantification of vacuole fusion and lipophagy in Saccharomyces cerevisiae from fluorescence and cryo-soft X-ray microscopy data using deep learning. Autophagy 2024; 20:902-922. [PMID: 37908116 PMCID: PMC11062380 DOI: 10.1080/15548627.2023.2270378] [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: 03/06/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023] Open
Abstract
During starvation in the yeast Saccharomyces cerevisiae vacuolar vesicles fuse and lipid droplets (LDs) can become internalized into the vacuole in an autophagic process named lipophagy. There is a lack of tools to quantitatively assess starvation-induced vacuole fusion and lipophagy in intact cells with high resolution and throughput. Here, we combine soft X-ray tomography (SXT) with fluorescence microscopy and use a deep-learning computational approach to visualize and quantify these processes in yeast. We focus on yeast homologs of mammalian NPC1 (NPC intracellular cholesterol transporter 1; Ncr1 in yeast) and NPC2 proteins, whose dysfunction leads to Niemann Pick type C (NPC) disease in humans. We developed a convolutional neural network (CNN) model which classifies fully fused versus partially fused vacuoles based on fluorescence images of stained cells. This CNN, named Deep Yeast Fusion Network (DYFNet), revealed that cells lacking Ncr1 (ncr1∆ cells) or Npc2 (npc2∆ cells) have a reduced capacity for vacuole fusion. Using a second CNN model, we implemented a pipeline named LipoSeg to perform automated instance segmentation of LDs and vacuoles from high-resolution reconstructions of X-ray tomograms. From that, we obtained 3D renderings of LDs inside and outside of the vacuole in a fully automated manner and additionally measured droplet volume, number, and distribution. We find that ncr1∆ and npc2∆ cells could ingest LDs into vacuoles normally but showed compromised degradation of LDs and accumulation of lipid vesicles inside vacuoles. Our new method is versatile and allows for analysis of vacuole fusion, droplet size and lipophagy in intact cells.Abbreviations: BODIPY493/503: 4,4-difluoro-1,3,5,7,8-pentamethyl-4-bora-3a,4a-diaza-s-Indacene; BPS: bathophenanthrolinedisulfonic acid disodium salt hydrate; CNN: convolutional neural network; DHE; dehydroergosterol; npc2∆, yeast deficient in Npc2; DSC, Dice similarity coefficient; EM, electron microscopy; EVs, extracellular vesicles; FIB-SEM, focused ion beam milling-scanning electron microscopy; FM 4-64, N-(3-triethylammoniumpropyl)-4-(6-[4-{diethylamino} phenyl] hexatrienyl)-pyridinium dibromide; LDs, lipid droplets; Ncr1, yeast homolog of human NPC1 protein; ncr1∆, yeast deficient in Ncr1; NPC, Niemann Pick type C; NPC2, Niemann Pick type C homolog; OD600, optical density at 600 nm; ReLU, rectifier linear unit; PPV, positive predictive value; NPV, negative predictive value; MCC, Matthews correlation coefficient; SXT, soft X-ray tomography; UV, ultraviolet; YPD, yeast extract peptone dextrose.
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Affiliation(s)
- Jacob Marcus Egebjerg
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense M, Denmark
| | - Maria Szomek
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Katja Thaysen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Alice Dupont Juhl
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Suzana Kozakijevic
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Stephan Werner
- Department of X‑Ray Microscopy, Helmholtz-Zentrum Berlin, Germany and Humboldt-Universität zu Berlin, Institut für Physik, Berlin, Germany
| | - Christoph Pratsch
- Department of X‑Ray Microscopy, Helmholtz-Zentrum Berlin, Germany and Humboldt-Universität zu Berlin, Institut für Physik, Berlin, Germany
| | - Gerd Schneider
- Department of X‑Ray Microscopy, Helmholtz-Zentrum Berlin, Germany and Humboldt-Universität zu Berlin, Institut für Physik, Berlin, Germany
| | - Sergey Kapishnikov
- SiriusXT, 9A Holly Ave. Stillorgan Industrial Park, Blackrock, Co, Dublin, Ireland
| | - Axel Ekman
- Department of Biological and Environmental Science and Nanoscience Centre, University of Jyväskylä, Jyväskylä, Finland
| | - Richard Röttger
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense M, Denmark
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
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2
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Hammond N, Snider J, Stagljar I, Mitchell K, Lagutin K, Jessulat M, Babu M, Teesdale-Spittle PH, Sheridan JP, Sturley SL, Munkacsi AB. Identification and characterization of protein interactions with the major Niemann-Pick type C disease protein in yeast reveals pathways of therapeutic potential. Genetics 2023; 225:iyad129. [PMID: 37440478 PMCID: PMC10471228 DOI: 10.1093/genetics/iyad129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 01/12/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Niemann-Pick type C (NP-C) disease is a rare lysosomal storage disease caused by mutations in NPC1 (95% cases) or NPC2 (5% cases). These proteins function together in cholesterol egress from the lysosome, whereby upon mutation, cholesterol and other lipids accumulate causing major pathologies. However, it is not fully understood how cholesterol is transported from NPC1 residing at the lysosomal membrane to the endoplasmic reticulum (ER) and plasma membrane. The yeast ortholog of NPC1, Niemann-Pick type C-related protein-1 (Ncr1), functions similarly to NPC1; when transfected into a mammalian cell lacking NPC1, Ncr1 rescues the diagnostic hallmarks of cholesterol and sphingolipid accumulation. Here, we aimed to identify and characterize protein-protein interactions (PPIs) with the yeast Ncr1 protein. A genome-wide split-ubiquitin membrane yeast two-hybrid (MYTH) protein interaction screen identified 11 ER membrane-localized, full-length proteins interacting with Ncr1 at the lysosomal/vacuolar membrane. These highlight the importance of ER-vacuole membrane interface and include PPIs with the Cyb5/Cbr1 electron transfer system, the ceramide synthase complex, and the Sec61/Sbh1 protein translocation complex. These PPIs were not detected in a sterol auxotrophy condition and thus depend on normal sterol metabolism. To provide biological context for the Ncr1-Cyb5 PPI, a yeast strain lacking this PPI (via gene deletions) exhibited altered levels of sterols and sphingolipids including increased levels of glucosylceramide that mimic NP-C disease. Overall, the results herein provide new physical and genetic interaction models to further use the yeast model of NP-C disease to better understand human NP-C disease.
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Affiliation(s)
- Natalie Hammond
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jamie Snider
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Mediterranean Institute for Life Sciences, Meštrovićevo Šetalište 45, HR-21000 Split, Croatia
| | | | | | - Matthew Jessulat
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Paul H Teesdale-Spittle
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jeffrey P Sheridan
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Stephen L Sturley
- Department of Biology, Barnard College-Columbia University, New York, NY 10027, USA
| | - Andrew B Munkacsi
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
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3
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Martins TS, Costa RS, Vilaça R, Lemos C, Teixeira V, Pereira C, Costa V. Iron Limitation Restores Autophagy and Increases Lifespan in the Yeast Model of Niemann–Pick Type C1. Int J Mol Sci 2023; 24:ijms24076221. [PMID: 37047194 PMCID: PMC10094029 DOI: 10.3390/ijms24076221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Niemann–Pick type C1 (NPC1) is an endolysosomal transmembrane protein involved in the export of cholesterol and sphingolipids to other cellular compartments such as the endoplasmic reticulum and plasma membrane. NPC1 loss of function is the major cause of NPC disease, a rare lysosomal storage disorder characterized by an abnormal accumulation of lipids in the late endosomal/lysosomal network, mitochondrial dysfunction, and impaired autophagy. NPC phenotypes are conserved in yeast lacking Ncr1, an orthologue of human NPC1, leading to premature aging. Herein, we performed a phosphoproteomic analysis to investigate the effect of Ncr1 loss on cellular functions mediated by the yeast lysosome-like vacuoles. Our results revealed changes in vacuolar membrane proteins that are associated mostly with vesicle biology (fusion, transport, organization), autophagy, and ion homeostasis, including iron, manganese, and calcium. Consistently, the cytoplasm to vacuole targeting (Cvt) pathway was increased in ncr1∆ cells and autophagy was compromised despite TORC1 inhibition. Moreover, ncr1∆ cells exhibited iron overload mediated by the low-iron sensing transcription factor Aft1. Iron deprivation restored the autophagic flux of ncr1∆ cells and increased its chronological lifespan and oxidative stress resistance. These results implicate iron overload on autophagy impairment, oxidative stress sensitivity, and cell death in the yeast model of NPC1.
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4
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Leite AC, Barbedo M, Costa V, Pereira C. The APC/C Activator Cdh1p Plays a Role in Mitochondrial Metabolic Remodelling in Yeast. Int J Mol Sci 2023; 24:ijms24044111. [PMID: 36835555 PMCID: PMC9967508 DOI: 10.3390/ijms24044111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Cdh1p is one of the two substrate adaptor proteins of the anaphase promoting complex/cyclosome (APC/C), a ubiquitin ligase that regulates proteolysis during cell cycle. In this work, using a proteomic approach, we found 135 mitochondrial proteins whose abundance was significantly altered in the cdh1Δ mutant, with 43 up-regulated proteins and 92 down-regulated proteins. The group of significantly up-regulated proteins included subunits of the mitochondrial respiratory chain, enzymes from the tricarboxylic acid cycle and regulators of mitochondrial organization, suggesting a metabolic remodelling towards an increase in mitochondrial respiration. In accordance, mitochondrial oxygen consumption and Cytochrome c oxidase activity increased in Cdh1p-deficient cells. These effects seem to be mediated by the transcriptional activator Yap1p, a major regulator of the yeast oxidative stress response. YAP1 deletion suppressed the increased Cyc1p levels and mitochondrial respiration in cdh1Δ cells. In agreement, Yap1p is transcriptionally more active in cdh1Δ cells and responsible for the higher oxidative stress tolerance of cdh1Δ mutant cells. Overall, our results unveil a new role for APC/C-Cdh1p in the regulation of the mitochondrial metabolic remodelling through Yap1p activity.
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Affiliation(s)
- Ana Cláudia Leite
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- IBMC—Instituto de Biologia Celular e Molecular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Maria Barbedo
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- IBMC—Instituto de Biologia Celular e Molecular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - Vítor Costa
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- IBMC—Instituto de Biologia Celular e Molecular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Clara Pereira
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- IBMC—Instituto de Biologia Celular e Molecular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
- Correspondence: ; Tel.: +351-220408800
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5
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Mirisola MG, Longo VD. Yeast Chronological Lifespan: Longevity Regulatory Genes and Mechanisms. Cells 2022; 11:cells11101714. [PMID: 35626750 PMCID: PMC9139625 DOI: 10.3390/cells11101714] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/14/2022] [Accepted: 05/18/2022] [Indexed: 02/04/2023] Open
Abstract
S. cerevisiae plays a pivotal role as a model system in understanding the biochemistry and molecular biology of mammals including humans. A considerable portion of our knowledge on the genes and pathways involved in cellular growth, resistance to toxic agents, and death has in fact been generated using this model organism. The yeast chronological lifespan (CLS) is a paradigm to study age-dependent damage and longevity. In combination with powerful genetic screening and high throughput technologies, the CLS has allowed the identification of longevity genes and pathways but has also introduced a unicellular “test tube” model system to identify and study macromolecular and cellular damage leading to diseases. In addition, it has played an important role in studying the nutrients and dietary regimens capable of affecting stress resistance and longevity and allowing the characterization of aging regulatory networks. The parallel description of the pro-aging roles of homologs of RAS, S6 kinase, adenylate cyclase, and Tor in yeast and in higher eukaryotes in S. cerevisiae chronological survival studies is valuable to understand human aging and disease. Here we review work on the S. cerevisiae chronological lifespan with a focus on the genes regulating age-dependent macromolecular damage and longevity extension.
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Affiliation(s)
- Mario G. Mirisola
- Department of Surgery, Oncology and Oral Sciences, University of Palermo, Via del Vespro 129, 90127 Palermo, Italy
- Correspondence: (M.G.M.); (V.D.L.)
| | - Valter D. Longo
- Department of Biological Sciences, Longevity Institute, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- IFOM, FIRC Institute of Molecular Oncology, 20139 Milan, Italy
- Correspondence: (M.G.M.); (V.D.L.)
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6
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Winkler MBL, Nel L, Frain KM, Dedic E, Olesen E, Pedersen BP. Sterol uptake by the NPC system in eukaryotes: a Saccharomyces cerevisiae perspective. FEBS Lett 2021; 596:160-179. [PMID: 34897668 DOI: 10.1002/1873-3468.14253] [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] [Received: 10/20/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 12/11/2022]
Abstract
Sterols are an essential component of membranes in all eukaryotic cells and the precursor of multiple indispensable cellular metabolites. After endocytotic uptake, sterols are integrated into the lysosomal membrane by the Niemann-Pick type C (NPC) system before redistribution to other membranes. The process is driven by two proteins that, together, compose the NPC system: the lysosomal sterol shuttle protein NPC2 and the membrane protein NPC1 (named NCR1 in fungi), which integrates sterols into the lysosomal membrane. The Saccharomyces cerevisiae NPC system provides a compelling model to study the molecular mechanism of sterol integration into membranes and sterol homeostasis. This review summarizes recent advances in the field, and by interpreting available structural data, we propose a unifying conceptual model for sterol loading, transfer and transport by NPC proteins.
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Affiliation(s)
- Mikael B L Winkler
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Lynette Nel
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Kelly M Frain
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Emil Dedic
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Esben Olesen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
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7
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Sun Y, Yu R, Guo HB, Qin H, Dang W. A quantitative yeast aging proteomics analysis reveals novel aging regulators. GeroScience 2021; 43:2573-2593. [PMID: 34241809 DOI: 10.1007/s11357-021-00412-3] [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] [Received: 07/18/2020] [Accepted: 06/23/2021] [Indexed: 11/29/2022] Open
Abstract
Calorie restriction (CR) is the most robust longevity intervention, extending lifespan from yeast to mammals. Numerous conserved pathways regulating aging and mediating CR have been identified; however, the overall proteomic changes during these conditions remain largely unexplored. We compared proteomes between young and replicatively aged yeast cells under normal and CR conditions using the Stable-Isotope Labeling by Amino acids in Cell culture (SILAC) quantitative proteomics and discovered distinct signatures in the aging proteome. We found remarkable proteomic similarities between aged and CR cells, including induction of stress response pathways, providing evidence that CR pathways are engaged in aged cells. These observations also uncovered aberrant changes in mitochondria membrane proteins as well as a proteolytic cellular state in old cells. These proteomics analyses help identify potential genes and pathways that have causal effects on longevity.
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Affiliation(s)
- Yu Sun
- Huffington Center On Aging and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ruofan Yu
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hao-Bo Guo
- Department of Computer Science and Engineering, Department of Biology, Geology and Environmental Science, SimCenter, The University of Tennessee At Chattanooga, Chattanooga, TN, 37403, USA
| | - Hong Qin
- Department of Computer Science and Engineering, Department of Biology, Geology and Environmental Science, SimCenter, The University of Tennessee At Chattanooga, Chattanooga, TN, 37403, USA
| | - Weiwei Dang
- Huffington Center On Aging and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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8
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Abed Rabbo M, Khodour Y, Kaguni LS, Stiban J. Sphingolipid lysosomal storage diseases: from bench to bedside. Lipids Health Dis 2021; 20:44. [PMID: 33941173 PMCID: PMC8094529 DOI: 10.1186/s12944-021-01466-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/14/2021] [Indexed: 01/13/2023] Open
Abstract
Johann Ludwig Wilhelm Thudicum described sphingolipids (SLs) in the late nineteenth century, but it was only in the past fifty years that SL research surged in importance and applicability. Currently, sphingolipids and their metabolism are hotly debated topics in various biochemical fields. Similar to other macromolecular reactions, SL metabolism has important implications in health and disease in most cells. A plethora of SL-related genetic ailments has been described. Defects in SL catabolism can cause the accumulation of SLs, leading to many types of lysosomal storage diseases (LSDs) collectively called sphingolipidoses. These diseases mainly impact the neuronal and immune systems, but other systems can be affected as well. This review aims to present a comprehensive, up-to-date picture of the rapidly growing field of sphingolipid LSDs, their etiology, pathology, and potential therapeutic strategies. We first describe LSDs biochemically and briefly discuss their catabolism, followed by general aspects of the major diseases such as Gaucher, Krabbe, Fabry, and Farber among others. We conclude with an overview of the available and potential future therapies for many of the diseases. We strive to present the most important and recent findings from basic research and clinical applications, and to provide a valuable source for understanding these disorders.
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Affiliation(s)
- Muna Abed Rabbo
- Department of Biology and Biochemistry, Birzeit University, P.O. Box 14, Ramallah, West Bank, 627, Palestine
| | - Yara Khodour
- Department of Biology and Biochemistry, Birzeit University, P.O. Box 14, Ramallah, West Bank, 627, Palestine
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Johnny Stiban
- Department of Biology and Biochemistry, Birzeit University, P.O. Box 14, Ramallah, West Bank, 627, Palestine.
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9
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Jürs AV, Völkner C, Liedtke M, Huth K, Lukas J, Hermann A, Frech MJ. Oxidative Stress and Alterations in the Antioxidative Defense System in Neuronal Cells Derived from NPC1 Patient-Specific Induced Pluripotent Stem Cells. Int J Mol Sci 2020; 21:ijms21207667. [PMID: 33081384 PMCID: PMC7593914 DOI: 10.3390/ijms21207667] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 01/10/2023] Open
Abstract
Oxidative stress (OS) represents a state of an imbalanced amount of reactive oxygen species (ROS) and/or a hampered efficacy of the antioxidative defense system. Cells of the central nervous system are particularly sensitive to OS, as they have a massive need of oxygen to maintain proper function. Consequently, OS represents a common pathophysiological hallmark of neurodegenerative diseases and is discussed to contribute to the neurodegeneration observed amongst others in Alzheimer’s disease and Parkinson’s disease. In this context, accumulating evidence suggests that OS is involved in the pathophysiology of Niemann-Pick type C1 disease (NPC1). NPC1, a rare hereditary neurodegenerative disease, belongs to the family of lysosomal storage disorders. A major hallmark of the disease is the accumulation of cholesterol and other glycosphingolipids in lysosomes. Several studies describe OS both in murine in vivo and in vitro NPC1 models. However, studies based on human cells are limited to NPC1 patient-derived fibroblasts. Thus, we analyzed OS in a human neuronal model based on NPC1 patient-specific induced pluripotent stem cells (iPSCs). Higher ROS levels, as determined by DCF (dichlorodihydrofluorescein) fluorescence, indicated oxidative stress in all NPC1-deficient cell lines. This finding was further supported by reduced superoxide dismutase (SOD) activity. The analysis of mRNA and protein levels of SOD1 and SOD2 did not reveal any difference between control cells and NPC1-deficient cells. Interestingly, we observed a striking decrease in catalase mRNA and protein levels in all NPC1-deficient cell lines. As catalase is a key enzyme of the cellular antioxidative defense system, we concluded that the lack of catalase contributes to the elevated ROS levels observed in NPC1-deficient cells. Thus, a restitution of a physiological catalase level may pose an intervention strategy to rescue NPC1-deficient cells from the repercussions of oxidative stress contributing to the neurodegeneration observed in NPC1.
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Affiliation(s)
- Alexandra V. Jürs
- Translational Neurodegeneration Section Albrecht Kossel, Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany; (A.V.J.); (C.V.); (M.L.); (K.H.); (J.L.); (A.H.)
| | - Christin Völkner
- Translational Neurodegeneration Section Albrecht Kossel, Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany; (A.V.J.); (C.V.); (M.L.); (K.H.); (J.L.); (A.H.)
| | - Maik Liedtke
- Translational Neurodegeneration Section Albrecht Kossel, Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany; (A.V.J.); (C.V.); (M.L.); (K.H.); (J.L.); (A.H.)
| | - Katharina Huth
- Translational Neurodegeneration Section Albrecht Kossel, Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany; (A.V.J.); (C.V.); (M.L.); (K.H.); (J.L.); (A.H.)
| | - Jan Lukas
- Translational Neurodegeneration Section Albrecht Kossel, Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany; (A.V.J.); (C.V.); (M.L.); (K.H.); (J.L.); (A.H.)
- Center for Transdisciplinary Neurosciences Rostock (CTNR), Rostock University Medical Center, University of Rostock, 18147 Rostock, Germany
| | - Andreas Hermann
- Translational Neurodegeneration Section Albrecht Kossel, Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany; (A.V.J.); (C.V.); (M.L.); (K.H.); (J.L.); (A.H.)
- Center for Transdisciplinary Neurosciences Rostock (CTNR), Rostock University Medical Center, University of Rostock, 18147 Rostock, Germany
- German Center for Neurodegenerative Diseases (DZNE) Rostock/Greifswald, 18147 Rostock, Germany
| | - Moritz J. Frech
- Translational Neurodegeneration Section Albrecht Kossel, Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany; (A.V.J.); (C.V.); (M.L.); (K.H.); (J.L.); (A.H.)
- Center for Transdisciplinary Neurosciences Rostock (CTNR), Rostock University Medical Center, University of Rostock, 18147 Rostock, Germany
- Correspondence:
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10
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Colaco A, Fernández-Suárez ME, Shepherd D, Gal L, Bibi C, Chuartzman S, Diot A, Morten K, Eden E, Porter FD, Poulton J, Platt N, Schuldiner M, Platt FM. Unbiased yeast screens identify cellular pathways affected in Niemann-Pick disease type C. Life Sci Alliance 2020; 3:e201800253. [PMID: 32487688 PMCID: PMC7283134 DOI: 10.26508/lsa.201800253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 01/14/2023] Open
Abstract
Niemann-Pick disease type C (NPC) is a rare lysosomal storage disease caused by mutations in either the NPC1 or NPC2 genes. Mutations in the NPC1 gene lead to the majority of clinical cases (95%); however, the function of NPC1 remains unknown. To gain further insights into the biology of NPC1, we took advantage of the homology between the human NPC1 protein and its yeast orthologue, Niemann-Pick C-related protein 1 (Ncr1). We recreated the NCR1 mutant in yeast and performed screens to identify compensatory or redundant pathways that may be involved in NPC pathology, as well as proteins that were mislocalized in NCR1-deficient yeast. We also identified binding partners of the yeast Ncr1 orthologue. These screens identified several processes and pathways that may contribute to NPC pathogenesis. These included alterations in mitochondrial function, cytoskeleton organization, metal ion homeostasis, lipid trafficking, calcium signalling, and nutrient sensing. The mitochondrial and cytoskeletal abnormalities were validated in patient cells carrying mutations in NPC1, confirming their dysfunction in NPC disease.
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Affiliation(s)
| | | | - Dawn Shepherd
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Lihi Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Chen Bibi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Silvia Chuartzman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Alan Diot
- Nuffield Department of Obstetrics and Gynecology, University of Oxford, Oxford, UK
| | - Karl Morten
- Nuffield Department of Obstetrics and Gynecology, University of Oxford, Oxford, UK
| | - Emily Eden
- Institute of Ophthalmology-Cell Biology, University College London, London, UK
| | - Forbes D Porter
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institute of Health, Bethesda, MD, USA
| | - Joanna Poulton
- Nuffield Department of Obstetrics and Gynecology, University of Oxford, Oxford, UK
| | - Nick Platt
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Frances M Platt
- Department of Pharmacology, University of Oxford, Oxford, UK
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11
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Fiorenza MT, Moro E, Erickson RP. The pathogenesis of lysosomal storage disorders: beyond the engorgement of lysosomes to abnormal development and neuroinflammation. Hum Mol Genet 2019; 27:R119-R129. [PMID: 29718288 DOI: 10.1093/hmg/ddy155] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 04/24/2018] [Indexed: 01/03/2023] Open
Abstract
There is growing evidence that the complex clinical manifestations of lysosomal storage diseases (LSDs) are not fully explained by the engorgement of the endosomal-autophagic-lysosomal system. In this review, we explore current knowledge of common pathogenetic mechanisms responsible for the early onset of tissue abnormalities of two LSDs, Mucopolysaccharidosis type II (MPSII) and Niemann-Pick type C (NPC) diseases. In particular, perturbations of the homeostasis of glycosaminoglycans (GAGs) and cholesterol (Chol) in MPSII and NPC diseases, respectively, affect key biological processes, including morphogen signaling. Both GAGs and Chol finely regulate the release, reception and tissue distribution of Shh. Hence, not surprisingly, developmental processes depending on correct Shh signaling have been found altered in both diseases. Besides abnormal signaling, exaggerated activation of microglia and impairment of autophagy and mitophagy occur in both diseases, largely before the appearance of typical pathological signs.
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Affiliation(s)
- Maria Teresa Fiorenza
- Division of Neuroscience, Department of Psychology and "Daniel Bovet" Neurobiology Research Center, Sapienza University of Rome, Rome, Italy.,IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Enrico Moro
- Department of Molecular Medicine, University of Padova, Padova, Italy
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12
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Meske V, Albert F, Gerstenberg S, Kallwellis K, Ohm TG. NPC1-deficient neurons are selectively vulnerable for statin treatment. Neuropharmacology 2019; 151:159-170. [DOI: 10.1016/j.neuropharm.2019.04.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 03/07/2019] [Accepted: 04/10/2019] [Indexed: 10/27/2022]
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13
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McKenna MC, Schuck PF, Ferreira GC. Fundamentals of CNS energy metabolism and alterations in lysosomal storage diseases. J Neurochem 2018; 148:590-599. [PMID: 30144055 DOI: 10.1111/jnc.14577] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/05/2018] [Accepted: 08/22/2018] [Indexed: 01/03/2023]
Abstract
The brain has a very high requirement for energy. Adult brain relies on glucose as an energy substrate, whereas developing brain can utilize alternative substrates as well as glucose for energy and for the biosynthesis of lipids and proteins required for brain development. Metabolism provides the energy required to support all cellular functions and brain development and building blocks for macromolecules. Lysosomes are organelles involved in breakdown of biological compounds including proteins and complex lipids in the body and brain. Recent studies suggest that lysosomal dysfunction can damage neurons and/or alter neurotransmitter homeostasis. Several studies also implicate mitochondrial dysfunction in the pathophysiology of brain damage in lysosomal storage diseases. This manuscript provides a brief review of energy metabolism and the key pathways involved in metabolism in brain. Roles of lysosomes related to metabolism and neurotransmission are discussed, and evidence for mitochondrial dysfunction in several lysosomal storage diseases is presented. This article is part of the Special Issue "Lysosomal Storage Disorders".
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Affiliation(s)
- Mary C McKenna
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Program in Neuroscience, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Patricia F Schuck
- School of Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Gustavo C Ferreira
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, Rio Grande do Sul, Brazil
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14
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Ruetenik A, Barrientos A. Exploiting Post-mitotic Yeast Cultures to Model Neurodegeneration. Front Mol Neurosci 2018; 11:400. [PMID: 30450036 PMCID: PMC6224518 DOI: 10.3389/fnmol.2018.00400] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/12/2018] [Indexed: 12/19/2022] Open
Abstract
Over the last few decades, the budding yeast Saccharomyces cerevisiae has been extensively used as a valuable organism to explore mechanisms of aging and human age-associated neurodegenerative disorders. Yeast models can be used to study loss of function of disease-related conserved genes and to investigate gain of function activities, frequently proteotoxicity, exerted by non-conserved human mutant proteins responsible for neurodegeneration. Most published models of proteotoxicity have used rapidly dividing cells and suffer from a high level of protein expression resulting in acute growth arrest or cell death. This contrasts with the slow development of neurodegenerative proteotoxicity during aging and the characteristic post-mitotic state of the affected cell type, the neuron. Here, we will review the efforts to create and characterize yeast models of neurodegeneration using the chronological life span model of aging, and the specific information they can provide regarding the chronology of physiological events leading to neurotoxic proteotoxicity-induced cell death and the identification of new pathways involved.
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Affiliation(s)
- Andrea Ruetenik
- Department of Neurology, School of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States.,Neuroscience Graduate Program, School of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Antonio Barrientos
- Department of Neurology, School of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States.,Neuroscience Graduate Program, School of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States.,Department of Biochemistry, School of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
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15
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Yi JK, Xu R, Jeong E, Mileva I, Truman JP, Lin CL, Wang K, Snider J, Wen S, Obeid LM, Hannun YA, Mao C. Aging-related elevation of sphingoid bases shortens yeast chronological life span by compromising mitochondrial function. Oncotarget 2018; 7:21124-44. [PMID: 27008706 PMCID: PMC5008273 DOI: 10.18632/oncotarget.8195] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/04/2016] [Indexed: 01/08/2023] Open
Abstract
Sphingoid bases (SBs) as bioactive sphingolipids, have been implicated in aging in yeast. However, we know neither how SBs are regulated during yeast aging nor how they, in turn, regulate it. Herein, we demonstrate that the yeast alkaline ceramidases (YPC1 and YDC1) and SB kinases (LCB4 and LCB5) cooperate in regulating SBs during the aging process and that SBs shortens chronological life span (CLS) by compromising mitochondrial functions. With a lipidomics approach, we found that SBs were increased in a time-dependent manner during yeast aging. We also demonstrated that among the enzymes known for being responsible for the metabolism of SBs, YPC1 was upregulated whereas LCB4/5 were downregulated in the course of aging. This inverse regulation of YPC1 and LCB4/5 led to the aging-related upregulation of SBs in yeast and a reduction in CLS. With the proteomics-based approach (SILAC), we revealed that increased SBs altered the levels of proteins related to mitochondria. Further mechanistic studies demonstrated that increased SBs inhibited mitochondrial fusion and caused fragmentation, resulting in decreases in mtDNA copy numbers, ATP levels, mitochondrial membrane potentials, and oxygen consumption. Taken together, these results suggest that increased SBs mediate the aging process by impairing mitochondrial structural integrity and functions.
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Affiliation(s)
- Jae Kyo Yi
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY, USA.,Department of Medicine, Stony Brook University, Stony Brook, NY, USA.,Stony Brook Cancer Center, Stony Brook, NY, USA
| | - Ruijuan Xu
- Department of Medicine, Stony Brook University, Stony Brook, NY, USA.,Stony Brook Cancer Center, Stony Brook, NY, USA
| | - Eunmi Jeong
- Department of Medicine, Stony Brook University, Stony Brook, NY, USA.,Stony Brook Cancer Center, Stony Brook, NY, USA
| | - Izolda Mileva
- Department of Medicine, Stony Brook University, Stony Brook, NY, USA.,Stony Brook Cancer Center, Stony Brook, NY, USA
| | | | - Chih-Li Lin
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY, USA.,Department of Medicine, Stony Brook University, Stony Brook, NY, USA.,Stony Brook Cancer Center, Stony Brook, NY, USA
| | - Kai Wang
- Department of Medicine, Stony Brook University, Stony Brook, NY, USA.,Stony Brook Cancer Center, Stony Brook, NY, USA
| | - Justin Snider
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY, USA.,Department of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Sally Wen
- Department of Medicine, Stony Brook University, Stony Brook, NY, USA.,Stony Brook Cancer Center, Stony Brook, NY, USA
| | - Lina M Obeid
- Department of Medicine, Stony Brook University, Stony Brook, NY, USA.,Stony Brook Cancer Center, Stony Brook, NY, USA.,Northport Veterans Affairs Medical Center, Northport, NY, USA
| | - Yusuf A Hannun
- Department of Medicine, Stony Brook University, Stony Brook, NY, USA.,Stony Brook Cancer Center, Stony Brook, NY, USA
| | - Cungui Mao
- Department of Medicine, Stony Brook University, Stony Brook, NY, USA.,Stony Brook Cancer Center, Stony Brook, NY, USA
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16
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Vilaça R, Barros I, Matmati N, Silva E, Martins T, Teixeira V, Hannun YA, Costa V. The ceramide activated protein phosphatase Sit4 impairs sphingolipid dynamics, mitochondrial function and lifespan in a yeast model of Niemann-Pick type C1. Biochim Biophys Acta Mol Basis Dis 2017; 1864:79-88. [PMID: 28988886 DOI: 10.1016/j.bbadis.2017.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 09/29/2017] [Accepted: 10/05/2017] [Indexed: 12/20/2022]
Abstract
The Niemann-Pick type C is a rare neurodegenerative disease that results from loss-of-function point mutations in NPC1 or NPC2, which affect the homeostasis of sphingolipids and sterols in human cells. We have previously shown that yeast lacking Ncr1, the orthologue of human NPC1 protein, display a premature ageing phenotype and higher sensitivity to oxidative stress associated with mitochondrial dysfunctions and accumulation of long chain bases. In this study, a lipidomic analysis revealed specific changes in the levels of ceramide species in ncr1Δ cells, including decreases in dihydroceramides and increases in phytoceramides. Moreover, the activation of Sit4, a ceramide-activated protein phosphatase, increased in ncr1Δ cells. Deletion of SIT4 or CDC55, its regulatory subunit, increased the chronological lifespan and hydrogen peroxide resistance of ncr1Δ cells and suppressed its mitochondrial defects. Notably, Sch9 and Pkh1-mediated phosphorylation of Sch9 decreased significantly in ncr1Δsit4Δ cells. These results suggest that phytoceramide accumulation and Sit4-dependent signaling mediate the mitochondrial dysfunction and shortened lifespan in the yeast model of Niemann-Pick type C1, in part through modulation of the Pkh1-Sch9 pathway.
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Affiliation(s)
- Rita Vilaça
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal; Departamento de Biologia Molecular, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Ivo Barros
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal; Departamento de Biologia Molecular, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Nabil Matmati
- Stony Brook Cancer Center, Stony Brook University, Health Science Center, Stony Brook, NY, USA
| | - Elísio Silva
- Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal; Departamento de Biologia Molecular, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Telma Martins
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Vítor Teixeira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal; Departamento de Biologia Molecular, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Yusuf A Hannun
- Stony Brook Cancer Center, Stony Brook University, Health Science Center, Stony Brook, NY, USA
| | - Vítor Costa
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal; Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal; Departamento de Biologia Molecular, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal.
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17
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Rajakumar T, Munkacsi AB, Sturley SL. Exacerbating and reversing lysosomal storage diseases: from yeast to humans. MICROBIAL CELL 2017; 4:278-293. [PMID: 28913343 PMCID: PMC5597791 DOI: 10.15698/mic2017.09.588] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Lysosomal storage diseases (LSDs) arise from monogenic deficiencies in lysosomal proteins and pathways and are characterized by a tissue-wide accumulation of a vast variety of macromolecules, normally specific to each genetic lesion. Strategies for treatment of LSDs commonly depend on reduction of the offending metabolite(s) by substrate depletion or enzyme replacement. However, at least 44 of the ~50 LSDs are currently recalcitrant to intervention. Murine models have provided significant insights into our understanding of many LSD mechanisms; however, these systems do not readily permit phenotypic screening of compound libraries, or the establishment of genetic or gene-environment interaction networks. Many of the genes causing LSDs are evolutionarily conserved, thus facilitating the application of models system to provide additional insight into LSDs. Here, we review the utility of yeast models of 3 LSDs: Batten disease, cystinosis, and Niemann-Pick type C disease. We will focus on the translation of research from yeast models into human patients suffering from these LSDs. We will also discuss the use of yeast models to investigate the penetrance of LSDs, such as Niemann-Pick type C disease, into more prevalent syndromes including viral infection and obesity.
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Affiliation(s)
- Tamayanthi Rajakumar
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand 6012
| | - Andrew B Munkacsi
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand 6012.,Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand 6012
| | - Stephen L Sturley
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032
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18
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Mitochondrial Dysfunction and Neurodegeneration in Lysosomal Storage Disorders. Trends Mol Med 2017; 23:116-134. [DOI: 10.1016/j.molmed.2016.12.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/12/2016] [Accepted: 12/13/2016] [Indexed: 12/22/2022]
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19
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Exploring the power of yeast to model aging and age-related neurodegenerative disorders. Biogerontology 2016; 18:3-34. [PMID: 27804052 DOI: 10.1007/s10522-016-9666-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/24/2016] [Indexed: 12/12/2022]
Abstract
Aging is a multifactorial process determined by molecular, cellular and systemic factors and it is well established that advancing age is a leading risk factor for several neurodegenerative diseases. In fact, the close association of aging and neurodegenerative disorders has placed aging as the greatest social and economic challenge of the 21st century, and age-related diseases have also become a key priority for countries worldwide. The growing need to better understand both aging and neurodegenerative processes has led to the development of simple eukaryotic models amenable for mechanistic studies. Saccharomyces cerevisiae has proven to be an unprecedented experimental model to study the fundamental aspects of aging and to decipher the intricacies of neurodegenerative disorders greatly because the molecular mechanisms underlying these processes are evolutionarily conserved from yeast to human. Moreover, yeast offers several methodological advantages allowing a rapid and relatively easy way of establishing gene-protein-function associations. Here we review different aging theories, common cellular pathways driving aging and neurodegenerative diseases and discuss the major contributions of yeast to the state-of-art knowledge in both research fields.
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20
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Woś M, Szczepanowska J, Pikuła S, Tylki-Szymańska A, Zabłocki K, Bandorowicz-Pikuła J. Mitochondrial dysfunction in fibroblasts derived from patients with Niemann-Pick type C disease. Arch Biochem Biophys 2016; 593:50-9. [PMID: 26869201 DOI: 10.1016/j.abb.2016.02.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 02/05/2016] [Accepted: 02/06/2016] [Indexed: 01/01/2023]
Abstract
Mutations in the NPC1 or NPC2 genes lead to Niemann-Pick type C (NPC) disease, a rare lysosomal storage disorder characterized by progressive neurodegeneration. These mutations result in cholesterol and glycosphingolipid accumulation in the late endosomal/lysosomal compartment. Complications in the storage of cholesterol in NPC1 mutant cells are associated with other anomalies, such as altered distribution of intracellular organelles and properties of the plasma membrane. The pathomechanism of NPC disease is largely unknown. Interestingly, other storage diseases such as Gaucher and Farber diseases are accompanied by severe mitochondrial dysfunction. This prompted us to investigate the effect of absence or dysfunction of the NPC1 protein on mitochondrial properties to confirm or deny a putative relationship between NPC1 mutations and mitochondrial function. This study was performed on primary skin fibroblasts derived from skin biopsies of two NPC patients, carrying mutations in the NPC1 gene. We observed altered organization of mitochondria in NPC1 mutant cells, significant enrichment in mitochondrial cholesterol content, increased respiration, altered composition of the respiratory chain complex, and substantial reduction in cellular ATP level. Thus, a primary lysosomal defect in NPC1 mutant fibroblasts is accompanied by deregulation of the organization and function of the mitochondrial network.
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Affiliation(s)
- Marcin Woś
- Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, PL-02093, Warsaw, Poland
| | - Joanna Szczepanowska
- Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, PL-02093, Warsaw, Poland
| | - Sławomir Pikuła
- Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, PL-02093, Warsaw, Poland
| | - Anna Tylki-Szymańska
- Clinic of Metabolic Diseases, Endocrinology and Diabetology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Krzysztof Zabłocki
- Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, PL-02093, Warsaw, Poland
| | - Joanna Bandorowicz-Pikuła
- Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, PL-02093, Warsaw, Poland.
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21
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Teixeira V, Costa V. Unraveling the role of the Target of Rapamycin signaling in sphingolipid metabolism. Prog Lipid Res 2015; 61:109-33. [PMID: 26703187 DOI: 10.1016/j.plipres.2015.11.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 11/04/2015] [Accepted: 11/09/2015] [Indexed: 02/06/2023]
Abstract
Sphingolipids are important bioactive molecules that regulate basic aspects of cellular metabolism and physiology, including cell growth, adhesion, migration, senescence, apoptosis, endocytosis, and autophagy in yeast and higher eukaryotes. Since they have the ability to modulate the activation of several proteins and signaling pathways, variations in the relative levels of different sphingolipid species result in important changes in overall cellular functions and fate. Sphingolipid metabolism and their route of synthesis are highly conserved from yeast to mammalian cells. Studies using the budding yeast Saccharomyces cerevisiae have served in many ways to foster our understanding of sphingolipid dynamics and their role in the regulation of cellular processes. In the past decade, studies in S. cerevisiae have unraveled a functional association between the Target of Rapamycin (TOR) pathway and sphingolipids, showing that both TOR Complex 1 (TORC1) and TOR Complex 2 (TORC2) branches control temporal and spatial aspects of sphingolipid metabolism in response to physiological and environmental cues. In this review, we report recent findings in this emerging and exciting link between the TOR pathway and sphingolipids and implications in human health and disease.
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Affiliation(s)
- Vitor Teixeira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; IBMC, Instituto de Biologia Molecular e Celular, Porto, Portugal; ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Departamento de Biologia Molecular, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Vítor Costa
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; IBMC, Instituto de Biologia Molecular e Celular, Porto, Portugal; ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Departamento de Biologia Molecular, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
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22
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Pastor-Flores D, Ferrer-Dalmau J, Bahí A, Boleda M, Biondi RM, Casamayor A. Depletion of yeast PDK1 orthologs triggers a stress-like transcriptional response. BMC Genomics 2015; 16:719. [PMID: 26391581 PMCID: PMC4578605 DOI: 10.1186/s12864-015-1903-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 09/09/2015] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Pkh proteins are the PDK1 orthologs in S. cerevisiae. They have redundant and essential activity and are responsible for the phosphorylation of several members of the AGC family of protein kinases. Pkh proteins have been involved in several cellular functions, including cell wall integrity and endocytosis. However the global expression changes caused by their depletion are still unknown. RESULTS A doxycycline-repressible tetO7 promoter driving the expression of PKH2 in cells carrying deletions of the PKH1 and PKH3 genes allowed us to progressively deplete cells from Pkh proteins when treated with doxycycline. Global gene expression analysis indicate that depletion of Pkh results in the up-regulation of genes involved in the accumulation of glycogen and also of those related to stress responses. Moreover, genes involved in the ion transport were quickly down-regulated when the levels of Pkh decreased. The reduction in the mRNA levels required for protein translation, however, was only observed after longer doxycycline treatment (24 h). We uncovered that Pkh is important for the proper transcriptional response to heat shock, and is mostly required for the effects driven by the transcription factors Hsf1 and Msn2/Msn4, but is not required for down-regulation of the mRNA coding for ribosomal proteins. CONCLUSIONS By using the tetO7 promoter we elucidated for the first time the transcriptomic changes directly or indirectly caused by progressive depletion of Pkh. Furthermore, this system enabled the characterization of the transcriptional response triggered by heat shock in wild-type and Pkh-depleted cells, showing that about 40 % of the observed expression changes were, to some degree, dependent on Pkh.
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Affiliation(s)
- Daniel Pastor-Flores
- Research Group PhosphoSites, Medizinische Klinik I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany. .,Present address: Division of Redox Regulation, German Cancer Research Center, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
| | - Jofre Ferrer-Dalmau
- Departament de Bioquímica i Biologia Molecular, Facultat de Veterinària, Universitat Autònoma de Barcelona, Cerdanyola 08193, Barcelona, Spain. .,Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola 08193, Barcelona, Spain.
| | - Anna Bahí
- Departament de Bioquímica i Biologia Molecular, Facultat de Veterinària, Universitat Autònoma de Barcelona, Cerdanyola 08193, Barcelona, Spain. .,Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola 08193, Barcelona, Spain.
| | - Martí Boleda
- Departament de Bioquímica i Biologia Molecular, Facultat de Veterinària, Universitat Autònoma de Barcelona, Cerdanyola 08193, Barcelona, Spain. .,Laboratoire d'Ecologie Alpine (LECA), UMR 5553, CNRS-Université Joseph Fourie, BP 53, 38041, Grenoble, France.
| | - Ricardo M Biondi
- Research Group PhosphoSites, Medizinische Klinik I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.
| | - Antonio Casamayor
- Departament de Bioquímica i Biologia Molecular, Facultat de Veterinària, Universitat Autònoma de Barcelona, Cerdanyola 08193, Barcelona, Spain. .,Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola 08193, Barcelona, Spain.
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23
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Hartman JL, Stisher C, Outlaw DA, Guo J, Shah NA, Tian D, Santos SM, Rodgers JW, White RA. Yeast Phenomics: An Experimental Approach for Modeling Gene Interaction Networks that Buffer Disease. Genes (Basel) 2015; 6:24-45. [PMID: 25668739 PMCID: PMC4377832 DOI: 10.3390/genes6010024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 01/12/2015] [Indexed: 01/10/2023] Open
Abstract
The genome project increased appreciation of genetic complexity underlying disease phenotypes: many genes contribute each phenotype and each gene contributes multiple phenotypes. The aspiration of predicting common disease in individuals has evolved from seeking primary loci to marginal risk assignments based on many genes. Genetic interaction, defined as contributions to a phenotype that are dependent upon particular digenic allele combinations, could improve prediction of phenotype from complex genotype, but it is difficult to study in human populations. High throughput, systematic analysis of S. cerevisiae gene knockouts or knockdowns in the context of disease-relevant phenotypic perturbations provides a tractable experimental approach to derive gene interaction networks, in order to deduce by cross-species gene homology how phenotype is buffered against disease-risk genotypes. Yeast gene interaction network analysis to date has revealed biology more complex than previously imagined. This has motivated the development of more powerful yeast cell array phenotyping methods to globally model the role of gene interaction networks in modulating phenotypes (which we call yeast phenomic analysis). The article illustrates yeast phenomic technology, which is applied here to quantify gene X media interaction at higher resolution and supports use of a human-like media for future applications of yeast phenomics for modeling human disease.
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Affiliation(s)
- John L Hartman
- Department of Genetics, University of Alabama at Birmingham, 730 Hugh Kaul Human Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA.
| | - Chandler Stisher
- Department of Genetics, University of Alabama at Birmingham, 730 Hugh Kaul Human Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA.
| | - Darryl A Outlaw
- Department of Genetics, University of Alabama at Birmingham, 730 Hugh Kaul Human Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA.
| | - Jingyu Guo
- Department of Genetics, University of Alabama at Birmingham, 730 Hugh Kaul Human Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA.
| | - Najaf A Shah
- Department of Genetics, University of Alabama at Birmingham, 730 Hugh Kaul Human Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA.
| | - Dehua Tian
- Department of Genetics, University of Alabama at Birmingham, 730 Hugh Kaul Human Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA.
| | - Sean M Santos
- Department of Genetics, University of Alabama at Birmingham, 730 Hugh Kaul Human Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA.
| | - John W Rodgers
- Department of Genetics, University of Alabama at Birmingham, 730 Hugh Kaul Human Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA.
| | - Richard A White
- Department of Statistics and Michael Smith Laboratories, University of British Columbia, 3182 Earth Sciences Building, 2207 Main Mall, Vancouver, BC V6T-1Z4, Canada.
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Spincemaille P, Matmati N, Hannun YA, Cammue BPA, Thevissen K. Sphingolipids and mitochondrial function in budding yeast. Biochim Biophys Acta Gen Subj 2014; 1840:3131-7. [PMID: 24973565 DOI: 10.1016/j.bbagen.2014.06.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/09/2014] [Accepted: 06/19/2014] [Indexed: 02/07/2023]
Abstract
BACKGROUND Sphingolipids (SLs) are not only key components of cellular membranes, but also play an important role as signaling molecules in orchestrating both cell growth and apoptosis. In Saccharomyces cerevisiae, three complex SLs are present and hydrolysis of either of these species is catalyzed by the inositol phosphosphingolipid phospholipase C (Isc1p). Strikingly, mutants deficient in Isc1p display several hallmarks of mitochondrial dysfunction such as the inability to grow on a non-fermentative carbon course, increased oxidative stress and aberrant mitochondrial morphology. SCOPE OF REVIEW In this review, we focus on the pivotal role of Isc1p in regulating mitochondrial function via SL metabolism, and on Sch9p as a central signal transducer. Sch9p is one of the main effectors of the target of rapamycin complex 1 (TORC1), which is regarded as a crucial signaling axis for the regulation of Isc1p-mediated events. Finally, we describe the retrograde response, a signaling event originating from mitochondria to the nucleus, which results in the induction of nuclear target genes. Intriguingly, the retrograde response also interacts with SL homeostasis. MAJOR CONCLUSIONS All of the above suggests a pivotal signaling role for SLs in maintaining correct mitochondrial function in budding yeast. GENERAL SIGNIFICANCE Studies with budding yeast provide insight on SL signaling events that affect mitochondrial function.
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Affiliation(s)
- Pieter Spincemaille
- Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
| | - Nabil Matmati
- Department of Medicine and the Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yusuf A Hannun
- Department of Medicine and the Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA
| | - Bruno P A Cammue
- Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium; Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium.
| | - Karin Thevissen
- Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
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Spincemaille P, Cammue BP, Thevissen K. Sphingolipids and mitochondrial function, lessons learned from yeast. MICROBIAL CELL (GRAZ, AUSTRIA) 2014; 1:210-224. [PMID: 28357246 PMCID: PMC5349154 DOI: 10.15698/mic2014.07.156] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 06/10/2014] [Indexed: 01/22/2023]
Abstract
Mitochondrial dysfunction is a hallmark of several neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease, but also of cancer, diabetes and rare diseases such as Wilson's disease (WD) and Niemann Pick type C1 (NPC). Mitochondrial dysfunction underlying human pathologies has often been associated with an aberrant cellular sphingolipid metabolism. Sphingolipids (SLs) are important membrane constituents that also act as signaling molecules. The yeast Saccharomyces cerevisiae has been pivotal in unraveling mammalian SL metabolism, mainly due to the high degree of conservation of SL metabolic pathways. In this review we will first provide a brief overview of the major differences in SL metabolism between yeast and mammalian cells and the use of SL biosynthetic inhibitors to elucidate the contribution of specific parts of the SL metabolic pathway in response to for instance stress. Next, we will discuss recent findings in yeast SL research concerning a crucial signaling role for SLs in orchestrating mitochondrial function, and translate these findings to relevant disease settings such as WD and NPC. In summary, recent research shows that S. cerevisiae is an invaluable model to investigate SLs as signaling molecules in modulating mitochondrial function, but can also be used as a tool to further enhance our current knowledge on SLs and mitochondria in mammalian cells.
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Affiliation(s)
- Pieter Spincemaille
- Centre of Microbial and Plant Genetics (CMPG), KU Leuven,
Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
| | - Bruno P. Cammue
- Centre of Microbial and Plant Genetics (CMPG), KU Leuven,
Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052,
Ghent, Belgium
| | - Karin Thevissen
- Centre of Microbial and Plant Genetics (CMPG), KU Leuven,
Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
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