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Singin Ö, Astapenka A, Costina V, Kühl S, Bonekamp N, Drews O, Islinger M. Analysis of the Mouse Hepatic Peroxisome Proteome-Identification of Novel Protein Constituents Using a Semi-Quantitative SWATH-MS Approach. Cells 2024; 13:176. [PMID: 38247867 PMCID: PMC10814758 DOI: 10.3390/cells13020176] [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: 12/21/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024] Open
Abstract
Ongoing technical and bioinformatics improvements in mass spectrometry (MS) allow for the identifying and quantifying of the enrichment of increasingly less-abundant proteins in individual fractions. Accordingly, this study reassessed the proteome of mouse liver peroxisomes by the parallel isolation of peroxisomes from a mitochondria- and a microsome-enriched prefraction, combining density-gradient centrifugation with a semi-quantitative SWATH-MS proteomics approach to unveil novel peroxisomal or peroxisome-associated proteins. In total, 1071 proteins were identified using MS and assessed in terms of their distribution in either high-density peroxisomal or low-density gradient fractions, containing the bulk of organelle material. Combining the data from both fractionation approaches allowed for the identification of specific protein profiles characteristic of mitochondria, the ER and peroxisomes. Among the proteins significantly enriched in the peroxisomal cluster were several novel peroxisomal candidates. Five of those were validated by colocalization in peroxisomes, using confocal microscopy. The peroxisomal import of HTATIP2 and PAFAH2, which contain a peroxisome-targeting sequence 1 (PTS1), could be confirmed by overexpression in HepG2 cells. The candidates SAR1B and PDCD6, which are known ER-exit-site proteins, did not directly colocalize with peroxisomes, but resided at ER sites, which frequently surrounded peroxisomes. Hence, both proteins might concentrate at presumably co-purified peroxisome-ER membrane contacts. Intriguingly, the fifth candidate, OCIA domain-containing protein 1, was previously described as decreasing mitochondrial network formation. In this work, we confirmed its peroxisomal localization and further observed a reduction in peroxisome numbers in response to OCIAD1 overexpression. Hence, OCIAD1 appears to be a novel protein, which has an impact on both mitochondrial and peroxisomal maintenance.
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Affiliation(s)
- Öznur Singin
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
| | - Artur Astapenka
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
| | - Victor Costina
- Institute of Clinical Chemistry, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (V.C.); (O.D.)
| | - Sandra Kühl
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
| | - Nina Bonekamp
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
| | - Oliver Drews
- Institute of Clinical Chemistry, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (V.C.); (O.D.)
- Biomedical Mass Spectrometry, Center for Medical Research, Johannes Kepler University Linz, 4020 Linz, Austria
| | - Markus Islinger
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
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2
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Zhang J, Ye ZW, Bräutigam L, Chakraborty P, Luo Z, Culpepper J, Aslam M, Zhang L, Johansson K, Haeggström JZ, Xu J, Olsson M, Townsend DM, Mehrotra S, Morgenstern R, Tew KD. A role for microsomal glutathione transferase 1 in melanin biosynthesis and melanoma progression. J Biol Chem 2023; 299:104920. [PMID: 37321450 PMCID: PMC10372821 DOI: 10.1016/j.jbc.2023.104920] [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: 10/26/2022] [Revised: 03/31/2023] [Accepted: 05/06/2023] [Indexed: 06/17/2023] Open
Abstract
Recent advancements in the treatment of melanoma are encouraging, but there remains a need to identify additional therapeutic targets. We identify a role for microsomal glutathione transferase 1 (MGST1) in biosynthetic pathways for melanin and as a determinant of tumor progression. Knockdown (KD) of MGST1 depleted midline-localized, pigmented melanocytes in zebrafish embryos, while in both mouse and human melanoma cells, loss of MGST1 resulted in a catalytically dependent, quantitative, and linear depigmentation, associated with diminished conversion of L-dopa to dopachrome (eumelanin precursor). Melanin, especially eumelanin, has antioxidant properties, and MGST1 KD melanoma cells are under higher oxidative stress, with increased reactive oxygen species, decreased antioxidant capacities, reduced energy metabolism and ATP production, and lower proliferation rates in 3D culture. In mice, when compared to nontarget control, Mgst1 KD B16 cells had less melanin, more active CD8+ T cell infiltration, slower growing tumors, and enhanced animal survival. Thus, MGST1 is an integral enzyme in melanin synthesis and its inhibition adversely influences tumor growth.
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Affiliation(s)
- Jie Zhang
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, United States.
| | - Zhi-Wei Ye
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Lars Bräutigam
- Department of Comparative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Paramita Chakraborty
- Department of Surgery, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Zhenwu Luo
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, United States
| | - John Culpepper
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Muhammad Aslam
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Leilei Zhang
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, United States
| | | | - Jesper Z Haeggström
- Divisions of Biochemistry and Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jianqiang Xu
- School of Life and Pharmaceutical Sciences (LPS) & Panjin Institute of Industrial Technology (PIIT), Dalian University of Technology, Panjin, China
| | - Magnus Olsson
- Division of Biochemical Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Danyelle M Townsend
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Shikhar Mehrotra
- Department of Surgery, Medical University of South Carolina, Charleston, South Carolina, United States
| | - Ralf Morgenstern
- Division of Biochemical Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kenneth D Tew
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, United States.
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3
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Zhang J, Ye ZW, Morgenstern R, Townsend DM, Tew KD. Microsomal glutathione transferase 1 in cancer and the regulation of ferroptosis. Adv Cancer Res 2023; 160:107-132. [PMID: 37704286 PMCID: PMC10586476 DOI: 10.1016/bs.acr.2023.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Microsomal glutathione transferase 1 (MGST1) is a member of the MAPEG family (membrane associated proteins in eicosanoid and glutathione metabolism), defined according to enzymatic activities, sequence motifs, and structural properties. MGST1 is a homotrimer which can bind three molecules of glutathione (GSH), with one modified to a thiolate anion displaying one-third-of-sites-reactivity. MGST1 has both glutathione transferase and peroxidase activities. Each is based on stabilizing the GSH thiolate in the same active site. MGST1 is abundant in the liver and displays a broad subcellular distribution with high levels in endoplasmic reticulum and mitochondrial membranes, consistent with a physiological role in protection from reactive electrophilic intermediates and oxidative stress. In this review paper, we particularly focus on recent advances made in understanding MGST1 activation, induction, broad subcellular distribution, and the role of MGST1 in apoptosis, ferroptosis, cancer progression, and therapeutic responses.
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Affiliation(s)
- Jie Zhang
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States.
| | - Zhi-Wei Ye
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - Ralf Morgenstern
- Institute of Environmental Medicine, Division of Biochemical Toxicology, Karolinska Institutet, Stockholm, Sweden
| | - Danyelle M Townsend
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Kenneth D Tew
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
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4
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Schrader TA, Carmichael RE, Schrader M. Immunolabeling for Detection of Endogenous and Overexpressed Peroxisomal Proteins in Mammalian Cells. Methods Mol Biol 2023; 2643:47-63. [PMID: 36952177 DOI: 10.1007/978-1-0716-3048-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Peroxisomes are dynamic subcellular organelles in mammals, playing essential roles in cellular lipid metabolism and redox homeostasis. They perform a wide spectrum of functions in human health and disease, with new roles, mechanisms, and regulatory pathways still being discovered. Recently elucidated biological roles of peroxisomes include as antiviral defense hubs, intracellular signaling platforms, immunomodulators, and protective organelles in sensory cells. Furthermore, peroxisomes are part of a complex inter-organelle interaction network, which involves metabolic cooperation and cross talk via membrane contacts. The detection of endogenous and/or overexpressed proteins within a cell by immunolabelling informs us about the organellar and even sub-organellar localization of both known and putative peroxisomal proteins. In turn, this can be exploited to characterize the effects of experimental manipulations on the morphology, distribution, and/or number of peroxisomes in a cell, which are key properties controlling peroxisome function. Here, we present a protocol used successfully in our laboratory for the immunolabelling of peroxisomal proteins in cultured mammalian cells. We present immunofluorescence and transfection techniques as well as reagents to determine the localization of endogenous and overexpressed peroxisomal proteins.
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Affiliation(s)
- Tina A Schrader
- Faculty of Health and Life Sciences, Biosciences, University of Exeter, Exeter, Devon, UK
| | - Ruth E Carmichael
- Faculty of Health and Life Sciences, Biosciences, University of Exeter, Exeter, Devon, UK
| | - Michael Schrader
- Faculty of Health and Life Sciences, Biosciences, University of Exeter, Exeter, Devon, UK.
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5
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Manner A, Islinger M. Isolation of Mammalian Peroxisomes by Density Gradient Centrifugation. Methods Mol Biol 2023; 2643:1-12. [PMID: 36952174 DOI: 10.1007/978-1-0716-3048-8_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Sophisticated organelle fractionation strategies were the workhorse of early peroxisome research and led to the characterization of the principal functions of the organelle. However, even in the era of molecular biology and "omics" technologies, they are still of importance to unravel peroxisome-specific proteomes, confirm the localization of still uncharacterized proteins, analyze peroxisome metabolism or lipid composition, or study their protein import mechanism. To isolate and analyze peroxisomes for these purposes, density gradient centrifugation still represents a highly reliable and reproducible technique. This article describes two protocols to purify peroxisomes from either liver tissue or the HepG2 hepatoma cell line. The protocol for liver enables purification of peroxisome fractions with high purity (95%) and is therefore suitable to study low-abundant peroxisomal proteins or analyze their lipid composition, for example. The protocol presented for HepG2 cells is not suitable to gain highly pure peroxisomal fractions but is intended to be used for gradient profiling experiments and allows easier manipulation of the peroxisomal compartment, e.g., by gene knockdown or protein overexpression for functional studies. Both purification methods therefore represent complementary tools to be used to analyze different aspects of peroxisome physiology. Please note that this is an updated version of a protocol, which has been published in a former volume of Methods in Molecular Biology.
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Affiliation(s)
- Andreas Manner
- Institute of Neuroanatomy, Medical Faculty Mannheim, Mannheim Centre for Translational Neuroscience, Mannheim, Germany
| | - Markus Islinger
- Institute of Neuroanatomy, Medical Faculty Mannheim, Mannheim Centre for Translational Neuroscience, Mannheim, Germany.
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Perrot N, Dessaux D, Rignani A, Gillet C, Orlowski S, Jamin N, Garrigos M, Jaxel C. Caveolin-1β promotes the production of active human microsomal glutathione S-transferase in induced intracellular vesicles inSpodoptera frugiperda21 insect cells. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183922. [PMID: 35367202 DOI: 10.1016/j.bbamem.2022.183922] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
The heterologous expression in Spodoptera frugiperda 21 (Sf21) insect cells of the β isoform of canine caveolin-1 (caveolin-1β), using a baculovirus-based vector, resulted in intracellular vesicles enriched in caveolin-1β. We investigated whether these vesicles could act as membrane reservoirs, and promote the production of an active membrane protein (MP) when co-expressed with caveolin-1β. We chose hMGST1 (human microsomal glutathione S-transferase 1) as the co-expressed MP. It belongs to the membrane-associated proteins in eicosanoid and glutathione metabolism (MAPEG) family of integral MPs, and, as a phase II detoxification enzyme, it catalyzes glutathione conjugation of lipophilic drugs present in the lipid membranes. In addition to its pharmaceutical interest, its GST activity can be conveniently measured. The expression of both MPs were followed by Western blots and membrane fractionation on density gradient, and their cell localization by immunolabeling and transmission electron microscopy. We showed that caveolin-1β kept its capacity to induce intracellular vesicles in the host when co-expressed with hMGST1, and that hMGST1 is in part addressed to these vesicles. Remarkably, a fourfold increase in the amount of active hMGST1 was found in the most enriched membrane fraction, along with an increase of its specific activity by 60% when it was co-expressed with caveolin-1β. Thus, heterologously expressed caveolin-1β was able to induce cytoplasmic vesicles in which a co-expressed exogenous MP is diverted and sequestered, providing a favorable environment for this cargo.
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Affiliation(s)
- Nahuel Perrot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Delphine Dessaux
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Anthony Rignani
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Cynthia Gillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Stéphane Orlowski
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Nadège Jamin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Manuel Garrigos
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Christine Jaxel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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7
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Pisetsky DS, Spencer DM, Mobarrez F, Fuzzi E, Gunnarsson I, Svenungsson E. The binding of SLE autoantibodies to mitochondria. Clin Immunol 2020; 212:108349. [PMID: 31982644 PMCID: PMC10538439 DOI: 10.1016/j.clim.2020.108349] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 02/08/2023]
Abstract
Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease characterized by immune complexes. Because these complexes contain mitochondrial components, we assessed the presence of antibodies to whole mitochondria (wMITO) using an ELISA in which mitochondria from mouse liver are bound to microtiter plates pre-coated with poly-l-lysine. Studies with this ELISA demonstrated that SLE plasmas contain abundant anti-wMITO activity. While digestion with DNase 1 did not affect anti-wMITO activity, adsorption of plasma on DNA affinity columns could reduce binding activity. Assay for anti-mitochondrial antibodies (AMA) by immunofluorescence and an ELISA with the M2 antigen (2-oxo-acid dehydrogenase protein complex) showed a low frequency of positivity, indicating that AMA and anti-wMITO are distinct specificities. In the study of 204 patients with SLE, the levels of anti-wMITO were higher in active SLE and correlated with levels of anti-DNA. These findings suggest that anti-wMITO can form immune complexes with mitochondria which may drive pathogenesis.
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Affiliation(s)
- David S Pisetsky
- Division of Rheumatology and Immunology, Duke University Medical Center, Durham, NC, United States of America; Medical Research Service, VA Medical Center, Durham, NC, United States of America.
| | - Diane M Spencer
- Division of Rheumatology and Immunology, Duke University Medical Center, Durham, NC, United States of America
| | - Fariborz Mobarrez
- Unit of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Enrico Fuzzi
- Unit of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Division of Rheumatology, Department of Medicine, University of Padua, Padua, Italy
| | - Iva Gunnarsson
- Unit of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Elisabet Svenungsson
- Unit of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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8
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Stastna M. Continuous flow electrophoretic separation - Recent developments and applications to biological sample analysis. Electrophoresis 2019; 41:36-55. [PMID: 31650578 DOI: 10.1002/elps.201900288] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 01/23/2023]
Abstract
Continuous flow electrophoretic separation with continuous sample loading provides the advantage of processing volumes of any sizes, as well as the benefit of a real-time monitoring and optimization of the separation process. In addition, the spatial separation of the sample enables collecting multiple separated components simultaneously and in a continuous manner. The separation is usually performed in mild buffers without organic solvents and detergents (sample biological activity is retained) and it is carried out without usage of a solid support in the separation space preventing the interaction of the sample with it (high sample recovery). The method is used for the separation of proteins/peptides in proteomic applications, and its great applicability is to the separation of the cells, cellular organelles, vesicles, membrane fragments, and DNA. This review focuses on the electrophoretic separation performed in a continuous flow and it describes various electrophoretic modes and instrumental setups. Recent developments in methodology and instrumentation, the integration with other techniques, and the application to the biological sample analysis are discussed as well.
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Affiliation(s)
- Miroslava Stastna
- Institute of Analytical Chemistry of the Czech Academy of Sciences, Brno, Czech Republic
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9
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Gordaliza-Alaguero I, Cantó C, Zorzano A. Metabolic implications of organelle-mitochondria communication. EMBO Rep 2019; 20:e47928. [PMID: 31418169 DOI: 10.15252/embr.201947928] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/10/2019] [Accepted: 05/28/2019] [Indexed: 12/31/2022] Open
Abstract
Cellular organelles are not static but show dynamism-a property that is likely relevant for their function. In addition, they interact with other organelles in a highly dynamic manner. In this review, we analyze the proteins involved in the interaction between mitochondria and other cellular organelles, especially the endoplasmic reticulum, lipid droplets, and lysosomes. Recent results indicate that, on one hand, metabolic alterations perturb the interaction between mitochondria and other organelles, and, on the other hand, that deficiency in proteins involved in the tethering between mitochondria and the ER or in specific functions of the interaction leads to metabolic alterations in a variety of tissues. The interaction between organelles is an emerging field that will permit to identify key proteins, to delineate novel modulation pathways, and to elucidate their implications in human disease.
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Affiliation(s)
- Isabel Gordaliza-Alaguero
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,CIBER de Diabetes y Enfermedades Metabolicas Asociadas, Barcelona, Spain.,Departamento de Bioquimica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Carlos Cantó
- Nestle Institute of Health Sciences (NIHS), Lausanne, Switzerland.,School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Antonio Zorzano
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,CIBER de Diabetes y Enfermedades Metabolicas Asociadas, Barcelona, Spain.,Departamento de Bioquimica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
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10
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Yu SB, Pekkurnaz G. Mechanisms Orchestrating Mitochondrial Dynamics for Energy Homeostasis. J Mol Biol 2018; 430:3922-3941. [PMID: 30089235 DOI: 10.1016/j.jmb.2018.07.027] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 07/23/2018] [Accepted: 07/30/2018] [Indexed: 12/13/2022]
Abstract
To maintain homeostasis, every cell must constantly monitor its energy level and appropriately adjust energy, in the form of ATP, production rates based on metabolic demand. Continuous fulfillment of this energy demand depends on the ability of cells to sense, metabolize, and convert nutrients into chemical energy. Mitochondria are the main energy conversion sites for many cell types. Cellular metabolic states dictate the mitochondrial size, shape, function, and positioning. Mitochondrial shape varies from singular discrete organelles to interconnected reticular networks within cells. The morphological adaptations of mitochondria to metabolic cues are facilitated by the dynamic events categorized as transport, fusion, fission, and quality control. By changing their dynamics and strategic positioning within the cytoplasm, mitochondria carry out critical functions and also participate actively in inter-organelle cross-talk, assisting metabolite transfer, degradation, and biogenesis. Mitochondrial dynamics has become an active area of research because of its particular importance in cancer, metabolic diseases, and neurological disorders. In this review, we will highlight the molecular pathways involved in the regulation of mitochondrial dynamics and their roles in maintaining energy homeostasis.
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Affiliation(s)
- Seungyoon B Yu
- Neurobiology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, United States
| | - Gulcin Pekkurnaz
- Neurobiology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, United States.
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Islinger M, Manner A, Völkl A. The Craft of Peroxisome Purification-A Technical Survey Through the Decades. Subcell Biochem 2018; 89:85-122. [PMID: 30378020 DOI: 10.1007/978-981-13-2233-4_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Purification technologies are one of the working horses in organelle proteomics studies as they guarantee the separation of organelle-specific proteins from the background contamination by other subcellular compartments. The development of methods for the separation of organelles was a major prerequisite for the initial detection and characterization of peroxisome as a discrete entity of the cell. Since then, isolated peroxisomes fractions have been used in numerous studies in order to characterize organelle-specific enzyme functions, to allocate the peroxisome-specific proteome or to unravel the organellar membrane composition. This review will give an overview of the fractionation methods used for the isolation of peroxisomes from animals, plants and fungi. In addition to "classic" centrifugation-based isolation methods, relying on the different densities of individual organelles, the review will also summarize work on alternative technologies like free-flow-electrophoresis or flow field fractionation which are based on distinct physicochemical parameters. A final chapter will further describe how different separation methods and quantitative mass spectrometry have been used in proteomics studies to assign the proteome of PO.
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Affiliation(s)
- Markus Islinger
- Institute for Neuroanatomy, Centre for Biomedicine and Medical Technology Mannheim, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany.
| | - Andreas Manner
- Institute for Neuroanatomy, Centre for Biomedicine and Medical Technology Mannheim, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Alfred Völkl
- Department of Medical Cell Biology, Institute of Anatomy, University of Heidelberg, Heidelberg, Germany
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12
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Kunze M. Predicting Peroxisomal Targeting Signals to Elucidate the Peroxisomal Proteome of Mammals. Subcell Biochem 2018; 89:157-199. [PMID: 30378023 DOI: 10.1007/978-981-13-2233-4_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peroxisomes harbor a plethora of proteins, but the peroxisomal proteome as the entirety of all peroxisomal proteins is still unknown for mammalian species. Computational algorithms can be used to predict the subcellular localization of proteins based on their amino acid sequence and this method has been amply used to forecast the intracellular fate of individual proteins. However, when applying such algorithms systematically to all proteins of an organism the prediction of its peroxisomal proteome in silico should be possible. Therefore, a reliable detection of peroxisomal targeting signals (PTS ) acting as postal codes for the intracellular distribution of the encoding protein is crucial. Peroxisomal proteins can utilize different routes to reach their destination depending on the type of PTS. Accordingly, independent prediction algorithms have been developed for each type of PTS, but only those for type-1 motifs (PTS1) have so far reached a satisfying predictive performance. This is partially due to the low number of peroxisomal proteins limiting the power of statistical analyses and partially due to specific properties of peroxisomal protein import, which render functional PTS motifs inactive in specific contexts. Moreover, the prediction of the peroxisomal proteome is limited by the high number of proteins encoded in mammalian genomes, which causes numerous false positive predictions even when using reliable algorithms and buries the few yet unidentified peroxisomal proteins. Thus, the application of prediction algorithms to identify all peroxisomal proteins is currently ineffective as stand-alone method, but can display its full potential when combined with other methods.
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Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
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13
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The Peroxisome-Mitochondria Connection: How and Why? Int J Mol Sci 2017; 18:ijms18061126. [PMID: 28538669 PMCID: PMC5485950 DOI: 10.3390/ijms18061126] [Citation(s) in RCA: 198] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/15/2017] [Accepted: 05/20/2017] [Indexed: 12/14/2022] Open
Abstract
Over the past decades, peroxisomes have emerged as key regulators in overall cellular lipid and reactive oxygen species metabolism. In mammals, these organelles have also been recognized as important hubs in redox-, lipid-, inflammatory-, and innate immune-signaling networks. To exert these activities, peroxisomes must interact both functionally and physically with other cell organelles. This review provides a comprehensive look of what is currently known about the interconnectivity between peroxisomes and mitochondria within mammalian cells. We first outline how peroxisomal and mitochondrial abundance are controlled by common sets of cis- and trans-acting factors. Next, we discuss how peroxisomes and mitochondria may communicate with each other at the molecular level. In addition, we reflect on how these organelles cooperate in various metabolic and signaling pathways. Finally, we address why peroxisomes and mitochondria have to maintain a healthy relationship and why defects in one organelle may cause dysfunction in the other. Gaining a better insight into these issues is pivotal to understanding how these organelles function in their environment, both in health and disease.
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Shimoji M, Figueroa RA, Neve E, Maksel D, Imreh G, Morgenstern R, Hallberg E. Molecular basis for the dual subcellular distribution of microsomal glutathione transferase 1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:238-244. [DOI: 10.1016/j.bbamem.2016.11.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 11/11/2016] [Accepted: 11/28/2016] [Indexed: 02/07/2023]
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Abstract
Peroxisomes are essential organelles in mammals which contribute to cellular lipid metabolism and redox homeostasis. The spectrum of their functions in human health and disease is far from being complete, and unexpected and novel roles of peroxisomes are being discovered. To date, those include novel biological roles in antiviral defence, as intracellular signaling platforms and as protective organelles in sensory cells. Furthermore, peroxisomes are part of a complex network of interacting subcellular compartments which involves metabolic cooperation, cross-talk and membrane contacts. As potentially novel peroxisomal proteins are continuously discovered, there is great interest in the verification of their peroxisomal localization. Here, we present protocols used successfully in our laboratory for the detection and immunolabeling of peroxisomal proteins in cultured mammalian cells. We present immunofluorescence and fluorescence-based techniques as well as reagents to determine peroxisome-specific targeting and localization of candidate proteins.
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Affiliation(s)
- Tina A Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Markus Islinger
- Center for Biomedicine and Medical Technology Mannheim, Institute of Neuroanatomy, University of Heidelberg, Ludolf-Krehl Str. 13-17, 68137, Mannheim, Germany
| | - Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, United Kingdom.
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16
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Isolation of Peroxisomes from Rat Liver and Cultured Hepatoma Cells by Density Gradient Centrifugation. Methods Mol Biol 2017; 1595:1-11. [PMID: 28409446 DOI: 10.1007/978-1-4939-6937-1_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Subcellular fractionation is still a valuable technique to unravel organelle-specific proteomes, validate the location of uncharacterized proteins, or to functionally analyze import and metabolism in individual subcellular compartments. In this respect, density gradient centrifugation still represents a very classic, indispensable technique to isolate and analyze peroxisomes. Here, we present two independent protocols for the purification of peroxisomes from either liver tissue or the HepG2 hepatoma cell line. While the former permits the isolation of highly pure peroxisomes suitable for, e.g., subcellular proteomics experiments, the latter protocol yields peroxisomal fractions from considerably less purity but allows to easily modify metabolic conditions in the culture medium or to genetically manipulate the peroxisomal compartment. In this respect, both purification methods represent alternative tools to be applied in experiments investigating peroxisome physiology.
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17
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Rodríguez-Arribas M, Yakhine-Diop SMS, Pedro JMBS, Gómez-Suaga P, Gómez-Sánchez R, Martínez-Chacón G, Fuentes JM, González-Polo RA, Niso-Santano M. Mitochondria-Associated Membranes (MAMs): Overview and Its Role in Parkinson's Disease. Mol Neurobiol 2016; 54:6287-6303. [PMID: 27714635 DOI: 10.1007/s12035-016-0140-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/19/2016] [Indexed: 12/21/2022]
Abstract
Mitochondria-associated membranes (MAMs) are structures that regulate physiological functions between endoplasmic reticulum (ER) and mitochondria in order to maintain calcium signaling and mitochondrial biogenesis. Several proteins located in MAMs, including those encoded by PARK genes and some of neurodegeneration-related proteins (huntingtin, presenilin, etc.), ensure this regulation. In this regard, MAM alteration is associated with neurodegenerative diseases such as Parkinson's (PD), Alzheimer's (AD), and Huntington's diseases (HD) and contributes to the appearance of the pathogenesis features, i.e., autophagy dysregulation, mitochondrial dysfunction, oxidative stress, and lately, neuronal death. Moreover,, ER stress and/or damaged mitochondria can be the cause of these disruptions. Therefore, ER-mitochondria contact structure and function are crucial to multiple cellular processes. This review is focused on the molecular interaction between ER and mitochondria indispensable to MAM formation and on MAM alteration-induced etiology of neurodegenerative diseases.
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Affiliation(s)
- M Rodríguez-Arribas
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Universidad de Extremadura, Avda. De la Universidad S/N, C.P, 10003, Cáceres, Cáceres, Spain.,Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, Avda. de la Universidad s/n, C.P, 10003, Cáceres, Cáceres, Spain
| | - S M S Yakhine-Diop
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Universidad de Extremadura, Avda. De la Universidad S/N, C.P, 10003, Cáceres, Cáceres, Spain.,Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, Avda. de la Universidad s/n, C.P, 10003, Cáceres, Cáceres, Spain
| | - J M Bravo-San Pedro
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, 75006, Paris, France.,INSERM U1138, 75006, Paris, France.,Université Paris Descartes/Paris V, Sorbonne Paris Cité, 75006, Paris, France.,Université Pierre et Marie Curie/Paris VI, 75006, Paris, France.,Gustave Roussy Comprehensive Cancer Institute, 94805, Villejuif, France
| | - P Gómez-Suaga
- Department Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute Kings College London, London, SE5 9RX, UK
| | - R Gómez-Sánchez
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - G Martínez-Chacón
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Universidad de Extremadura, Avda. De la Universidad S/N, C.P, 10003, Cáceres, Cáceres, Spain.,Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, Avda. de la Universidad s/n, C.P, 10003, Cáceres, Cáceres, Spain
| | - J M Fuentes
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Universidad de Extremadura, Avda. De la Universidad S/N, C.P, 10003, Cáceres, Cáceres, Spain.,Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, Avda. de la Universidad s/n, C.P, 10003, Cáceres, Cáceres, Spain
| | - R A González-Polo
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Universidad de Extremadura, Avda. De la Universidad S/N, C.P, 10003, Cáceres, Cáceres, Spain. .,Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, Avda. de la Universidad s/n, C.P, 10003, Cáceres, Cáceres, Spain.
| | - M Niso-Santano
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Universidad de Extremadura, Avda. De la Universidad S/N, C.P, 10003, Cáceres, Cáceres, Spain. .,Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, Avda. de la Universidad s/n, C.P, 10003, Cáceres, Cáceres, Spain.
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Wanders RJA, Waterham HR, Ferdinandusse S. Metabolic Interplay between Peroxisomes and Other Subcellular Organelles Including Mitochondria and the Endoplasmic Reticulum. Front Cell Dev Biol 2016; 3:83. [PMID: 26858947 PMCID: PMC4729952 DOI: 10.3389/fcell.2015.00083] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/10/2015] [Indexed: 01/02/2023] Open
Abstract
Peroxisomes are unique subcellular organelles which play an indispensable role in several key metabolic pathways which include: (1.) etherphospholipid biosynthesis; (2.) fatty acid beta-oxidation; (3.) bile acid synthesis; (4.) docosahexaenoic acid (DHA) synthesis; (5.) fatty acid alpha-oxidation; (6.) glyoxylate metabolism; (7.) amino acid degradation, and (8.) ROS/RNS metabolism. The importance of peroxisomes for human health and development is exemplified by the existence of a large number of inborn errors of peroxisome metabolism in which there is an impairment in one or more of the metabolic functions of peroxisomes. Although the clinical signs and symptoms of affected patients differ depending upon the enzyme which is deficient and the extent of the deficiency, the disorders involved are usually (very) severe diseases with neurological dysfunction and early death in many of them. With respect to the role of peroxisomes in metabolism it is clear that peroxisomes are dependent on the functional interplay with other subcellular organelles to sustain their role in metabolism. Indeed, whereas mitochondria can oxidize fatty acids all the way to CO2 and H2O, peroxisomes are only able to chain-shorten fatty acids and the end products of peroxisomal beta-oxidation need to be shuttled to mitochondria for full oxidation to CO2 and H2O. Furthermore, NADH is generated during beta-oxidation in peroxisomes and beta-oxidation can only continue if peroxisomes are equipped with a mechanism to reoxidize NADH back to NAD+, which is now known to be mediated by specific NAD(H)-redox shuttles. In this paper we describe the current state of knowledge about the functional interplay between peroxisomes and other subcellular compartments notably the mitochondria and endoplasmic reticulum for each of the metabolic pathways in which peroxisomes are involved.
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Affiliation(s)
- Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Laboratory Division, Departments of Paediatrics and Clinical Chemistry, Academic Medical Center, Emma Children's Hospital, University of Amsterdam Amsterdam, Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Laboratory Division, Departments of Paediatrics and Clinical Chemistry, Academic Medical Center, Emma Children's Hospital, University of Amsterdam Amsterdam, Netherlands
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Laboratory Division, Departments of Paediatrics and Clinical Chemistry, Academic Medical Center, Emma Children's Hospital, University of Amsterdam Amsterdam, Netherlands
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Oeljeklaus S, Schummer A, Mastalski T, Platta HW, Warscheid B. Regulation of peroxisome dynamics by phosphorylation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:1027-37. [PMID: 26775584 DOI: 10.1016/j.bbamcr.2015.12.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/22/2015] [Accepted: 12/24/2015] [Indexed: 12/31/2022]
Abstract
Peroxisomes are highly dynamic organelles that can rapidly change in size, abundance, and protein content in response to alterations in nutritional and other environmental conditions. These dynamic changes in peroxisome features, referred to as peroxisome dynamics, rely on the coordinated action of several processes of peroxisome biogenesis. Revealing the regulatory mechanisms of peroxisome dynamics is an emerging theme in cell biology. These mechanisms are inevitably linked to and synchronized with the biogenesis and degradation of peroxisomes. To date, the key players and basic principles of virtually all steps in the peroxisomal life cycle are known, but regulatory mechanisms remained largely elusive. A number of recent studies put the spotlight on reversible protein phosphorylation for the control of peroxisome dynamics and highlighted peroxisomes as hubs for cellular signal integration and regulation. Here, we will present and discuss the results of several studies performed using yeast and mammalian cells that convey a sense of the impact protein phosphorylation may have on the modulation of peroxisome dynamics by regulating peroxisomal matrix and membrane protein import, proliferation, inheritance, and degradation. We further put forward the idea to make use of current data on phosphorylation sites of peroxisomal and peroxisome-associated proteins reported in advanced large-scale phosphoproteomic studies.
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Affiliation(s)
- Silke Oeljeklaus
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, 79104 Freiburg, Germany
| | - Andreas Schummer
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Mastalski
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Harald W Platta
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Bettina Warscheid
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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20
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C22-bronchial and T7-alveolar epithelial cell lines of the immortomouse are excellent murine cell culture model systems to study pulmonary peroxisome biology and metabolism. Histochem Cell Biol 2015; 145:287-304. [DOI: 10.1007/s00418-015-1385-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2015] [Indexed: 10/22/2022]
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21
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Schrader M, Godinho LF, Costello JL, Islinger M. The different facets of organelle interplay-an overview of organelle interactions. Front Cell Dev Biol 2015; 3:56. [PMID: 26442263 PMCID: PMC4585249 DOI: 10.3389/fcell.2015.00056] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/08/2015] [Indexed: 12/28/2022] Open
Abstract
Membrane-bound organelles such as mitochondria, peroxisomes, or the endoplasmic reticulum (ER) create distinct environments to promote specific cellular tasks such as ATP production, lipid breakdown, or protein export. During recent years, it has become evident that organelles are integrated into cellular networks regulating metabolism, intracellular signaling, cellular maintenance, cell fate decision, and pathogen defence. In order to facilitate such signaling events, specialized membrane regions between apposing organelles bear distinct sets of proteins to enable tethering and exchange of metabolites and signaling molecules. Such membrane associations between the mitochondria and a specialized site of the ER, the mitochondria associated-membrane (MAM), as well as between the ER and the plasma membrane (PAM) have been partially characterized at the molecular level. However, historical and recent observations imply that other organelles like peroxisomes, lysosomes, and lipid droplets might also be involved in the formation of such apposing membrane contact sites. Alternatively, reports on so-called mitochondria derived-vesicles (MDV) suggest alternative mechanisms of organelle interaction. Moreover, maintenance of cellular homeostasis requires the precise removal of aged organelles by autophagy—a process which involves the detection of ubiquitinated organelle proteins by the autophagosome membrane, representing another site of membrane associated-signaling. This review will summarize the available data on the existence and composition of organelle contact sites and the molecular specializations each site uses in order to provide a timely overview on the potential functions of organelle interaction.
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Affiliation(s)
- Michael Schrader
- Department of Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
| | - Luis F Godinho
- Centre for Cell Biology and Department of Biology, University of Aveiro Aveiro, Portugal
| | - Joseph L Costello
- Department of Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
| | - Markus Islinger
- Neuroanatomy, Center for Biomedicine and Medical Technology Mannheim, University of Heidelberg Mannheim, Germany
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22
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Klecker T, Böckler S, Westermann B. Making connections: interorganelle contacts orchestrate mitochondrial behavior. Trends Cell Biol 2014; 24:537-45. [PMID: 24786308 DOI: 10.1016/j.tcb.2014.04.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/01/2014] [Accepted: 04/02/2014] [Indexed: 01/07/2023]
Abstract
Mitochondria are highly dynamic organelles. During their life cycle they frequently fuse and divide, and damaged mitochondria are removed by autophagic degradation. These processes serve to maintain mitochondrial function and ensure optimal energy supply for the cell. It has recently become clear that this complex mitochondrial behavior is governed to a large extent by interactions with other organelles. In this review, we describe mitochondrial contacts with the endoplasmic reticulum (ER), plasma membrane, and peroxisomes. In particular, we highlight how mitochondrial fission, distribution, inheritance, and turnover are orchestrated by interorganellar contacts in yeast and metazoa. These interactions are pivotal for the integration of the dynamic mitochondrial network into the architecture of eukaryotic cells.
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Affiliation(s)
- Till Klecker
- Institut für Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Stefan Böckler
- Institut für Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
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23
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Contreras MA, Alzate O, Singh AK, Singh I. PPARα activation induces N(ε)-Lys-acetylation of rat liver peroxisomal multifunctional enzyme type 1. Lipids 2013; 49:119-31. [PMID: 24092543 DOI: 10.1007/s11745-013-3843-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/09/2013] [Indexed: 11/28/2022]
Abstract
Peroxisomes are ubiquitous subcellular organelles that participate in metabolic and disease processes, with few of its proteins undergoing posttranslational modifications. As the role of lysine-acetylation has expanded into the cellular intermediary metabolism, we used a combination of differential centrifugation, organelle isolation by linear density gradient centrifugation, western blot analysis, and peptide fingerprinting and amino acid sequencing by mass spectrometry to investigate protein acetylation in control and ciprofibrate-treated rat liver peroxisomes. Organelle protein samples isolated by density gradient centrifugation from PPARα-agonist treated rat liver screened with an anti-N(ε)-acetyl lysine antibody revealed a single protein band of 75 kDa. Immunoprecipitation with this antibody resulted in the precipitation of a protein from the protein pool of ciprofibrate-induced peroxisomes, but not from the protein pool of non-induced peroxisomes. Peptide mass fingerprinting analysis identified the protein as the peroxisomal multifunctional enzyme type 1. In addition, mass spectrometry-based amino acid sequencing resulted in the identification of unique peptides containing 4 acetylated-Lys residues (K¹⁵⁵, K¹⁷³, K¹⁹⁰, and K⁵⁸³). This is the first report that demonstrates posttranslational acetylation of a peroxisomal enzyme in PPARα-dependent proliferation of peroxisomes in rat liver.
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Affiliation(s)
- Miguel A Contreras
- Department of Pediatrics, The Darby Children's Research Institute, Medical University of South Carolina, Charleston, SC, 29425, USA,
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25
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Mammalian SOD2 is exclusively located in mitochondria and not present in peroxisomes. Histochem Cell Biol 2013; 140:105-17. [DOI: 10.1007/s00418-013-1099-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2013] [Indexed: 11/30/2022]
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Colasante C, Voncken F, Manful T, Ruppert T, Tielens AGM, van Hellemond JJ, Clayton C. Proteins and lipids of glycosomal membranes from Leishmania tarentolae and Trypanosoma brucei. F1000Res 2013; 2:27. [PMID: 24358884 PMCID: PMC3814921 DOI: 10.12688/f1000research.2-27.v1] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/19/2013] [Indexed: 01/20/2023] Open
Abstract
In kinetoplastid protists, several metabolic pathways, including glycolysis and purine salvage, are located in glycosomes, which are microbodies that are evolutionarily related to peroxisomes. With the exception of some potential transporters for fatty acids, and one member of the mitochondrial carrier protein family, proteins that transport metabolites across the glycosomal membrane have yet to be identified. We show here that the phosphatidylcholine species composition of
Trypanosoma brucei glycosomal membranes resembles that of other cellular membranes, which means that glycosomal membranes are expected to be impermeable to small hydrophilic molecules unless transport is facilitated by specialized membrane proteins. Further, we identified 464 proteins in a glycosomal membrane preparation from
Leishmania tarentolae. The proteins included approximately 40 glycosomal matrix proteins, and homologues of peroxisomal membrane proteins - PEX11, GIM5A and GIM5B; PXMP4, PEX2 and PEX16 - as well as the transporters GAT1 and GAT3. There were 27 other proteins that could not be unambiguously assigned to other compartments, and that had predicted trans-membrane domains. However, no clear candidates for transport of the major substrates and intermediates of energy metabolism were found. We suggest that, instead, these metabolites are transported via pores formed by the known glycosomal membrane proteins.
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Affiliation(s)
| | - Frank Voncken
- Department of Biological Sciences and Hull York Medical School, University of Hull, Hull, HU6 7RX, UK
| | - Theresa Manful
- Department of Biochemistry, Cell & Molecular Biology, University of Ghana, Accra, P.O. Box LG 54, Ghana
| | - Thomas Ruppert
- DKFZ-ZMBH Alliance, Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, D69120, Germany
| | - Aloysius G M Tielens
- Department of Medical Microbiology and Infectious Diseases, ErasmusMC University Medical Center, Rotterdam, PO box 2040, Netherlands.,Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, PO Box 80176, Netherlands
| | - Jaap J van Hellemond
- Department of Medical Microbiology and Infectious Diseases, ErasmusMC University Medical Center, Rotterdam, PO box 2040, Netherlands
| | - Christine Clayton
- DKFZ-ZMBH Alliance, Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, D69120, Germany
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Schrader M, Grille S, Fahimi HD, Islinger M. Peroxisome interactions and cross-talk with other subcellular compartments in animal cells. Subcell Biochem 2013; 69:1-22. [PMID: 23821140 DOI: 10.1007/978-94-007-6889-5_1] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Peroxisomes are remarkably plastic and dynamic organelles, which fulfil important functions in hydrogen peroxide and lipid metabolism rendering them essential for human health and development. Despite great advances in the identification and characterization of essential components and molecular mechanisms associated with the biogenesis and function of peroxisomes, our understanding of how peroxisomes are incorporated into metabolic pathways and cellular communication networks is just beginning to emerge. Here we address the interaction of peroxisomes with other subcellular compartments including the relationship with the endoplasmic reticulum, the peroxisome-mitochondria connection and the association with lipid droplets. We highlight metabolic cooperations and potential cross-talk and summarize recent findings on peroxisome-peroxisome interactions and the interaction of peroxisomes with microtubules in mammalian cells.
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Affiliation(s)
- Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK,
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28
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Role of peroxisomes in ROS/RNS-metabolism: Implications for human disease. Biochim Biophys Acta Mol Basis Dis 2012; 1822:1363-73. [DOI: 10.1016/j.bbadis.2011.12.001] [Citation(s) in RCA: 383] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/25/2011] [Accepted: 12/02/2011] [Indexed: 12/27/2022]
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Watkins PA, Ellis JM. Peroxisomal acyl-CoA synthetases. Biochim Biophys Acta Mol Basis Dis 2012; 1822:1411-20. [PMID: 22366061 DOI: 10.1016/j.bbadis.2012.02.010] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 01/12/2012] [Accepted: 02/10/2012] [Indexed: 01/26/2023]
Abstract
Peroxisomes carry out many essential lipid metabolic functions. Nearly all of these functions require that an acyl group-either a fatty acid or the acyl side chain of a steroid derivative-be thioesterified to coenzyme A (CoA) for subsequent reactions to proceed. This thioesterification, or "activation", reaction, catalyzed by enzymes belonging to the acyl-CoA synthetase family, is thus central to cellular lipid metabolism. However, despite our rather thorough understanding of peroxisomal metabolic pathways, surprisingly little is known about the specific peroxisomal acyl-CoA synthetases that participate in these pathways. Of the 26 acyl-CoA synthetases encoded by the human and mouse genomes, only a few have been reported to be peroxisomal, including ACSL4, SLC27A2, and SLC27A4. In this review, we briefly describe the primary peroxisomal lipid metabolic pathways in which fatty acyl-CoAs participate. Then, we examine the evidence for presence and functions of acyl-CoA synthetases in peroxisomes, much of which was obtained before the existence of multiple acyl-CoA synthetase isoenzymes was known. Finally, we discuss the role(s) of peroxisome-specific acyl-CoA synthetase isoforms in lipid metabolism.
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Expression and subcellular distribution of gephyrin in non-neuronal tissues and cells. Histochem Cell Biol 2012; 137:471-82. [PMID: 22270318 DOI: 10.1007/s00418-012-0914-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2012] [Indexed: 10/14/2022]
Abstract
Gephyrin is a scaffolding protein required for the accumulation of inhibitory neurotransmitter receptors at neuronal postsynaptic membranes. In non-neuronal tissues, gephyrin is indispensible for the biosynthesis of molybdenum cofactor, the prosthetic group of oxidoreductases including sulfite oxidase and xanthine oxidase. However, the molecular and cellular basis of gephyrin's non-neuronal function is poorly understood; in particular, the roles of its splice variants remain enigmatic. Here, we used cDNA screening as well as Northern and immunoblot analyses to show that mammalian liver contains only a limited number of gephyrin splice variants, with the C3-containing variant being the predominant isoform. Using new and established anti-gephyrin antibodies in immunofluorescence and subcellular fractionation studies, we report that gephyrin localizes to the cytoplasm of both tissue hepatocytes and cultured immortalized cells. These findings were corroborated by RNA interference studies in which the cytosolic distribution was found to be abolished. Finally, by blue-native PAGE we show that cytoplasmic gephyrin is part of a ~600 kDa protein complex of yet unknown composition. Our data suggest that the expression pattern of non-neuronal gephyrin is simpler than indicated by previous evidence. In addition, gephyrin's presence in a cytosolic 600 kDa protein complex suggests that its metabolic and/or other non-neuronal functions are exerted in the cytoplasm and are not confined to a particular subcellular compartment.
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Board PG, Anders MW. Glutathione transferase zeta: discovery, polymorphic variants, catalysis, inactivation, and properties of Gstz1-/- mice. Drug Metab Rev 2011; 43:215-25. [PMID: 21303221 DOI: 10.3109/03602532.2010.549132] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Glutathione transferase zeta (GSTZ1) is a member of the GST superfamily of proteins that catalyze the reaction of glutathione with endo- and xenobiotics. GSTZ1-1 was discovered by a bioinformatics strategy that searched the human-expressed sequence-tag database with a sequence that matched a putative plant GST. A sequence that was found was expressed and termed GSTZ1-1. In common with other GSTs, GSTZ1-1 showed some peroxidase activity, but lacked activity with most known GST substrates. GSTZ1-1 was also found to be identical with maleylacetoacetate isomerase, which catalyzes the penultimate step in the tyrosine-degradation pathway. Further studies showed that dichloroacetate (DCA) and a range of α-haloalkanoates and α,α-dihaloalkanoates were substrates. A subsequent search of the human-expressed sequence-tag database showed the presence of four polymorphic alleles: 1a, 1b, 1c, and 1d; GSTZ1c was the most common and was designated as the wild-type gene. DCA was shown to be a k(cat) inactivator of human, rat, and mouse GSTZ1-1; human GSTZ1-1 was more resistant to inactivation than mouse or rat GSTZ1-1. Proteomic analysis showed that hGSTZ1-1 was inactivated when Cys-16 was modified by glutathione and the carbon skeleton of DCA. The polymorphic variants of hGSTZ1-1 differ in their susceptibility to inactivation, with 1a-1a being more resistant to inactivation than the other variants. The targeted deletion of GSTZ1 yielded mice that were not phenotypically distinctive. Phenylalanine proved, however, to be toxic to Gstz1(-/-) mice, and these mice showed evidence of organ damage and leucopenia.
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Affiliation(s)
- Philip G Board
- Molecular Genetics Group, John Curtin School of Medical Research, Australian National University, Canberra, Australia
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Managadze D, Würtz C, Wiese S, Meyer HE, Niehaus G, Erdmann R, Warscheid B, Rottensteiner H. A proteomic approach towards the identification of the matrix protein content of the two types of microbodies in Neurospora crassa. Proteomics 2011; 10:3222-34. [PMID: 20707002 DOI: 10.1002/pmic.201000095] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Microbodies (peroxisomes) comprise a class of organelles with a similar biogenesis but remarkable biochemical heterogeneity. Here, we purified the two distinct microbody family members of filamentous fungi, glyoxysomes and Woronin bodies, from Neurospora crassa and analyzed their protein content by HPLC/ESI-MS/MS. In the purified Woronin bodies, we unambiguously identified only hexagonal 1 (HEX1), suggesting that the matrix is probably exclusively filled with the HEX1 hexagonal crystal. The proteomic analysis of highly purified glyoxysomes allowed the identification of 191 proteins. Among them were 16 proteins with a peroxisomal targeting signal type 1 (PTS1) and three with a PTS2. The collection also contained the previously described N. crassa glyoxysomal matrix proteins FOX2 and ICL1 that lack a typical PTS. Three PTS1 proteins were identified that likely represent the long sought glyoxysomal acyl-CoA dehydrogenases of filamentous fungi. Two of them were demonstrated by subcellular localization studies to be indeed glyoxysomal. Furthermore, two PTS proteins were identified that are suggested to be involved in the detoxification of nitroalkanes. Since the glyoxysomal localization was experimentally demonstrated for one of these enzymes, a new biochemical reaction is expected to be associated with microbody function.
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Affiliation(s)
- David Managadze
- Department of Systems Biochemistry, Institute of Physiological Chemistry, Ruhr-University of Bochum, Bochum, Germany
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Gianazza E, Eberini I, Sensi C, Barile M, Vergani L, Vanoni MA. Energy matters: mitochondrial proteomics for biomedicine. Proteomics 2011; 11:657-74. [PMID: 21241019 DOI: 10.1002/pmic.201000412] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 09/22/2010] [Accepted: 11/03/2010] [Indexed: 12/16/2022]
Abstract
This review compiles results of medical relevance from mitochondrial proteomics, grouped either according to the type of disease - genetic or degenerative - or to the involved mechanism - oxidative stress or apoptosis. The findings are commented in the light of our current understanding of uniformity/variability in cell responses to different stimuli. Specificities in the conceptual and technical approaches to human mitochondrial proteomics are also outlined.
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Affiliation(s)
- Elisabetta Gianazza
- Dipartimento di Scienze Farmacologiche, Università degli Studi di Milano, Milano, Italy.
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Abstract
Peroxisomes are multifunctional organelles with an important role in the generation and decomposition of reactive oxygen species (ROS). In this review, the ROS-producing enzymes, as well as the antioxidative defense system in mammalian peroxisomes, are described. In addition, various conditions leading to disturbances in peroxisomal ROS metabolism, such as abnormal peroxisomal biogenesis, hypocatalasemia, and proliferation of peroxisomes are discussed. We also review the role of mammalian peroxisomes in some physiological and pathological processes involving ROS that lead to mitochondrial abnormalities, defects in cell proliferation, and alterations in the central nervous system, alcoholic cardiomyopathy, and aging. Antioxid.
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Abstract
Peroxisomes are organelles bounded by a single membrane that can be found in all major groups of eukaryotes. A single evolutionary origin of this cellular compartment is supported by the presence, in diverse organisms, of a common set of proteins implicated in peroxisome biogenesis and maintenance. Their enzymatic content, however, can vary substantially across species, indicating a high level of evolutionary plasticity. Proteomic analyses have greatly expanded our knowledge on peroxisomes in some model organisms, including plants, mammals and yeasts. However, we still have a limited knowledge about the distribution and functionalities of peroxisomes in the vast majority of groups of microbial eukaryotes. Here, I review recent advances in our understanding of peroxisome diversity and evolution, with a special emphasis on peroxisomes in microbial eukaryotes.
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Affiliation(s)
- Toni Gabaldón
- Centre for Genomic Regulation (CRG), Dr Aiguader, 88 08003 Barcelona, Spain.
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Islinger M, Cardoso MJR, Schrader M. Be different--the diversity of peroxisomes in the animal kingdom. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:881-97. [PMID: 20347886 DOI: 10.1016/j.bbamcr.2010.03.013] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 03/15/2010] [Accepted: 03/18/2010] [Indexed: 10/19/2022]
Abstract
Peroxisomes represent so-called "multipurpose organelles" as they contribute to various anabolic as well as catabolic pathways. Thus, with respect to the physiological specialization of an individual organ or animal species, peroxisomes exhibit a functional diversity, which is documented by significant variations in their proteome. These differences are usually regarded as an adaptational response to the nutritional and environmental life conditions of a specific organism. Thus, human peroxisomes can be regarded as an in part physiologically unique organellar entity fulfilling metabolic functions that differ from our animal model systems. In line with this, a profound understanding on how peroxisomes acquired functional heterogeneity in terms of an evolutionary and mechanistic background is required. This review summarizes our current knowledge on the heterogeneity of peroxisomal physiology, providing insights into the genetic and cell biological mechanisms, which lead to the differential localization or expression of peroxisomal proteins and further gives an overview on peroxisomal biochemical pathways, which are specialized in different animal species and organs. Moreover, it addresses the impact of proteome studies on our understanding of differential peroxisome function describing the utility of mass spectrometry and computer-assisted algorithms to identify peroxisomal target sequences for the detection of new organ- or species-specific peroxisomal proteins.
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Affiliation(s)
- M Islinger
- Department of Anatomy and Cell Biology, Ruprecht-Karls University, 69120 Heidelberg, Germany
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Falcón-Pérez JM, Lu SC, Mato JM. Sub-proteome approach to the knowledge of liver. Proteomics Clin Appl 2010; 4:407-15. [PMID: 21137060 DOI: 10.1002/prca.200900123] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Accepted: 08/12/2009] [Indexed: 11/08/2022]
Abstract
In the recent years, global proteomics approaches have been widely used to characterize a number of tissue proteomes including plasma and liver; however, the elevated complexity of these samples in combination with the high abundance of some specific proteins make the study of the lowest abundant proteins difficult. This review is focused on different strategies that have been developed to extend the proteome focused on these two tissues, as, for example, the analysis of sub-cellular proteomes. In this regard, two special kind of extracellular vesicles--exosomes and membrane plasma shedding vesicles--are emerging as excellent biological source both to extend the liver and plasma proteomes and to be applied in the discovery of non-invasive liver-specific disease biomarkers.
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Affiliation(s)
- Juan M Falcón-Pérez
- Metabolomics Unit, CICbioGUNE, CIBERehd, Bizkaia Technology Park, Derio, Bizkaia, Spain.
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Islinger M, Li KW, Seitz J, Völkl A, Lüers GH. Hitchhiking of Cu/Zn Superoxide Dismutase to Peroxisomes - Evidence for a Natural Piggyback Import Mechanism in Mammals. Traffic 2009; 10:1711-21. [DOI: 10.1111/j.1600-0854.2009.00966.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Islinger M, Li KW, Loos M, Liebler S, Angermüller S, Eckerskorn C, Weber G, Abdolzade A, Völkl A. Peroxisomes from the Heavy Mitochondrial Fraction: Isolation by Zonal Free Flow Electrophoresis and Quantitative Mass Spectrometrical Characterization. J Proteome Res 2009; 9:113-24. [DOI: 10.1021/pr9004663] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Markus Islinger
- Department of Anatomy and Cell Biology, Ruprecht-Karl University, 69120 Heidelberg, Germany, Department of Molecular and Cellular Neurobiology, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, Netherlands, and BD Diagnostics - Preanalytical Systems, 82152 Planegg/Martinsried, Germany
| | - Ka Wan Li
- Department of Anatomy and Cell Biology, Ruprecht-Karl University, 69120 Heidelberg, Germany, Department of Molecular and Cellular Neurobiology, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, Netherlands, and BD Diagnostics - Preanalytical Systems, 82152 Planegg/Martinsried, Germany
| | - Maarten Loos
- Department of Anatomy and Cell Biology, Ruprecht-Karl University, 69120 Heidelberg, Germany, Department of Molecular and Cellular Neurobiology, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, Netherlands, and BD Diagnostics - Preanalytical Systems, 82152 Planegg/Martinsried, Germany
| | - Sven Liebler
- Department of Anatomy and Cell Biology, Ruprecht-Karl University, 69120 Heidelberg, Germany, Department of Molecular and Cellular Neurobiology, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, Netherlands, and BD Diagnostics - Preanalytical Systems, 82152 Planegg/Martinsried, Germany
| | - Sabine Angermüller
- Department of Anatomy and Cell Biology, Ruprecht-Karl University, 69120 Heidelberg, Germany, Department of Molecular and Cellular Neurobiology, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, Netherlands, and BD Diagnostics - Preanalytical Systems, 82152 Planegg/Martinsried, Germany
| | - Christoph Eckerskorn
- Department of Anatomy and Cell Biology, Ruprecht-Karl University, 69120 Heidelberg, Germany, Department of Molecular and Cellular Neurobiology, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, Netherlands, and BD Diagnostics - Preanalytical Systems, 82152 Planegg/Martinsried, Germany
| | - Gerhard Weber
- Department of Anatomy and Cell Biology, Ruprecht-Karl University, 69120 Heidelberg, Germany, Department of Molecular and Cellular Neurobiology, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, Netherlands, and BD Diagnostics - Preanalytical Systems, 82152 Planegg/Martinsried, Germany
| | - Afsaneh Abdolzade
- Department of Anatomy and Cell Biology, Ruprecht-Karl University, 69120 Heidelberg, Germany, Department of Molecular and Cellular Neurobiology, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, Netherlands, and BD Diagnostics - Preanalytical Systems, 82152 Planegg/Martinsried, Germany
| | - Alfred Völkl
- Department of Anatomy and Cell Biology, Ruprecht-Karl University, 69120 Heidelberg, Germany, Department of Molecular and Cellular Neurobiology, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, Netherlands, and BD Diagnostics - Preanalytical Systems, 82152 Planegg/Martinsried, Germany
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41
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Minden JS, Dowd SR, Meyer HE, Stühler K. Difference gel electrophoresis. Electrophoresis 2009; 30 Suppl 1:S156-61. [DOI: 10.1002/elps.200900098] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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42
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Kulinsky VI, Kolesnichenko LS. The glutathione system. I. Synthesis, transport, glutathione transferases, glutathione peroxidases. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2009. [DOI: 10.1134/s1990750809020036] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
Defining membrane proteomes is fundamental to our understanding of many physiological and pathophysiological processes. Their separation and identification is hence a key issue in basic and biomedical research. Due to their hydrophobic character, few high-resolution techniques for separation are available for qualitative and quantitative approaches. For gel-based methods, the two-dimensional 16-BAC/SDS-PAGE is the method of choice. This technique separates proteins in the first dimension using an acidic buffer system and the cationic detergent benzyldimethyl-n-hexadecylammonium chloride (16-BAC) and in the second dimension by SDS-PAGE. Here, we describe a detailed protocol for the separation of proteins by 16-BAC/SDS-PAGE.
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Affiliation(s)
- Hans Gerd Nothwang
- Abteilung Neurogenetik, Institut für Biologie und Umweltwissenschaften, Oldenburg, Germany
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44
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Abstract
Mitochondria are essential organelles in cellular metabolism. These organelles are bounded by two membranes, the outer and inner membrane. Especially the inner membrane comprises a high content of proteins, for example, the protein complexes of the respiratory chain. High-resolution separation and analysis of such membrane proteins, for example, by two-dimensional gel electrophoresis (2-DE), is hampered by their hydrophobicity and tendency for aggregation. Here, we describe the separation of mitochondrial membrane proteins of Saccharomyces cerevisiae by 16-benzyldimethyl-n-hexadecylammonium chloride/sodium dodecyl sulfate polyacrylamide gel electrophoresis (16-BAC/SDS-PAGE). This method enables the separation of membrane proteins owing to the solubilizing power of the ionic detergents 16-BAC and SDS, respectively. Mitochondria were isolated from yeast cultures by differential centrifugation and were further purified by free flow electrophoresis (FFE) in zone-electrophoretic mode (ZE). Subsequently, membrane proteins from ZE-FFE-purified mitochondria were enriched by carbonate extraction and subjected to 16-BAC/SDS-PAGE. The resulting protein spot patterns were visualized by a highly sensitive fluorescence stain with ruthenium-II-bathophenantroline disulfonate chelate (RuBP), and by colloidal Coomassie staining. Proteins were identified by Maldi-Tof mass spectrometry and peptide mass fingerprinting.
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Peroxisomes in mouse and human lung: their involvement in pulmonary lipid metabolism. Histochem Cell Biol 2008; 130:719-40. [PMID: 18665385 DOI: 10.1007/s00418-008-0462-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2008] [Indexed: 10/21/2022]
Abstract
Only sparse information is available from the literature on the peroxisomal compartment and its enzyme composition in mouse and human lungs. Therefore, in the present investigation we have characterized peroxisomes in different cell types of adult mouse (C57BL/6J) and human lungs in a comprehensive study using a variety of light-, fluorescence- and electron microscopic as well as biochemical techniques and by the use of various peroxisomal marker proteins (Pex13p, Pex14p, ABCD3, beta-oxidation enzymes and catalase). In contrast to previous reports, we have found that peroxisomes are present in all cell types in human and mouse lungs. However, they differ significantly and in a cell-type-specific manner in their structure, numerical abundance and enzyme composition. Whereas catalase showed significant differences between distinct cell types, Pex14p proved to be the marker of choice for labeling all lung peroxisomes. In alveolar type II cells and alveolar macrophages peroxisomes contained significant amounts of the lipid transporter ABCD3 and beta-oxidation enzymes, suggesting their involvement in the modification and recycling of surfactant lipids and in the control of lipid mediators and ligands for nuclear receptors of the PPAR family. Possible connections between ROS and lipid metabolism of lung peroxisomes are discussed.
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Abstract
More than half a century of research on peroxisomes has revealed unique features of this ubiquitous subcellular organelle, which have often been in disagreement with existing dogmas in cell biology. About 50 peroxisomal enzymes have so far been identified, which contribute to several crucial metabolic processes such as β-oxidation of fatty acids, biosynthesis of ether phospholipids and metabolism of reactive oxygen species, and render peroxisomes indispensable for human health and development. It became obvious that peroxisomes are highly dynamic organelles that rapidly assemble, multiply and degrade in response to metabolic needs. However, many aspects of peroxisome biology are still mysterious. This review addresses recent exciting discoveries on the biogenesis, formation and degradation of peroxisomes, on peroxisomal dynamics and division, as well as on the interaction and cross talk of peroxisomes with other subcellular compartments. Furthermore, recent advances on the role of peroxisomes in medicine and in the identification of novel peroxisomal proteins are discussed.
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Affiliation(s)
- Michael Schrader
- Centre for Cell Biology and Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal.
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Islinger M, Weber G. Free flow isoelectric focusing : a method for the separation of both hydrophilic and hydrophobic proteins of rat liver peroxisomes. Methods Mol Biol 2008; 432:199-215. [PMID: 18370020 DOI: 10.1007/978-1-59745-028-7_14] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Peroxisomes take part in various metabolic pathways related to the regulation of lipid homeostasis. Although detailed information on the enzymes involved in the peroxisomal lipid metabolism was acquired in the past, the mechanisms of metabolic exchange between peroxisomes and the cytosol or other organelles still remain an enigma. Therefore, a detailed analysis of the peroxisomal membrane proteome could help identify potential metabolite transporters. However, because of their highly hydrophobic character, membrane proteins tend to precipitate in aqueous media, making their fractionation still a challenging task. To overcome these obstacles, we have elaborated a protocol for the separation of both hydrophilic as well as hydrophobic proteins using free flow isoelectric focusing (FF-IEF). Similar to traditional gel-based isoelectric focusing, a denaturing electrophoresis buffer containing a mixture of urea, thiourea and detergents is applied to keep highly hydrophobic proteins in solution. Electrophoresis is conducted on a BD Free Flow Electrophoresis System with a linear pH gradient from 3 to 10 and sampled into 96 fractions. As a second dimension, sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) is used to further separate and visualize the protein pattern of the peroxisomal subfractions of matrix, peripheral and integral membrane proteins. The identification of the known peroxisomal membrane proteins PMP22, PMP70 as well as mGST in the subsequent matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) analysis of the 100 most prominent protein bands has documented the suitability of this new technique for the analysis of hydrophobic proteins.
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Affiliation(s)
- Markus Islinger
- Department of Anatomy and Cell Biology II, University of Heidelberg, Heidelberg, Germany
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48
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Wiese S, Gronemeyer T, Ofman R, Kunze M, Grou CP, Almeida JA, Eisenacher M, Stephan C, Hayen H, Schollenberger L, Korosec T, Waterham HR, Schliebs W, Erdmann R, Berger J, Meyer HE, Just W, Azevedo JE, Wanders RJA, Warscheid B. Proteomics characterization of mouse kidney peroxisomes by tandem mass spectrometry and protein correlation profiling. Mol Cell Proteomics 2007; 6:2045-57. [PMID: 17768142 DOI: 10.1074/mcp.m700169-mcp200] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The peroxisome represents a ubiquitous single membrane-bound key organelle that executes various metabolic pathways such as fatty acid degradation by alpha- and beta-oxidation, ether-phospholipid biosynthesis, metabolism of reactive oxygen species, and detoxification of glyoxylate in mammals. To fulfil this vast array of metabolic functions, peroxisomes accommodate approximately 50 different enzymes at least as identified until now. Interest in peroxisomes has been fueled by the discovery of a group of genetic diseases in humans, which are caused by either a defect in peroxisome biogenesis or the deficient activity of a distinct peroxisomal enzyme or transporter. Although this research has greatly improved our understanding of peroxisomes and their role in mammalian metabolism, deeper insight into biochemistry and functions of peroxisomes is required to expand our knowledge of this low abundance but vital organelle. In this work, we used classical subcellular fractionation in combination with MS-based proteomics methodologies to characterize the proteome of mouse kidney peroxisomes. We could identify virtually all known components involved in peroxisomal metabolism and biogenesis. Moreover through protein localization studies by using a quantitative MS screen combined with statistical analyses, we identified 15 new peroxisomal candidates. Of these, we further investigated five candidates by immunocytochemistry, which confirmed their localization in peroxisomes. As a result of this joint effort, we believe to have compiled the so far most comprehensive protein catalogue of mammalian peroxisomes.
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Affiliation(s)
- Sebastian Wiese
- Medizinisches Proteom-Center, Ruhr-Universitaet Bochum, Universitaetsstrasse 150, 44780 Bochum, Germany
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Braun RJ, Kinkl N, Beer M, Ueffing M. Two-dimensional electrophoresis of membrane proteins. Anal Bioanal Chem 2007; 389:1033-45. [PMID: 17680235 DOI: 10.1007/s00216-007-1514-6] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Revised: 07/10/2007] [Accepted: 07/13/2007] [Indexed: 01/26/2023]
Abstract
One third of all genes of various organisms encode membrane proteins, emphasizing their crucial cellular role. However, due to their high hydrophobicity, membrane proteins demonstrate low solubility and a high tendency for aggregation. Indeed, conventional two-dimensional gel electrophoresis (2-DE), a powerful electrophoretic method for the separation of complex protein samples that applies isoelectric focusing (IEF) in the first dimension and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension, has a strong bias against membrane proteins. This review describes two-dimensional electrophoretic techniques that can be used to separate membrane proteins. Alternative methods for performing conventional 2-DE are highlighted; these involve replacing the IEF with electrophoresis using cationic detergents, namely 16-benzyldimethyl-n-hexadecylammonium chloride (16-BAC) and cetyl trimethyl ammonium bromide (CTAB), or the anionic detergent SDS. Finally, the separation of native membrane protein complexes through the application of blue and clear native gel electrophoresis (BN/CN-PAGE) is reviewed, as well as the free-flow electrophoresis (FFE) of membranes.
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Affiliation(s)
- Ralf J Braun
- GSF-National Research Center for Environment and Health, Institute of Human Genetics, Ingolstaedter Landstrasse 1, 85764, Munich-Neuherberg, Germany
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50
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Islinger M, Lüers GH, Li KW, Loos M, Völkl A. Rat Liver Peroxisomes after Fibrate Treatment. J Biol Chem 2007; 282:23055-69. [PMID: 17522052 DOI: 10.1074/jbc.m610910200] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Fibrates are known to induce peroxisome proliferation and the expression of peroxisomal beta-oxidation enzymes. To analyze fibrate-induced changes of complex metabolic networks, we have compared the proteome of rat liver peroxisomes from control and bezafibrate-treated rats. Highly purified peroxisomes were subfractionated, and the proteins of the matrix, peripheral, and integral membrane subfractions thus obtained were analyzed by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry after labeling of tryptic peptides with the iTRAQ reagent. By means of this quantitative technique, we were able to identify 134 individual proteins, covering most of the known peroxisomal proteome. Ten predicted new open reading frames were verified by cDNA cloning, and seven of them could be localized to peroxisomes by immunocytochemistry. Moreover, quantitative mass spectrometry substantiated the induction of most of the known peroxisome proliferator-activated receptor alpha-regulated peroxisomal proteins upon treatment with bezafibrate, documenting the suitability of the iTRAQ procedure in larger scale experiments. However, not all proteins reacted to a similar extent but exerted a fibrate-specific induction scheme showing the variability of peroxisome proliferator-activated receptoralpha-transmitted responses to specific ligands. In view of our data, rat hepatic peroxisomes are apparently not specialized to sequester very long chain fatty acids (C22-C26) but rather metabolize preferentially long chain fatty acids (C16-18).
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Affiliation(s)
- Markus Islinger
- Department of Anatomy and Cell Biology, Ruprecht-Karl University, 69120 Heidelberg, Germany.
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