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Bajdzienko J, Bremm A. Mammalian pexophagy at a glance. J Cell Sci 2024; 137:jcs259775. [PMID: 38752931 PMCID: PMC11166455 DOI: 10.1242/jcs.259775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2024] Open
Abstract
Peroxisomes are highly plastic organelles that are involved in several metabolic processes, including fatty acid oxidation, ether lipid synthesis and redox homeostasis. Their abundance and activity are dynamically regulated in response to nutrient availability and cellular stress. Damaged or superfluous peroxisomes are removed mainly by pexophagy, the selective autophagy of peroxisomes induced by ubiquitylation of peroxisomal membrane proteins or ubiquitin-independent processes. Dysregulated pexophagy impairs peroxisome homeostasis and has been linked to the development of various human diseases. Despite many recent insights into mammalian pexophagy, our understanding of this process is still limited compared to our understanding of pexophagy in yeast. In this Cell Science at a Glance article and the accompanying poster, we summarize current knowledge on the control of mammalian pexophagy and highlight which aspects require further attention. We also discuss the role of ubiquitylation in pexophagy and describe the ubiquitin machinery involved in regulating signals for the recruitment of phagophores to peroxisomes.
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Affiliation(s)
- Justyna Bajdzienko
- Goethe University Frankfurt,Medical Faculty,Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Anja Bremm
- Goethe University Frankfurt,Medical Faculty,Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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Kumar R, Islinger M, Worthy H, Carmichael R, Schrader M. The peroxisome: an update on mysteries 3.0. Histochem Cell Biol 2024; 161:99-132. [PMID: 38244103 PMCID: PMC10822820 DOI: 10.1007/s00418-023-02259-5] [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] [Accepted: 12/09/2023] [Indexed: 01/22/2024]
Abstract
Peroxisomes are highly dynamic, oxidative organelles with key metabolic functions in cellular lipid metabolism, such as the β-oxidation of fatty acids and the synthesis of myelin sheath lipids, as well as the regulation of cellular redox balance. Loss of peroxisomal functions causes severe metabolic disorders in humans. Furthermore, peroxisomes also fulfil protective roles in pathogen and viral defence and immunity, highlighting their wider significance in human health and disease. This has sparked increasing interest in peroxisome biology and their physiological functions. This review presents an update and a continuation of three previous review articles addressing the unsolved mysteries of this remarkable organelle. We continue to highlight recent discoveries, advancements, and trends in peroxisome research, and address novel findings on the metabolic functions of peroxisomes, their biogenesis, protein import, membrane dynamics and division, as well as on peroxisome-organelle membrane contact sites and organelle cooperation. Furthermore, recent insights into peroxisome organisation through super-resolution microscopy are discussed. Finally, we address new roles for peroxisomes in immune and defence mechanisms and in human disorders, and for peroxisomal functions in different cell/tissue types, in particular their contribution to organ-specific pathologies.
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Grants
- BB/W015420/1, BB/V018167/1, BB/T002255/1, BB/R016844/1 Biotechnology and Biological Sciences Research Council
- BB/W015420/1, BB/V018167/1, BB/T002255/1, BB/R016844/1 Biotechnology and Biological Sciences Research Council
- BB/W015420/1, BB/V018167/1, BB/T002255/1, BB/R016844/1 Biotechnology and Biological Sciences Research Council
- European Union’s Horizon 2020 research and innovation programme
- Deutsches Zentrum für Herz-Kreislaufforschung
- German Research Foundation
- Medical Faculty Mannheim, University of Heidelberg
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Affiliation(s)
- Rechal Kumar
- Faculty of Health and Life Sciences, Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Markus Islinger
- Institute of Neuroanatomy, Medical Faculty Mannheim, Mannheim Centre for Translational Neuroscience, University of Heidelberg, 68167, Mannheim, Germany
| | - Harley Worthy
- Faculty of Health and Life Sciences, Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Ruth Carmichael
- Faculty of Health and Life Sciences, Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
| | - Michael Schrader
- Faculty of Health and Life Sciences, Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
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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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Colasante C, Bonilla-Martinez R, Berg T, Windhorst A, Baumgart-Vogt E. Peroxisomes during postnatal development of mouse endocrine and exocrine pancreas display cell-type- and stage-specific protein composition. Cell Tissue Res 2023:10.1007/s00441-023-03766-6. [PMID: 37126142 DOI: 10.1007/s00441-023-03766-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/15/2023] [Indexed: 05/02/2023]
Abstract
Peroxisomal dysfunction unhinges cellular metabolism by causing the accumulation of toxic metabolic intermediates (e.g. reactive oxygen species, very -chain fatty acids, phytanic acid or eicosanoids) and the depletion of important lipid products (e.g. plasmalogens, polyunsaturated fatty acids), leading to various proinflammatory and devastating pathophysiological conditions like metabolic syndrome and age-related diseases including diabetes. Because the peroxisomal antioxidative marker enzyme catalase is low abundant in Langerhans islet cells, peroxisomes were considered scarcely present in the endocrine pancreas. Recently, studies demonstrated that the peroxisomal metabolism is relevant for pancreatic cell functionality. During the postnatal period, significant changes occur in the cell structure and the metabolism to trigger the final maturation of the pancreas, including cell proliferation, regulation of energy metabolism, and activation of signalling pathways. Our aim in this study was to (i) morphometrically analyse the density of peroxisomes in mouse endocrine versus exocrine pancreas and (ii) investigate how the distribution and the abundance of peroxisomal proteins involved in biogenesis, antioxidative defence and fatty acid metabolism change during pancreatic maturation in the postnatal period. Our results prove that endocrine and exocrine pancreatic cells contain high amounts of peroxisomes with heterogeneous protein content indicating that distinct endocrine and exocrine cell types require a specific set of peroxisomal proteins depending on their individual physiological functions. We further show that significant postnatal changes occur in the peroxisomal compartment of different pancreatic cells that are most probably relevant for the metabolic maturation and differentiation of the pancreas during the development from birth to adulthood.
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Affiliation(s)
- Claudia Colasante
- Institute for Anatomy and Cell Biology, Medical Cell Biology, Justus Liebig -University, Aulweg 123, 35392, Giessen, Germany
| | - Rocio Bonilla-Martinez
- Institute for Anatomy and Cell Biology, Medical Cell Biology, Justus Liebig -University, Aulweg 123, 35392, Giessen, Germany
| | - Timm Berg
- Institute for Anatomy and Cell Biology, Medical Cell Biology, Justus Liebig -University, Aulweg 123, 35392, Giessen, Germany
| | - Anita Windhorst
- Institute for Medical Informatic, Justus Liebig University, Rudolf-Buchheim-Str. 6, 35392, Gießen, Germany
| | - Eveline Baumgart-Vogt
- Institute for Anatomy and Cell Biology, Medical Cell Biology, Justus Liebig -University, Aulweg 123, 35392, Giessen, Germany.
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Carmichael RE, Richards DM, Fahimi HD, Schrader M. Organelle Membrane Extensions in Mammalian Cells. BIOLOGY 2023; 12:biology12050664. [PMID: 37237478 DOI: 10.3390/biology12050664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023]
Abstract
Organelles within eukaryotic cells are not isolated static compartments, instead being morphologically diverse and highly dynamic in order to respond to cellular needs and carry out their diverse and cooperative functions. One phenomenon exemplifying this plasticity, and increasingly gaining attention, is the extension and retraction of thin tubules from organelle membranes. While these protrusions have been observed in morphological studies for decades, their formation, properties and functions are only beginning to be understood. In this review, we provide an overview of what is known and still to be discovered about organelle membrane protrusions in mammalian cells, focusing on the best-characterised examples of these membrane extensions arising from peroxisomes (ubiquitous organelles involved in lipid metabolism and reactive oxygen species homeostasis) and mitochondria. We summarise the current knowledge on the diversity of peroxisomal/mitochondrial membrane extensions, as well as the molecular mechanisms by which they extend and retract, necessitating dynamic membrane remodelling, pulling forces and lipid flow. We also propose broad cellular functions for these membrane extensions in inter-organelle communication, organelle biogenesis, metabolism and protection, and finally present a mathematical model that suggests that extending protrusions is the most efficient way for an organelle to explore its surroundings.
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Affiliation(s)
- Ruth E Carmichael
- Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - David M Richards
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
- Department of Physics and Astronomy, University of Exeter, Exeter EX4 4QL, UK
| | - H Dariush Fahimi
- Institute for Anatomy and Cell Biology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Michael Schrader
- Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter EX4 4QD, UK
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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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