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Skowyra ML, Feng P, Rapoport TA. Towards solving the mystery of peroxisomal matrix protein import. Trends Cell Biol 2024; 34:388-405. [PMID: 37743160 PMCID: PMC10957506 DOI: 10.1016/j.tcb.2023.08.005] [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: 06/12/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023]
Abstract
Peroxisomes are vital metabolic organelles that import their lumenal (matrix) enzymes from the cytosol using mobile receptors. Surprisingly, the receptors can even import folded proteins, but the underlying mechanism has been a mystery. Recent results reveal how import receptors shuttle cargo into peroxisomes. The cargo-bound receptors move from the cytosol across the peroxisomal membrane completely into the matrix by a mechanism that resembles transport through the nuclear pore. The receptors then return to the cytosol through a separate retrotranslocation channel, leaving the cargo inside the organelle. This cycle concentrates imported proteins within peroxisomes, and the energy for cargo import is supplied by receptor export. Peroxisomal protein import thus fundamentally differs from other previously known mechanisms for translocating proteins across membranes.
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Affiliation(s)
- Michael L Skowyra
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Peiqiang Feng
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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2
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Gaussmann S, Peschel R, Ott J, Zak KM, Sastre J, Delhommel F, Popowicz GM, Boekhoven J, Schliebs W, Erdmann R, Sattler M. Modulation of peroxisomal import by the PEX13 SH3 domain and a proximal FxxxF binding motif. Nat Commun 2024; 15:3317. [PMID: 38632234 PMCID: PMC11024197 DOI: 10.1038/s41467-024-47605-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
Import of proteins into peroxisomes depends on PEX5, PEX13 and PEX14. By combining biochemical methods and structural biology, we show that the C-terminal SH3 domain of PEX13 mediates intramolecular interactions with a proximal FxxxF motif. The SH3 domain also binds WxxxF peptide motifs in the import receptor PEX5, demonstrating evolutionary conservation of such interactions from yeast to human. Strikingly, intramolecular interaction of the PEX13 FxxxF motif regulates binding of PEX5 WxxxF/Y motifs to the PEX13 SH3 domain. Crystal structures reveal how FxxxF and WxxxF/Y motifs are recognized by a non-canonical surface on the SH3 domain. The PEX13 FxxxF motif also mediates binding to PEX14. Surprisingly, the potential PxxP binding surface of the SH3 domain does not recognize PEX14 PxxP motifs, distinct from its yeast ortholog. Our data show that the dynamic network of PEX13 interactions with PEX5 and PEX14, mediated by diaromatic peptide motifs, modulates peroxisomal matrix import.
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Affiliation(s)
- Stefan Gaussmann
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Rebecca Peschel
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
| | - Julia Ott
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
| | - Krzysztof M Zak
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Judit Sastre
- Technical University of Munich, TUM School of Natural Sciences, Department of Chemistry, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Florent Delhommel
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Grzegorz M Popowicz
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Job Boekhoven
- Technical University of Munich, TUM School of Natural Sciences, Department of Chemistry, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany.
| | - Michael Sattler
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany.
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
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3
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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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4
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Su L, Peng M, Chen X, Wu S, Liu L. Severe Zellweger spectrum disorder due to a novel missense variant in the PEX13 gene: A case report and the literature review. Mol Genet Genomic Med 2024; 12:e2315. [PMID: 37962062 PMCID: PMC10767603 DOI: 10.1002/mgg3.2315] [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: 06/15/2023] [Revised: 10/08/2023] [Accepted: 10/13/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Peroxisome biogenesis disorders (PBDs) are caused by variants in PEX genes that impair peroxisome function. Zellweger spectrum disorders (ZSDs) are the most severe and common subtype of PBDs, affecting multiple organ systems due to peroxisomal involvement in various metabolic functions. PEX13 gene variants are rare causes of ZSDs, with only 21 cases reported worldwide and none in China. METHODS We describe an infant with biochemically and molecularly confirmed ZSDs due to variants in the PEX13 gene, identified by whole exome sequencing and validated by Sanger sequencing. The patient's treatment and prognosis were followed up. We also reviewed the literature on previously reported cases with PEX13 variants. RESULTS The patient had severe hypotonia, seizures, hepatic dysfunction, failure to thrive, and dysmorphic features. Serum analysis revealed elevated levels of very long-chain fatty acids (VLCFA), phytanic acid, and pipecolic acid. We detected a novel homozygous missense variant c.493G>C (p. Ala165Pro) in the PEX13 gene (NM_002618.3), which caused severe clinical manifestations and was inherited from the consanguineous parents. The patient died at the age of 14 months. CONCLUSION We report the first case of ZSDs due to the PEX13 variant in China. Our findings broaden the mutational spectrum of the PEX13 gene and indicate that missense variants can lead to severe ZSDs phenotypes, which has implications for genotype-phenotype correlations and genetic counseling.
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Affiliation(s)
- Ling Su
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouP. R. China
| | - Min‐Zhi Peng
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouP. R. China
| | - Xiao‐Dan Chen
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouP. R. China
| | - Shuang Wu
- School of PediatricsGuangzhou Medical UniversityGuangzhouP. R. China
| | - Li Liu
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouP. R. China
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5
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Waterham HR, Koster J, Ebberink MS, Ješina P, Zeman J, Nosková L, Kmoch S, Devic P, Cheillan D, Wanders RJA, Ferdinandusse S. Autosomal dominant Zellweger spectrum disorder caused by de novo variants in PEX14 gene. Genet Med 2023; 25:100944. [PMID: 37493040 DOI: 10.1016/j.gim.2023.100944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 07/27/2023] Open
Abstract
PURPOSE Zellweger spectrum disorders (ZSDs) are known as autosomal recessive disorders caused by defective peroxisome biogenesis due to bi-allelic pathogenic variants in any of at least 13 different PEX genes. Here, we report 2 unrelated patients who present with an autosomal dominant ZSD. METHODS We performed biochemical and genetic studies in blood and skin fibroblasts of the patients and demonstrated the pathogenicity of the identified PEX14 variants by functional cell studies. RESULTS We identified 2 different single heterozygous de novo variants in the PEX14 genes of 2 patients diagnosed with ZSD. Both variants cause messenger RNA mis-splicing, leading to stable expression of similar C-terminally truncated PEX14 proteins. Functional studies indicated that the truncated PEX14 proteins lost their function in peroxisomal matrix protein import and cause increased degradation of peroxisomes, ie, pexophagy, thus exerting a dominant-negative effect on peroxisome functioning. Inhibition of pexophagy by different autophagy inhibitors or genetic knockdown of the peroxisomal autophagy receptor NBR1 resulted in restoration of peroxisomal functions in the patients' fibroblasts. CONCLUSION Our finding of an autosomal dominant ZSD expands the genetic repertoire of ZSDs. Our study underscores that single heterozygous variants should not be ignored as possible genetic cause of diseases with an established autosomal recessive mode of inheritance.
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Affiliation(s)
- Hans R Waterham
- Amsterdam UMC - AMC, Department of Laboratory Medicine, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Amsterdam Reproduction & Development, Amsterdam, The Netherlands; United for Metabolic Diseases, The Netherlands.
| | - Janet Koster
- Amsterdam UMC - AMC, Department of Laboratory Medicine, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Merel S Ebberink
- Amsterdam UMC - AMC, Department of Laboratory Medicine, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Pavel Ješina
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague 2, Czech Republic
| | - Jiri Zeman
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague 2, Czech Republic
| | - Lenka Nosková
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague 2, Czech Republic
| | - Stanislav Kmoch
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague 2, Czech Republic
| | - Perrine Devic
- Centre Hospitalier Universitaire de Lyon, CHU Lyon·U 301, Hopital Neurologique, Bron, France
| | - David Cheillan
- Service Biochimie et Biologie Moléculaire Grand Est, UM Pathologies Métaboliques, Erythrocytaires et Dépistage Périnatal, Centre de Biologie et de Pathologie Est, Groupement Hospitalier Est - Hospices Civils de Lyon, Bron Cedex, France
| | - Ronald J A Wanders
- Amsterdam UMC - AMC, Department of Laboratory Medicine, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Amsterdam Reproduction & Development, Amsterdam, The Netherlands; United for Metabolic Diseases, The Netherlands
| | - Sacha Ferdinandusse
- Amsterdam UMC - AMC, Department of Laboratory Medicine, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
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6
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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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7
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Rüttermann M, Gatsogiannis C. Good things come to those who bait: the peroxisomal docking complex. Biol Chem 2023; 404:107-119. [PMID: 36117327 DOI: 10.1515/hsz-2022-0161] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/25/2022] [Indexed: 11/15/2022]
Abstract
Peroxisomal integrity and function are highly dependent on its membrane and soluble (matrix) components. Matrix enzymes are imported post-translationally in a folded or even oligomeric state, via a still mysterious protein translocation mechanism. They are guided to peroxisomes via the Peroxisomal Targeting Signal (PTS) sequences which are recognized by specific cytosolic receptors, Pex5, Pex7 and Pex9. Subsequently, cargo-loaded receptors bind to the docking complex in an initial step, followed by channel formation, cargo-release, receptor-recycling and -quality control. The docking complexes of different species share Pex14 as their core component but differ in composition and oligomeric state of Pex14. Here we review and highlight the latest insights on the structure and function of the peroxisomal docking complex. We summarize differences between yeast and mammals and then we integrate this knowledge into our current understanding of the import machinery.
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Affiliation(s)
- Maximilian Rüttermann
- Institute for Medical Physics and Biophysics and Center for Soft Nanoscience, Westfälische Wilhelms Universität Münster, D-48149 Münster, Germany
| | - Christos Gatsogiannis
- Institute for Medical Physics and Biophysics and Center for Soft Nanoscience, Westfälische Wilhelms Universität Münster, D-48149 Münster, Germany
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8
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Ferreira MJ, Rodrigues TA, Pedrosa AG, Francisco T, Azevedo JE. A Cell-Free In Vitro Import System for Peroxisomal Proteins Containing a Type 2 Targeting Signal (PTS2). Methods Mol Biol 2023; 2643:333-343. [PMID: 36952196 DOI: 10.1007/978-1-0716-3048-8_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Cell-free in vitro systems are invaluable tools to study the molecular mechanisms of protein translocation across biological membranes. We have been using such a strategy to dissect the mechanism of the mammalian peroxisomal matrix protein import machinery. Here, we provide a detailed protocol to import proteins containing a peroxisomal targeting signal type 2 (PTS2) into the organelle. The in vitro system consists of incubating a 35S-labeled reporter protein with a post-nuclear supernatant from rat/mouse liver. At the end of the incubation, the organelle suspensions are generally treated with an aggressive protease to degrade reporter proteins that did not enter peroxisomes, and the organelles are isolated by centrifugation and analyzed by SDS-PAGE and autoradiography. This in vitro system is particularly suited to characterize the functional consequences of PEX5 and PEX7 mutations found in patients affected with a peroxisomal biogenesis disorder.
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Affiliation(s)
- Maria J Ferreira
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Tony A Rodrigues
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Ana G Pedrosa
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Tânia Francisco
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Jorge E Azevedo
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Porto, Portugal.
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal.
- Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal.
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9
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Demers ND, Riccio V, Jo DS, Bhandari S, Law KB, Liao W, Kim C, McQuibban GA, Choe SK, Cho DH, Kim PK. PEX13 prevents pexophagy by regulating ubiquitinated PEX5 and peroxisomal ROS. Autophagy 2023:1-22. [PMID: 36541703 DOI: 10.1080/15548627.2022.2160566] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Peroxisomes are rapidly degraded during amino acid and oxygen deprivation by a type of selective autophagy called pexophagy. However, how damaged peroxisomes are detected and removed from the cell is poorly understood. Recent studies suggest that the peroxisomal matrix protein import machinery may serve double duty as a quality control machinery, where they are directly involved in activating pexophagy. Here, we explored whether any matrix import factors are required to prevent pexophagy, such that their loss designates peroxisomes for degradation. Using gene editing and quantitative fluorescence microscopy on culture cells and a zebrafish model system, we found that PEX13, a component of the peroxisomal matrix import system, is required to prevent the degradation of otherwise healthy peroxisomes. The loss of PEX13 caused an accumulation of ubiquitinated PEX5 on peroxisomes and an increase in peroxisome-dependent reactive oxygen species that coalesce to induce pexophagy. We also found that PEX13 protein level is downregulated to aid in the induction of pexophagy during amino acid starvation. Together, our study points to PEX13 as a novel pexophagy regulator that is modulated to maintain peroxisome homeostasis.Abbreviations: AAA ATPases: ATPases associated with diverse cellular activities; ABCD3: ATP binding cassette subfamily D member; 3ACOX1: acyl-CoA oxidase; 1ACTA1: actin alpha 1, skeletal muscle; ACTB: actin beta; ATG5: autophagy related 5; ATG7: autophagy related 7; ATG12: autophagy related 12; ATG16L1: autophagy related 16 like 1; CAT: catalase; CQ: chloroquine; Dpf: days post fertilization: FBS: fetal bovine serum; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; H2O2: hydrogen peroxide; HA - human influenza hemagglutinin; HBSS: Hanks' Balanced Salt Solution; HCQ; hydroxychloroquine; KANL: lysine alanine asparagine leucine; KO: knockout; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; MEF: mouse embryonic fibroblast; MTOR: mechanistic target of rapamycin kinase; MTORC1: mechanistic target of rapamycin kinase complex 1; MTORC2: mechanistic target of rapamycin kinase complex 2; MYC: MYC proto-oncogene, bHLH transcription factor; MZ: maternal and zygotic; NAC: N-acetyl cysteine; NBR1 - NBR1 autophagy cargo receptor; PBD: peroxisome biogenesis disorder; PBS: phosphate-buffered saline; PEX: peroxisomal biogenesis factor; PTS1: peroxisome targeting sequence 1; RFP: red fluorescent protein; ROS: reactive oxygen speciess; iRNA: short interfering RNA; SKL: serine lysine leucine; SLC25A17/PMP34: solute carrier family 25 member 17; Ub: ubiquitin; USP30: ubiquitin specific peptidase 30.
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Affiliation(s)
- Nicholas D Demers
- Cell Biology Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Victoria Riccio
- Cell Biology Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Doo Sin Jo
- School of Life Sciences, BK21 Four Knu Creative BioResearch Group Kyungpook National University, Republic of Korea
| | - Sushil Bhandari
- Department of Microbiology, Wonkwang University School of Medicine, Iksan, Republic of Korea
| | - Kelsey B Law
- Cell Biology Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Weifang Liao
- Department of Microbiology, Wonkwang University School of Medicine, Iksan, Republic of Korea
| | - Choy Kim
- Department of Microbiology, Wonkwang University School of Medicine, Iksan, Republic of Korea
| | - G Angus McQuibban
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Seong-Kyu Choe
- Department of Microbiology, Wonkwang University School of Medicine, Iksan, Republic of Korea
| | - Dong-Hyung Cho
- School of Life Sciences, BK21 Four Knu Creative BioResearch Group Kyungpook National University, Republic of Korea
| | - Peter K Kim
- Cell Biology Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada.,Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, South Korea
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10
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Wanders RJA, Baes M, Ribeiro D, Ferdinandusse S, Waterham HR. The physiological functions of human peroxisomes. Physiol Rev 2023; 103:957-1024. [PMID: 35951481 DOI: 10.1152/physrev.00051.2021] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Peroxisomes are subcellular organelles that play a central role in human physiology by catalyzing a range of unique metabolic functions. The importance of peroxisomes for human health is exemplified by the existence of a group of usually severe diseases caused by an impairment in one or more peroxisomal functions. Among others these include the Zellweger spectrum disorders, X-linked adrenoleukodystrophy, and Refsum disease. To fulfill their role in metabolism, peroxisomes require continued interaction with other subcellular organelles including lipid droplets, lysosomes, the endoplasmic reticulum, and mitochondria. In recent years it has become clear that the metabolic alliance between peroxisomes and other organelles requires the active participation of tethering proteins to bring the organelles physically closer together, thereby achieving efficient transfer of metabolites. This review intends to describe the current state of knowledge about the metabolic role of peroxisomes in humans, with particular emphasis on the metabolic partnership between peroxisomes and other organelles and the consequences of genetic defects in these processes. We also describe the biogenesis of peroxisomes and the consequences of the multiple genetic defects therein. In addition, we discuss the functional role of peroxisomes in different organs and tissues and include relevant information derived from model systems, notably peroxisomal mouse models. Finally, we pay particular attention to a hitherto underrated role of peroxisomes in viral infections.
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Affiliation(s)
- Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, Amsterdam, The Netherlands
| | - Myriam Baes
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Daniela Ribeiro
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, Amsterdam, The Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, Amsterdam, The Netherlands
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11
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Gao Y, Skowyra ML, Feng P, Rapoport TA. Protein import into peroxisomes occurs through a nuclear pore-like phase. Science 2022; 378:eadf3971. [PMID: 36520918 PMCID: PMC9795577 DOI: 10.1126/science.adf3971] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Peroxisomes are ubiquitous organelles whose dysfunction causes fatal human diseases. Most peroxisomal proteins are imported from the cytosol in a folded state by the soluble receptor PEX5. How folded cargo crosses the membrane is unknown. Here, we show that peroxisomal import is similar to nuclear transport. The peroxisomal membrane protein PEX13 contains a conserved tyrosine (Y)- and glycine (G)-rich YG domain, which forms a selective phase resembling that formed by phenylalanine-glycine (FG) repeats within nuclear pores. PEX13 resides in the membrane in two orientations that oligomerize and suspend the YG meshwork within the lipid bilayer. Purified YG domains form hydrogels into which PEX5 selectively partitions, by using conserved aromatic amino acid motifs, bringing cargo along. The YG meshwork thus forms an aqueous conduit through which PEX5 delivers folded proteins into peroxisomes.
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Affiliation(s)
- Yuan Gao
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Michael L. Skowyra
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Peiqiang Feng
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Tom A. Rapoport
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA.,Corresponding author.
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12
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Skowyra ML, Rapoport TA. PEX5 translocation into and out of peroxisomes drives matrix protein import. Mol Cell 2022; 82:3209-3225.e7. [PMID: 35931083 PMCID: PMC9444985 DOI: 10.1016/j.molcel.2022.07.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/30/2022] [Accepted: 07/08/2022] [Indexed: 12/12/2022]
Abstract
Peroxisomes are ubiquitous organelles whose dysfunction causes fatal human diseases. Most peroxisomal enzymes are imported from the cytosol by the receptor PEX5, which interacts with a docking complex in the peroxisomal membrane and then returns to the cytosol after monoubiquitination by a membrane-embedded ubiquitin ligase. The mechanism by which PEX5 shuttles between cytosol and peroxisomes and releases cargo inside the lumen is unclear. Here, we use Xenopus egg extract to demonstrate that PEX5 accompanies cargo completely into the lumen, utilizing WxxxF/Y motifs near its N terminus that bind a lumenal domain of the docking complex. PEX5 recycling is initiated by an amphipathic helix that binds to the lumenal side of the ubiquitin ligase. The N terminus then emerges in the cytosol for monoubiquitination. Finally, PEX5 is extracted from the lumen, resulting in the unfolding of the receptor and cargo release. Our results reveal the unique mechanism by which PEX5 ferries proteins into peroxisomes.
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Affiliation(s)
- Michael L Skowyra
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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13
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Borgia P, Baldassari S, Pedemonte N, Alkhunaizi E, D'Onofrio G, Tortora D, Calì E, Scudieri P, Balagura G, Musante I, Diana MC, Pedemonte M, Vari MS, Iacomino M, Riva A, Chimenz R, Mangano GD, Mohammadi MH, Toosi MB, Ashrafzadeh F, Imannezhad S, Karimiani EG, Accogli A, Schiaffino MC, Maghnie M, Soler MA, Echiverri K, Abrams CK, Striano P, Fortuna S, Maroofian R, Houlden H, Zara F, Fiorillo C, Salpietro V. Genotype-phenotype correlations and disease mechanisms in PEX13-related Zellweger spectrum disorders. Orphanet J Rare Dis 2022; 17:286. [PMID: 35854306 PMCID: PMC9295491 DOI: 10.1186/s13023-022-02415-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/26/2022] [Indexed: 11/26/2022] Open
Abstract
Background Pathogenic variants in PEX-genes can affect peroxisome assembly and function and cause Zellweger spectrum disorders (ZSDs), characterized by variable phenotypes in terms of disease severity, age of onset and clinical presentations. So far, defects in at least 15 PEX-genes have been implicated in Mendelian diseases, but in some of the ultra-rare ZSD subtypes genotype–phenotype correlations and disease mechanisms remain elusive. Methods We report five families carrying biallelic variants in PEX13. The identified variants were initially evaluated by using a combination of computational approaches. Immunofluorescence and complementation studies on patient-derived fibroblasts were performed in two patients to investigate the cellular impact of the identified mutations. Results Three out of five families carried a recurrent p.Arg294Trp non-synonymous variant. Individuals affected with PEX13-related ZSD presented heterogeneous clinical features, including hypotonia, developmental regression, hearing/vision impairment, progressive spasticity and brain leukodystrophy. Computational predictions highlighted the involvement of the Arg294 residue in PEX13 homodimerization, and the analysis of blind docking predicted that the p.Arg294Trp variant alters the formation of dimers, impairing the stability of the PEX13/PEX14 translocation module. Studies on muscle tissues and patient-derived fibroblasts revealed biochemical alterations of mitochondrial function and identified mislocalized mitochondria and a reduced number of peroxisomes with abnormal PEX13 concentration. Conclusions This study expands the phenotypic and mutational spectrum of PEX13-related ZSDs and also highlight a variety of disease mechanisms contributing to PEX13-related clinical phenotypes, including the emerging contribution of secondary mitochondrial dysfunction to the pathophysiology of ZSDs.
Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02415-5.
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Affiliation(s)
- Paola Borgia
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy.,Pediatric Neurology and Muscular Diseases Unit, IRCCS Giannina Gaslini Institute, 16147, Genoa, Italy
| | - Simona Baldassari
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Nicoletta Pedemonte
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Ebba Alkhunaizi
- Department of Genetics, North York General Hospital, University of Toronto, Toronto, ON, Canada
| | - Gianluca D'Onofrio
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy.,Pediatric Neurology and Muscular Diseases Unit, IRCCS Giannina Gaslini Institute, 16147, Genoa, Italy
| | - Domenico Tortora
- Neuroradiology Unit, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Elisa Calì
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Paolo Scudieri
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Ganna Balagura
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy
| | - Ilaria Musante
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Maria Cristina Diana
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Giannina Gaslini Institute, 16147, Genoa, Italy
| | - Marina Pedemonte
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Giannina Gaslini Institute, 16147, Genoa, Italy
| | - Maria Stella Vari
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Giannina Gaslini Institute, 16147, Genoa, Italy
| | - Michele Iacomino
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Antonella Riva
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy.,Pediatric Neurology and Muscular Diseases Unit, IRCCS Giannina Gaslini Institute, 16147, Genoa, Italy
| | - Roberto Chimenz
- Unit of Pediatric Nephrology and Dialysis, Department of Human Pathology in Adult and Developmental Age "Gaetano Barresi", University of Messina, Via Consolare Valeria 1, 98125, Messina, Italy
| | - Giuseppe D Mangano
- Department Pro.M.I.S.E. "G. D'Alessandro", University of Palermo, Palermo, Italy
| | | | - Mehran Beiraghi Toosi
- Pediatric Neurology Department, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farah Ashrafzadeh
- Department of Pediatrics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Shima Imannezhad
- Pediatric Neurology Department, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St. George's, University of London, Cranmer Terrace, London, SW170RE, UK.,Innovative Medical Research Center, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Andrea Accogli
- Division of Medical Genetics, Department of Specialized Medicine, Montreal Children's Hospital, McGill University Health Centre (MUHC), Montreal, QC, H4A 3J1, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Maria Cristina Schiaffino
- Pediatric Clinic and Endocrinology Unit, Department of General and Specialist Pediatric Sciences, University of Genoa, 16147, Genoa, Italy
| | - Mohamad Maghnie
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy.,Pediatric Clinic and Endocrinology Unit, Department of General and Specialist Pediatric Sciences, University of Genoa, 16147, Genoa, Italy
| | - Miguel Angel Soler
- Computational Modelling of Nanoscale and Biophysical Systems Laboratory, Italian Institute of Technology, 16163, Genoa, Italy
| | - Karl Echiverri
- Departments of Neurology and Ophthalmology, University of Kentucky, Lexington, 40506, USA
| | - Charles K Abrams
- Department of Neurology and Rehabilitation, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy.,Pediatric Neurology and Muscular Diseases Unit, IRCCS Giannina Gaslini Institute, 16147, Genoa, Italy
| | - Sara Fortuna
- Computational Modelling of Nanoscale and Biophysical Systems Laboratory, Italian Institute of Technology, 16163, Genoa, Italy.,Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34134, Trieste, Italy
| | - Reza Maroofian
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy.,Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, 16147, Genoa, Italy
| | - Chiara Fiorillo
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132, Genoa, Italy. .,Pediatric Neurology and Muscular Diseases Unit, IRCCS Giannina Gaslini Institute, 16147, Genoa, Italy.
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK. .,Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, 67100, L'Aquila, Italy.
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14
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Insights into the Structure and Function of the Pex1/Pex6 AAA-ATPase in Peroxisome Homeostasis. Cells 2022; 11:cells11132067. [PMID: 35805150 PMCID: PMC9265785 DOI: 10.3390/cells11132067] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/25/2022] [Accepted: 06/26/2022] [Indexed: 02/01/2023] Open
Abstract
The AAA-ATPases Pex1 and Pex6 are required for the formation and maintenance of peroxisomes, membrane-bound organelles that harbor enzymes for specialized metabolism. Together, Pex1 and Pex6 form a heterohexameric AAA-ATPase capable of unfolding substrate proteins via processive threading through a central pore. Here, we review the proposed roles for Pex1/Pex6 in peroxisome biogenesis and degradation, discussing how the unfolding of potential substrates contributes to peroxisome homeostasis. We also consider how advances in cryo-EM, computational structure prediction, and mechanisms of related ATPases are improving our understanding of how Pex1/Pex6 converts ATP hydrolysis into mechanical force. Since mutations in PEX1 and PEX6 cause the majority of known cases of peroxisome biogenesis disorders such as Zellweger syndrome, insights into Pex1/Pex6 structure and function are important for understanding peroxisomes in human health and disease.
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15
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Verner Z, Žárský V, Le T, Narayanasamy RK, Rada P, Rozbeský D, Makki A, Belišová D, Hrdý I, Vancová M, Lender C, König C, Bruchhaus I, Tachezy J. Anaerobic peroxisomes in Entamoeba histolytica metabolize myo-inositol. PLoS Pathog 2021; 17:e1010041. [PMID: 34780573 PMCID: PMC8629394 DOI: 10.1371/journal.ppat.1010041] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 11/29/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022] Open
Abstract
Entamoeba histolytica is believed to be devoid of peroxisomes, like most anaerobic protists. In this work, we provided the first evidence that peroxisomes are present in E. histolytica, although only seven proteins responsible for peroxisome biogenesis (peroxins) were identified (Pex1, Pex6, Pex5, Pex11, Pex14, Pex16, and Pex19). Targeting matrix proteins to peroxisomes is reduced to the PTS1-dependent pathway mediated via the soluble Pex5 receptor, while the PTS2 receptor Pex7 is absent. Immunofluorescence microscopy showed that peroxisomal markers (Pex5, Pex14, Pex16, Pex19) are present in vesicles distinct from mitosomes, the endoplasmic reticulum, and the endosome/phagosome system, except Pex11, which has dual localization in peroxisomes and mitosomes. Immunoelectron microscopy revealed that Pex14 localized to vesicles of approximately 90-100 nm in diameter. Proteomic analyses of affinity-purified peroxisomes and in silico PTS1 predictions provided datasets of 655 and 56 peroxisomal candidates, respectively; however, only six proteins were shared by both datasets, including myo-inositol dehydrogenase (myo-IDH). Peroxisomal NAD-dependent myo-IDH appeared to be a dimeric enzyme with high affinity to myo-inositol (Km 0.044 mM) and can utilize also scyllo-inositol, D-glucose and D-xylose as substrates. Phylogenetic analyses revealed that orthologs of myo-IDH with PTS1 are present in E. dispar, E. nutalli and E. moshkovskii but not in E. invadens, and form a monophyletic clade of mostly peroxisomal orthologs with free-living Mastigamoeba balamuthi and Pelomyxa schiedti. The presence of peroxisomes in E. histolytica and other archamoebae breaks the paradigm of peroxisome absence in anaerobes and provides a new potential target for the development of antiparasitic drugs.
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Affiliation(s)
- Zdeněk Verner
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vojtěch Žárský
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Tien Le
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ravi Kumar Narayanasamy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Petr Rada
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Daniel Rozbeský
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Abhijith Makki
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Darja Belišová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Marie Vancová
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, Ceske Budejovice, Czech Republic
| | - Corinna Lender
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Constantin König
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Iris Bruchhaus
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
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16
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Park WY, Park J, Lee S, Song G, Nam IK, Ahn KS, Choe SK, Um JY. PEX13 is required for thermogenesis of white adipose tissue in cold-exposed mice. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1867:159046. [PMID: 34517131 DOI: 10.1016/j.bbalip.2021.159046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 11/28/2022]
Abstract
Non-shivering thermogenesis (NST) is a heat generating process controlled by the mitochondria of brown adipose tissue (BAT). In the recent decade, 'functionally' acting brown adipocytes in white adipose tissue (WAT) has been identified as well: the so-called process of the 'browning' of WAT. While the importance of uncoupling protein 1 (UCP1)-oriented mitochondrial activation has been intensely studied, the role of peroxisomes during the browning of white adipocytes is poorly understood. Here, we assess the change in peroxisomal membrane proteins, or peroxins (PEXs), during cold stimulation and importantly, the role of PEX13 in the cold-induced remodeling of white adipocytes. PEX13, a protein that originally functions as a docking factor and is involved in protein import into peroxisome matrix, was highly increased during cold-induced recruitment of beige adipocytes within the inguinal WAT of C57BL/6 mice. Moreover, beige-induced 3 T3-L1 adipocytes and stromal vascular fraction (SVF) cells by exposure to the peroxisome proliferator-activated receptor gamma (PPARγ) agonist rosiglitazone showed a significant increase in mitochondrial thermogenic factors along with peroxisomal proteins including PEX13, and these were confirmed in SVF cells with the beta 3 adrenergic receptor (β3AR)-selective agonist CL316,243. To verify the relevance of PEX13, we used the RNA silencing method targeting the Pex13 gene and evaluated the subsequent beige development in SVF cells. Interestingly, siPex13 treatment suppressed expression of thermogenic proteins such as UCP1 and PPARγ coactivator 1 alpha (PGC1α). Overall, our data provide evidence supporting the role of peroxisomal proteins, in particular PEX13, during beige remodeling of white adipocytes.
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Affiliation(s)
- Woo Yong Park
- Department of Science in Korean Medicine, Graduate School, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-Gu, Seoul 02447, Republic of Korea
| | - Jinbong Park
- Department of Pharmacology, College of Korean Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; Basic Research Laboratory for Comorbidity Regulation and Department of Comorbodity Research, KyungHee Institute of Convergence Korean Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Sujin Lee
- Department of Science in Korean Medicine, Graduate School, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-Gu, Seoul 02447, Republic of Korea
| | - Gahee Song
- Department of Science in Korean Medicine, Graduate School, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-Gu, Seoul 02447, Republic of Korea
| | - In-Koo Nam
- Department of Microbiology, Wonkwang University School of Medicine, Iksan 54538, Republic of Korea
| | - Kwang Seok Ahn
- Department of Science in Korean Medicine, Graduate School, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-Gu, Seoul 02447, Republic of Korea; Basic Research Laboratory for Comorbidity Regulation and Department of Comorbodity Research, KyungHee Institute of Convergence Korean Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Seong-Kyu Choe
- Department of Microbiology, Wonkwang University School of Medicine, Iksan 54538, Republic of Korea
| | - Jae-Young Um
- Department of Pharmacology, College of Korean Medicine, Kyung Hee University, Seoul 02447, Republic of Korea; Basic Research Laboratory for Comorbidity Regulation and Department of Comorbodity Research, KyungHee Institute of Convergence Korean Medicine, Kyung Hee University, Seoul 02447, Korea..
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17
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Jansen RLM, Santana-Molina C, van den Noort M, Devos DP, van der Klei IJ. Comparative Genomics of Peroxisome Biogenesis Proteins: Making Sense of the PEX Proteins. Front Cell Dev Biol 2021; 9:654163. [PMID: 34095119 PMCID: PMC8172628 DOI: 10.3389/fcell.2021.654163] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/21/2021] [Indexed: 11/29/2022] Open
Abstract
PEX genes encode proteins involved in peroxisome biogenesis and proliferation. Using a comparative genomics approach, we clarify the evolutionary relationships between the 37 known PEX proteins in a representative set of eukaryotes, including all common model organisms, pathogenic unicellular eukaryotes and human. A large number of previously unknown PEX orthologs were identified. We analyzed all PEX proteins, their conservation and domain architecture and defined the core set of PEX proteins that is required to make a peroxisome. The molecular processes in peroxisome biogenesis in different organisms were put into context, showing that peroxisomes are not static organelles in eukaryotic evolution. Organisms that lack peroxisomes still contain a few PEX proteins, which probably play a role in alternative processes. Finally, the relationships between PEX proteins of two large families, the Pex11 and Pex23 families, were analyzed, thereby contributing to the understanding of their complicated and sometimes incorrect nomenclature. We provide an exhaustive overview of this important eukaryotic organelle.
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Affiliation(s)
- Renate L M Jansen
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Carlos Santana-Molina
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Seville, Spain
| | - Marco van den Noort
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Seville, Spain
| | - Ida J van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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18
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Gaussmann S, Gopalswamy M, Eberhardt M, Reuter M, Zou P, Schliebs W, Erdmann R, Sattler M. Membrane Interactions of the Peroxisomal Proteins PEX5 and PEX14. Front Cell Dev Biol 2021; 9:651449. [PMID: 33937250 PMCID: PMC8086558 DOI: 10.3389/fcell.2021.651449] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/11/2021] [Indexed: 11/17/2022] Open
Abstract
Human PEX5 and PEX14 are essential components of the peroxisomal translocon, which mediates import of cargo enzymes into peroxisomes. PEX5 is a soluble receptor for cargo enzymes comprised of an N-terminal intrinsically disordered domain (NTD) and a C-terminal tetratricopeptide (TPR) domain, which recognizes peroxisomal targeting signal 1 (PTS1) peptide motif in cargo proteins. The PEX5 NTD harbors multiple WF peptide motifs (WxxxF/Y or related motifs) that are recognized by a small globular domain in the NTD of the membrane-associated protein PEX14. How the PEX5 or PEX14 NTDs bind to the peroxisomal membrane and how the interaction between the two proteins is modulated at the membrane is unknown. Here, we characterize the membrane interactions of the PEX5 NTD and PEX14 NTD in vitro by membrane mimicking bicelles and nanodiscs using NMR spectroscopy and isothermal titration calorimetry. The PEX14 NTD weakly interacts with membrane mimicking bicelles with a surface that partially overlaps with the WxxxF/Y binding site. The PEX5 NTD harbors multiple interaction sites with the membrane that involve a number of amphipathic α-helical regions, which include some of the WxxxF/Y-motifs. The partially formed α-helical conformation of these regions is stabilized in the presence of bicelles. Notably, ITC data show that the interaction between the PEX5 and PEX14 NTDs is largely unaffected by the presence of the membrane. The PEX5/PEX14 interaction exhibits similar free binding enthalpies, where reduced binding enthalpy in the presence of bicelles is compensated by a reduced entropy loss. This demonstrates that docking of PEX5 to PEX14 at the membrane does not reduce the overall binding affinity between the two proteins, providing insights into the initial phase of PEX5-PEX14 docking in the assembly of the peroxisome translocon.
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Affiliation(s)
- Stefan Gaussmann
- Bavarian NMR Center, Department Chemie, Technische Universität München, Munich, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Mohanraj Gopalswamy
- Bavarian NMR Center, Department Chemie, Technische Universität München, Munich, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Maike Eberhardt
- Bavarian NMR Center, Department Chemie, Technische Universität München, Munich, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Maren Reuter
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Peijian Zou
- Bavarian NMR Center, Department Chemie, Technische Universität München, Munich, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Michael Sattler
- Bavarian NMR Center, Department Chemie, Technische Universität München, Munich, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
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19
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Dahan N, Francisco T, Falter C, Rodrigues T, Kalel V, Kunze M, Hansen T, Schliebs W, Erdmann R. Current advances in the function and biogenesis of peroxisomes and their roles in health and disease. Histochem Cell Biol 2021; 155:513-524. [PMID: 33818645 PMCID: PMC8062356 DOI: 10.1007/s00418-021-01982-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2021] [Indexed: 12/20/2022]
Affiliation(s)
- Noa Dahan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tania Francisco
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Christian Falter
- Plant Biochemistry and Infection Biology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
| | - Tony Rodrigues
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Vishal Kalel
- Department System Biochemistry, Institute of Biochemistry and Pathobiochemistry, Medical Faculty, Ruhr-University of Bochum, Universitätstr.150, 44780, Bochum, Germany
| | - Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria
| | - Tobias Hansen
- Department System Biochemistry, Institute of Biochemistry and Pathobiochemistry, Medical Faculty, Ruhr-University of Bochum, Universitätstr.150, 44780, Bochum, Germany
| | - Wolfgang Schliebs
- Department System Biochemistry, Institute of Biochemistry and Pathobiochemistry, Medical Faculty, Ruhr-University of Bochum, Universitätstr.150, 44780, Bochum, Germany
| | - Ralf Erdmann
- Department System Biochemistry, Institute of Biochemistry and Pathobiochemistry, Medical Faculty, Ruhr-University of Bochum, Universitätstr.150, 44780, Bochum, Germany.
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20
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Yamashita K, Tamura S, Honsho M, Yada H, Yagita Y, Kosako H, Fujiki Y. Mitotic phosphorylation of Pex14p regulates peroxisomal import machinery. J Cell Biol 2021; 219:152047. [PMID: 32854114 PMCID: PMC7659713 DOI: 10.1083/jcb.202001003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/28/2020] [Accepted: 07/13/2020] [Indexed: 01/27/2023] Open
Abstract
Peroxisomal matrix proteins are imported into peroxisomes via membrane-bound docking/translocation machinery. One central component of this machinery is Pex14p, a peroxisomal membrane protein involved in the docking of Pex5p, the receptor for peroxisome targeting signal type 1 (PTS1). Studies in several yeast species have shown that Pex14p is phosphorylated in vivo, whereas no function has been assigned to Pex14p phosphorylation in yeast and mammalian cells. Here, we investigated peroxisomal protein import and its dynamics in mitotic mammalian cells. In mitotically arrested cells, Pex14p is phosphorylated at Ser-232, resulting in a lower import efficiency of catalase, but not the majority of proteins including canonical PTS1 proteins. Conformational change induced by the mitotic phosphorylation of Pex14p more likely increases homomeric interacting affinity and suppresses topological change of its N-terminal part, thereby giving rise to the retardation of Pex5p export in mitotic cells. Taken together, these data show that mitotic phosphorylation of Pex14p and consequent suppression of catalase import are a mechanism of protecting DNA upon nuclear envelope breakdown at mitosis.
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Affiliation(s)
- Koichiro Yamashita
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | | | - Masanori Honsho
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.,Institute of Rheological Functions of Food, Fukuoka, Japan
| | - Hiroto Yada
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Yuichi Yagita
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, Japan
| | - Yukio Fujiki
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.,Institute of Rheological Functions of Food, Fukuoka, Japan
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21
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Towards the molecular architecture of the peroxisomal receptor docking complex. Proc Natl Acad Sci U S A 2020; 117:33216-33224. [PMID: 33323485 DOI: 10.1073/pnas.2009502117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Import of yeast peroxisomal matrix proteins is initiated by cytosolic receptors, which specifically recognize and bind the respective cargo proteins. At the peroxisomal membrane, the cargo-loaded receptor interacts with the docking protein Pex14p that is tightly associated with Pex17p. Previous data suggest that this interaction triggers the formation of an import pore for further translocation of the cargo. The mechanistic principles, however, are unclear, mainly because structures of higher-order assemblies are still lacking. Here, using an integrative approach, we provide the structural characterization of the major components of the peroxisomal docking complex Pex14p/Pex17p, in a native bilayer environment, and reveal its subunit organization. Our data show that three copies of Pex14p and a single copy of Pex17p assemble to form a 20-nm rod-like particle. The different subunits are arranged in a parallel manner, showing interactions along their complete sequences and providing receptor binding sites on both membrane sides. The long rod facing the cytosol is mainly formed by the predicted coiled-coil domains of Pex14p and Pex17p, possibly providing the necessary structural support for the formation of the import pore. Further implications of Pex14p/Pex17p for formation of the peroxisomal translocon are discussed.
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22
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Covill-Cooke C, Toncheva VS, Kittler JT. Regulation of peroxisomal trafficking and distribution. Cell Mol Life Sci 2020; 78:1929-1941. [PMID: 33141311 PMCID: PMC7966214 DOI: 10.1007/s00018-020-03687-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/02/2020] [Accepted: 10/19/2020] [Indexed: 12/18/2022]
Abstract
Peroxisomes are organelles that perform a wide range of essential metabolic processes. To ensure that peroxisomes are optimally positioned in the cell, they must be transported by both long- and short-range trafficking events in response to cellular needs. Here, we review our current understanding of the mechanisms by which the cytoskeleton and organelle contact sites alter peroxisomal distribution. Though the focus of the review is peroxisomal transport in mammalian cells, findings from flies and fungi are used for comparison and to inform the gaps in our understanding. Attention is given to the apparent overlap in regulatory mechanisms for mitochondrial and peroxisomal trafficking, along with the recently discovered role of the mitochondrial Rho-GTPases, Miro, in peroxisomal dynamics. Moreover, we outline and discuss the known pathological and pharmacological conditions that perturb peroxisomal positioning. We conclude by highlighting several gaps in our current knowledge and suggest future directions that require attention.
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Affiliation(s)
| | - Viktoriya S Toncheva
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, WC1E 6BT, UK
| | - Josef T Kittler
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, WC1E 6BT, UK.
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23
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Uzor NE, Scheihing DM, Kim GS, Moruno-Manchon JF, Zhu L, Reynolds CR, Stephenson JM, Holmes A, McCullough LD, Tsvetkov AS. Aging lowers PEX5 levels in cortical neurons in male and female mouse brains. Mol Cell Neurosci 2020; 107:103536. [PMID: 32777345 PMCID: PMC7484460 DOI: 10.1016/j.mcn.2020.103536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/14/2020] [Accepted: 08/03/2020] [Indexed: 01/10/2023] Open
Abstract
Peroxisomes exist in nearly every cell, oxidizing fats, synthesizing lipids and maintaining redox balance. As the brain ages, multiple pathways are negatively affected, but it is currently unknown if peroxisomal proteins are affected by aging in the brain. While recent studies have investigated a PEX5 homolog in aging C. elegans models and found that it is reduced in aging, it is unclear if PEX5, a mammalian peroxisomal protein that plays a role in peroxisomal homeostasis and degradation, is affected in the aging brain. To answer this question, we first determined the amount of PEX5, in brain homogenates from young (3 months) and aged (26 through 32+ months of age) wild-type mice of both sexes. PEX5 protein was decreased in aged male brains, but this reduction was not significant in female brains. RNAScope and real-time qPCR analyses showed that Pex5 mRNA was also reduced in aged male brain cortices, but not in females. Immunohistochemistry assays of cortical neurons in young and aged male brains showed that the amount of neuronal PEX5 was reduced in aged male brains. Cortical neurons in aged female mice also had reduced PEX5 levels in comparison to younger female mice. In conclusion, total PEX5 levels and Pex5 gene expression both decrease with age in male brains, and neuronal PEX5 levels lower in an age-dependent manner in the cortices of animals of both sexes.
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Affiliation(s)
- Ndidi-Ese Uzor
- University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Department of Neurology, the University of Texas McGovern Medical School at Houston, Houston 77030, TX, USA
| | - Diego Morales Scheihing
- Department of Neurology, the University of Texas McGovern Medical School at Houston, Houston 77030, TX, USA
| | - Gab Seok Kim
- Department of Neurology, the University of Texas McGovern Medical School at Houston, Houston 77030, TX, USA
| | - Jose Felix Moruno-Manchon
- Department of Neurology, the University of Texas McGovern Medical School at Houston, Houston 77030, TX, USA
| | - Liang Zhu
- Biostatistics and Epidemiology Research Design, University of Texas Health Science Center at Houston, Houston 77030, TX, USA
| | - Caroline R Reynolds
- Department of Neurology, the University of Texas McGovern Medical School at Houston, Houston 77030, TX, USA
| | - Jessica M Stephenson
- Department of Neurology, the University of Texas McGovern Medical School at Houston, Houston 77030, TX, USA
| | - Aleah Holmes
- Department of Neurology, the University of Texas McGovern Medical School at Houston, Houston 77030, TX, USA
| | - Louise D McCullough
- University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Department of Neurology, the University of Texas McGovern Medical School at Houston, Houston 77030, TX, USA; UTHealth Consortium on Aging, the University of Texas McGovern Medical School, Houston 77030, TX, USA
| | - Andrey S Tsvetkov
- University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Department of Neurology, the University of Texas McGovern Medical School at Houston, Houston 77030, TX, USA; UTHealth Consortium on Aging, the University of Texas McGovern Medical School, Houston 77030, TX, USA.
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24
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Partial proteolysis improves the identification of the extracellular segments of transmembrane proteins by surface biotinylation. Sci Rep 2020; 10:8880. [PMID: 32483232 PMCID: PMC7264363 DOI: 10.1038/s41598-020-65831-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/08/2020] [Indexed: 01/11/2023] Open
Abstract
Transmembrane proteins (TMP) play a crucial role in several physiological processes. Despite their importance and diversity, only a few TMP structures have been determined by high-resolution protein structure characterization methods so far. Due to the low number of determined TMP structures, the parallel development of various bioinformatics and experimental methods was necessary for their topological characterization. The combination of these methods is a powerful approach in the determination of TMP topology as in the Constrained Consensus TOPology prediction. To support the prediction, we previously developed a high-throughput topology characterization method based on primary amino group-labelling that is still limited in identifying all TMPs and their extracellular segments on the surface of a particular cell type. In order to generate more topology information, a new step, a partial proteolysis of the cell surface has been introduced to our method. This step results in new primary amino groups in the proteins that can be biotinylated with a membrane-impermeable agent while the cells still remain intact. Pre-digestion also promotes the emergence of modified peptides that are more suitable for MS/MS analysis. The modified sites can be utilized as extracellular constraints in topology predictions and may contribute to the refined topology of these proteins.
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25
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Passmore JB, Carmichael RE, Schrader TA, Godinho LF, Ferdinandusse S, Lismont C, Wang Y, Hacker C, Islinger M, Fransen M, Richards DM, Freisinger P, Schrader M. Mitochondrial fission factor (MFF) is a critical regulator of peroxisome maturation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118709. [PMID: 32224193 PMCID: PMC7262603 DOI: 10.1016/j.bbamcr.2020.118709] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 02/21/2020] [Accepted: 03/24/2020] [Indexed: 12/14/2022]
Abstract
Peroxisomes are highly dynamic subcellular compartments with important functions in lipid and ROS metabolism. Impaired peroxisomal function can lead to severe metabolic disorders with developmental defects and neurological abnormalities. Recently, a new group of disorders has been identified, characterised by defects in the membrane dynamics and division of peroxisomes rather than by loss of metabolic functions. However, the contribution of impaired peroxisome plasticity to the pathophysiology of those disorders is not well understood. Mitochondrial fission factor (MFF) is a key component of both the peroxisomal and mitochondrial division machinery. Patients with MFF deficiency present with developmental and neurological abnormalities. Peroxisomes (and mitochondria) in patient fibroblasts are highly elongated as a result of impaired organelle division. The majority of studies into MFF-deficiency have focused on mitochondrial dysfunction, but the contribution of peroxisomal alterations to the pathophysiology is largely unknown. Here, we show that MFF deficiency does not cause alterations to overall peroxisomal biochemical function. However, loss of MFF results in reduced import-competency of the peroxisomal compartment and leads to the accumulation of pre-peroxisomal membrane structures. We show that peroxisomes in MFF-deficient cells display alterations in peroxisomal redox state and intra-peroxisomal pH. Removal of elongated peroxisomes through induction of autophagic processes is not impaired. A mathematical model describing key processes involved in peroxisome dynamics sheds further light into the physical processes disturbed in MFF-deficient cells. The consequences of our findings for the pathophysiology of MFF-deficiency and related disorders with impaired peroxisome plasticity are discussed. Peroxisomes are highly elongated in cells from patients lacking fission factor MFF. Peroxisomal proteins are not uniformly distributed in highly elongated peroxisomes. Peroxisomal metabolism is unaltered in MFF-deficient patients. Peroxisomal elongations are stabilised through interaction with microtubules. Highly elongated peroxisomes are not spared from degradation.
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Affiliation(s)
| | | | | | | | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centre, University of Amsterdam, the Netherlands
| | - Celien Lismont
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Yunhong Wang
- Institute of Neuroanatomy, Medical Faculty Manheim, University of Heidelberg, Mannheim, Germany
| | | | - Markus Islinger
- Institute of Neuroanatomy, Medical Faculty Manheim, University of Heidelberg, Mannheim, Germany
| | - Marc Fransen
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | | | - Peter Freisinger
- Department of Pediatrics, Kreiskliniken Reutlingen, Reutlingen, Germany
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26
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Crowe LP, Wilkinson CL, Nicholson KR, Morris MT. Trypanosoma brucei Pex13.2 Is an Accessory Peroxin That Functions in the Import of Peroxisome Targeting Sequence Type 2 Proteins and Localizes to Subdomains of the Glycosome. mSphere 2020; 5:e00744-19. [PMID: 32075879 PMCID: PMC7031615 DOI: 10.1128/msphere.00744-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/30/2020] [Indexed: 01/30/2023] Open
Abstract
Kinetoplastid parasites, including Trypanosoma brucei, Trypanosoma cruzi, and Leishmania, harbor unique organelles known as glycosomes, which are evolutionarily related to peroxisomes. Glycosome/peroxisome biogenesis is mediated by proteins called peroxins that facilitate organelle formation, proliferation, and degradation and import of proteins housed therein. Import of matrix proteins occurs via one of two pathways that are dictated by their peroxisome targeting sequence (PTS). In PTS1 import, a C-terminal tripeptide sequence, most commonly SKL, is recognized by the soluble receptor Pex5. In PTS2 import, a less conserved N-terminal sequence is recognized by Pex7. The soluble receptors deliver their cargo to the import channel consisting minimally of Pex13 and Pex14. While much of the import process is conserved, kinetoplastids are the only organisms to have two Pex13s, Pex13.1 and Pex13.2. It is unclear why trypanosomes require two Pex13s when one is sufficient for most eukaryotes. To interrogate the role of Pex13.2, we have employed biochemical approaches to partially resolve the composition of the Pex13/Pex14 import complexes in T. brucei and characterized glycosome morphology and protein import in Pex13.2-deficient parasites. Here, we show that Pex13.2 is an integral glycosome membrane protein that interacts with Pex13.1 and Pex14. The N terminus of Pex13.2 faces the cytoplasmic side of the membrane, where it can facilitate interactions required for protein import. Two-dimensional gel electrophoresis revealed three glycosome membrane complexes containing combinations of Pex13.1, Pex13.2, and Pex14. The silencing of Pex13.2 resulted in parasites with fewer, larger glycosomes and disrupted glycosome protein import, suggesting the protein is involved in glycosome biogenesis as well as protein import. Furthermore, superresolution microscopy demonstrated that Pex13.2 localizes to discrete foci in the glycosome periphery, indicating that the glycosome periphery is not homogenous.IMPORTANCETrypanosoma brucei causes human African trypanosomiasis and a wasting disease called Nagana in livestock. Current treatments are expensive, toxic, and difficult to administer. Because of this, the search for new drug targets is essential. T. brucei has glycosomes that are essential to parasite survival; however, our ability to target them in drug development is hindered by our lack of understanding about how these organelles are formed and maintained. This work forwards our understanding of how the parasite-specific protein Pex13.2 functions in glycosome protein import and lays the foundation for future studies focused on blocking Pex13.2 function, which would be lethal to bloodstream-form parasites that reside in the mammalian bloodstream.
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Affiliation(s)
- Logan P Crowe
- Eukaryotic Innovations Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Christina L Wilkinson
- Eukaryotic Innovations Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Kathleen R Nicholson
- Eukaryotic Innovations Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Meredith T Morris
- Eukaryotic Innovations Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
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27
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Abstract
Blobel and coworkers discovered in 1978 that peroxisomal proteins are synthesized on free ribosomes in the cytosol and thus provided the grounds for the conception of peroxisomes as self-containing organelles. Peroxisomes are highly adaptive and versatile organelles carrying out a wide variety of metabolic functions. A striking feature of the peroxisomal import machinery is that proteins can traverse the peroxisomal membrane in a folded and even oligomeric state via cycling receptors. We outline essential steps of peroxisomal matrix protein import, from targeting of the proteins to the peroxisomal membrane, their translocation via transient pores and export of the corresponding cycling import receptors with emphasis on the situation in yeast. Peroxisomes can contribute to the adaptation of cells to different environmental conditions. This is realized by changes in metabolic functions and thus the enzyme composition of the organelles is adopted according to the cellular needs. In recent years, it turned out that this organellar diversity is based on an elaborate regulation of gene expression and peroxisomal protein import. The latter is in the focus of this review that summarizes our knowledge on the composition and function of the peroxisomal protein import machinery with emphasis on novel alternative protein import pathways.
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Affiliation(s)
- Thomas Walter
- Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr-University Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Ralf Erdmann
- Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr-University Bochum, Universitätsstr. 150, 44780, Bochum, Germany.
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28
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Kunze M. The type-2 peroxisomal targeting signal. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1867:118609. [PMID: 31751594 DOI: 10.1016/j.bbamcr.2019.118609] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/08/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022]
Abstract
The type-2 peroxisomal targeting signal (PTS2) is one of two peptide motifs destining soluble proteins for peroxisomes. This signal acts as amphiphilic α-helix exposing the side chains of all conserved residues to the same side. PTS2 motifs are recognized by a bipartite protein complex consisting of the receptor PEX7 and a co-receptor. Cargo-loaded receptor complexes are translocated across the peroxisomal membrane by a transient pore and inside peroxisomes, cargo proteins are released and processed in many, but not all species. The components of the bipartite receptor are re-exported into the cytosol by a ubiquitin-mediated and ATP-driven export mechanism. Structurally, PTS2 motifs resemble other N-terminal targeting signals, whereas the functional relation to the second peroxisomal targeting signal (PTS1) is unclear. Although only a few PTS2-carrying proteins are known in humans, subjects lacking a functional import mechanism for these proteins suffer from the severe inherited disease rhizomelic chondrodysplasia punctata.
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Affiliation(s)
- Markus Kunze
- Medical University of Vienna, Center for Brain Research, Department of Pathobiology of the Nervous System, Spitalgasse 4, 1090 Vienna, Austria.
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29
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A Mechanistic Perspective on PEX1 and PEX6, Two AAA+ Proteins of the Peroxisomal Protein Import Machinery. Int J Mol Sci 2019; 20:ijms20215246. [PMID: 31652724 PMCID: PMC6862443 DOI: 10.3390/ijms20215246] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 12/11/2022] Open
Abstract
In contrast to many protein translocases that use ATP or GTP hydrolysis as the driving force to transport proteins across biological membranes, the peroxisomal matrix protein import machinery relies on a regulated self-assembly mechanism for this purpose and uses ATP hydrolysis only to reset its components. The ATP-dependent protein complex in charge of resetting this machinery—the Receptor Export Module (REM)—comprises two members of the “ATPases Associated with diverse cellular Activities” (AAA+) family, PEX1 and PEX6, and a membrane protein that anchors the ATPases to the organelle membrane. In recent years, a large amount of data on the structure/function of the REM complex has become available. Here, we discuss the main findings and their mechanistic implications.
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30
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Barros-Barbosa A, Rodrigues TA, Ferreira MJ, Pedrosa AG, Teixeira NR, Francisco T, Azevedo JE. The intrinsically disordered nature of the peroxisomal protein translocation machinery. FEBS J 2018; 286:24-38. [PMID: 30443986 DOI: 10.1111/febs.14704] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/14/2018] [Indexed: 12/18/2022]
Abstract
Despite having a membrane that is impermeable to all but the smallest of metabolites, peroxisomes acquire their newly synthesized (cytosolic) matrix proteins in an already folded conformation. In some cases, even oligomeric proteins have been reported to translocate the organelle membrane. The protein sorting machinery that accomplishes this feat must be rather flexible and, unsurprisingly, several of its key components have large intrinsically disordered domains. Here, we provide an overview on these domains and their interactions trying to infer their functional roles in this protein sorting pathway.
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Affiliation(s)
- Aurora Barros-Barbosa
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Tony A Rodrigues
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Maria J Ferreira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Ana G Pedrosa
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Nélson R Teixeira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Tânia Francisco
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
| | - Jorge E Azevedo
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal
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