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Abstract
Peroxisomes are involved in a multitude of metabolic and catabolic pathways, as well as the innate immune system. Their dysfunction is linked to severe peroxisome-specific diseases, as well as cancer and neurodegenerative diseases. To ensure the ability of peroxisomes to fulfill their many roles in the organism, more than 100 different proteins are post-translationally imported into the peroxisomal membrane and matrix, and their functionality must be closely monitored. In this Review, we briefly discuss the import of peroxisomal membrane proteins, and we emphasize an updated view of both classical and alternative peroxisomal matrix protein import pathways. We highlight different quality control pathways that ensure the degradation of dysfunctional peroxisomal proteins. Finally, we compare peroxisomal matrix protein import with other systems that transport folded proteins across membranes, in particular the twin-arginine translocation (Tat) system and the nuclear pore.
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Affiliation(s)
- Markus Rudowitz
- Systems Biochemistry , Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Ralf Erdmann
- Systems Biochemistry , Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
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Karnati S, Oruqaj G, Janga H, Tumpara S, Colasante C, Van Veldhoven PP, Braverman N, Pilatz A, Mariani TJ, Baumgart-Vogt E. PPARα-mediated peroxisome induction compensates PPARγ-deficiency in bronchiolar club cells. PLoS One 2018; 13:e0203466. [PMID: 30212482 PMCID: PMC6136741 DOI: 10.1371/journal.pone.0203466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 08/21/2018] [Indexed: 11/18/2022] Open
Abstract
Despite the important functions of PPARγ in various cell types of the lung, PPARγ-deficiency in club cells induces only mild emphysema. Peroxisomes are distributed in a similar way as PPARγ in the lung and are mainly enriched in club and AECII cells. To date, the effects of PPARγ-deficiency on the overall peroxisomal compartment and its metabolic alterations in pulmonary club cells are unknown. Therefore, we characterized wild-type and club cell-specific PPARγ knockout-mice lungs and used C22 cells to investigate the peroxisomal compartment and its metabolic roles in the distal airway epithelium by means of 1) double-immunofluorescence labelling for peroxisomal proteins, 2) laser-assisted microdissection of the bronchiolar epithelium and subsequent qRT-PCR, 3) siRNA-transfection of PPARγand PPRE dual-luciferase reporter activity in C22 cells, 4) PPARg inhibition by GW9662, 5) GC-MS based lipid analysis. Our results reveal elevated levels of fatty acids, increased expression of PPARα and PPRE activity, a strong overall upregulation of the peroxisomal compartment and its associated gene expression (biogenesis, α-oxidation, β-oxidation, and plasmalogens) in PPARγ-deficient club cells. Interestingly, catalase was significantly increased and mistargeted into the cytoplasm, suggestive for oxidative stress by the PPARγ-deficiency in club cells. Taken together, PPARα-mediated metabolic induction and proliferation of peroxisomes via a PPRE-dependent mechanism could compensate PPARγ-deficiency in club cells.
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Affiliation(s)
- Srikanth Karnati
- Institute for Anatomy and Cell Biology II, Division of Medical Cell Biology, Justus Liebig University, Giessen, Germany
- * E-mail: ,
| | - Gani Oruqaj
- Institute for Anatomy and Cell Biology II, Division of Medical Cell Biology, Justus Liebig University, Giessen, Germany
| | - Harshavardhan Janga
- Institute for Anatomy and Cell Biology II, Division of Medical Cell Biology, Justus Liebig University, Giessen, Germany
| | - Srinu Tumpara
- Institute for Anatomy and Cell Biology II, Division of Medical Cell Biology, Justus Liebig University, Giessen, Germany
| | - Claudia Colasante
- Institute for Anatomy and Cell Biology II, Division of Medical Cell Biology, Justus Liebig University, Giessen, Germany
| | - Paul P. Van Veldhoven
- Laboratory of Lipid Biochemistry and Protein Interactions, KU Leuven, Leuven, Belgium
| | - Nancy Braverman
- Depts. of Human Genetics and Pediatrics, McGill University-Montreal Children’s Hospital Research Institute, Montreal, Canada
| | - Adrian Pilatz
- Department of Urology, Pediatric Urology and Andrology, Justus Liebig University Giessen, Giessen, Germany
| | - Thomas J. Mariani
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Eveline Baumgart-Vogt
- Institute for Anatomy and Cell Biology II, Division of Medical Cell Biology, Justus Liebig University, Giessen, Germany
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Schwerter D, Grimm I, Girzalsky W, Erdmann R. Receptor recognition by the peroxisomal AAA complex depends on the presence of the ubiquitin moiety and is mediated by Pex1p. J Biol Chem 2018; 293:15458-15470. [PMID: 30097517 DOI: 10.1074/jbc.ra118.003936] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/23/2018] [Indexed: 01/14/2023] Open
Abstract
The receptor cycle of type I peroxisomal matrix protein import is completed by ubiquitination of the membrane-bound peroxisome biogenesis factor 5 (Pex5p) and its subsequent export back to the cytosol. The receptor export is the only ATP-dependent step of the whole process and is facilitated by two members of the AAA family of proteins (ATPases associated with various cellular activities), namely Pex1p and Pex6p. To gain further insight into substrate recognition by the AAA complex, we generated an N-terminally linked ubiquitin-Pex5p fusion protein. This fusion protein displayed biological activity because it is able to functionally complement a PEX5-deletion in Saccharomyces cerevisiae. In vitro assays revealed its interaction at WT level with the native cargo protein Pcs60p and Pex14p, a constituent of the receptor docking complex. We also demonstrate in vitro deubiquitination by the deubiquitinating enzyme Ubp15p. In vitro pulldown assays and cross-linking studies demonstrate that Pex5p recognition by the AAA complex depends on the presence of the ubiquitin moiety and is mediated by Pex1p.
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Affiliation(s)
- Daniel Schwerter
- From the Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Systems Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Immanuel Grimm
- From the Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Systems Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Wolfgang Girzalsky
- From the Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Systems Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Ralf Erdmann
- From the Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Systems Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
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Peroxisomal protein import pores. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:821-7. [DOI: 10.1016/j.bbamcr.2015.10.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/14/2015] [Accepted: 10/16/2015] [Indexed: 02/06/2023]
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Human disorders of peroxisome metabolism and biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:922-33. [DOI: 10.1016/j.bbamcr.2015.11.015] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/16/2015] [Accepted: 11/17/2015] [Indexed: 12/22/2022]
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Kunze M, Berger J. The similarity between N-terminal targeting signals for protein import into different organelles and its evolutionary relevance. Front Physiol 2015; 6:259. [PMID: 26441678 PMCID: PMC4585086 DOI: 10.3389/fphys.2015.00259] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/04/2015] [Indexed: 12/04/2022] Open
Abstract
The proper distribution of proteins between the cytosol and various membrane-bound compartments is crucial for the functionality of eukaryotic cells. This requires the cooperation between protein transport machineries that translocate diverse proteins from the cytosol into these compartments and targeting signal(s) encoded within the primary sequence of these proteins that define their cellular destination. The mechanisms exerting protein translocation differ remarkably between the compartments, but the predominant targeting signals for mitochondria, chloroplasts and the ER share the N-terminal position, an α-helical structural element and the removal from the core protein by intraorganellar cleavage. Interestingly, similar properties have been described for the peroxisomal targeting signal type 2 mediating the import of a fraction of soluble peroxisomal proteins, whereas other peroxisomal matrix proteins encode the type 1 targeting signal residing at the extreme C-terminus. The structural similarity of N-terminal targeting signals poses a challenge to the specificity of protein transport, but allows the generation of ambiguous targeting signals that mediate dual targeting of proteins into different compartments. Dual targeting might represent an advantage for adaptation processes that involve a redistribution of proteins, because it circumvents the hierarchy of targeting signals. Thus, the co-existence of two equally functional import pathways into peroxisomes might reflect a balance between evolutionary constant and flexible transport routes.
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Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna Vienna, Austria
| | - Johannes Berger
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna Vienna, Austria
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Hagen S, Drepper F, Fischer S, Fodor K, Passon D, Platta HW, Zenn M, Schliebs W, Girzalsky W, Wilmanns M, Warscheid B, Erdmann R. Structural insights into cargo recognition by the yeast PTS1 receptor. J Biol Chem 2015; 290:26610-26. [PMID: 26359497 DOI: 10.1074/jbc.m115.657973] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Indexed: 11/06/2022] Open
Abstract
The peroxisomal matrix protein import is facilitated by cycling import receptors that shuttle between the cytosol and the peroxisomal membrane. The import receptor Pex5p mediates the import of proteins harboring a peroxisomal targeting signal of type I (PTS1). Purified recombinant Pex5p forms a dimeric complex with the PTS1-protein Pcs60p in vitro with a KD of 0.19 μm. To analyze the structural basis for receptor-cargo recognition, the PTS1 and adjacent amino acids of Pcs60p were systematically scanned for Pex5p binding by an in vitro site-directed photo-cross-linking approach. The cross-linked binding regions of the receptor were subsequently identified by high resolution mass spectrometry. Most cross-links were found with TPR6, TPR7, as well as the 7C-loop of Pex5p. Surface plasmon resonance analysis revealed a bivalent interaction mode for Pex5p and Pcs60p. Interestingly, Pcs60p lacking its C-terminal tripeptide sequence was efficiently cross-linked to the same regions of Pex5p. The KD value of the interaction of truncated Pcs60p and Pex5p was in the range of 7.7 μm. Isothermal titration calorimetry and surface plasmon resonance measurements revealed a monovalent binding mode for the interaction of Pex5p and Pcs60p lacking the PTS1. Our data indicate that Pcs60p contains a second contact site for its receptor Pex5p, beyond the C-terminal tripeptide. The physiological relevance of the ancillary binding region was supported by in vivo import studies. The bivalent binding mode might be explained by a two-step concept as follows: first, cargo recognition and initial tethering by the PTS1-receptor Pex5p; second, lock-in of receptor and cargo.
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Affiliation(s)
- Stefanie Hagen
- From the Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, System Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Friedel Drepper
- the Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Sven Fischer
- the Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Krisztian Fodor
- the Department of Biochemistry, Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Daniel Passon
- the European Molecular Biology Laboratory at Hamburg, D-22607 Hamburg, Germany
| | - Harald W Platta
- the Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Biochemistry of Intracellular Transport Mechanism, Ruhr-University Bochum, D-44781 Bochum, Germany, and
| | - Michael Zenn
- the Biaffin GmbH and Co., KG, D-34132 Kassel, Germany
| | - Wolfgang Schliebs
- From the Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, System Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Wolfgang Girzalsky
- From the Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, System Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Matthias Wilmanns
- the European Molecular Biology Laboratory at Hamburg, D-22607 Hamburg, Germany
| | - Bettina Warscheid
- the Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Ralf Erdmann
- From the Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, System Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany,
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Brown LA, Baker A. Shuttles and cycles: transport of proteins into the peroxisome matrix (review). Mol Membr Biol 2008; 25:363-75. [PMID: 18651315 DOI: 10.1080/09687680802130583] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Peroxisomes are organelles that carry out diverse biochemical processes in eukaryotic cells, including the core pathways of beta-oxidation of lipid molecules and detoxification of reactive oxygen species. In multicellular organisms defects in peroxisome assembly result in multiple biochemical and developmental abnormalities. As peroxisomes do not contain genetic material, their protein content, and therefore function, is determined by the import of nuclearly encoded proteins from the cytosol and, presumably, removal of damaged or obsolete proteins. Import of matrix proteins can be broken down into four steps: targeting signal recognition by the cycling import receptors; receptor-cargo docking at the peroxisome membrane; translocation and cargo unloading; and receptor recycling. Import is mediated by a set of evolutionarily conserved proteins called peroxins that have been identified primarily via genetic screens, but knowledge of their biochemical activities remains largely unresolved. Recent studies have filled in some of the blanks regarding receptor recycling and the role of ubiquitination but outstanding questions remain concerning the nature of the translocon and its ability to accommodate folded, even oligomeric proteins, and the mechanism of cargo unloading and turnover of peroxisomal proteins. This review seeks to integrate recent findings from yeast, mammalian and plant systems to present an up to date account of how proteins enter the peroxisome matrix.
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Abstract
Peroxisomes are important organelles of eukaryote cells. Although these structures are of relatively small size, they display an unprecedented functional versatility. The principles of their biogenesis and function are strongly conserved from very simple eukaryotes to humans. Peroxisome-borne proteins are synthesized in the cytosol and posttranslationally incorporated into the organelle. The protein-sorting signal for matrix proteins, peroxisomal targeting signal (PTS), and for membrane proteins (mPTS), are also conserved. Several genes involved in peroxisomal matrix protein import have been identified (PEX genes), but the details of the molecular mechanisms of this translocation process are still unclear. Here we describe procedures to study the subcellular location of peroxisomal matrix and membrane proteins in yeast and fungi. Emphasis is placed on protocols developed for the methylotrophic yeast Hansenula polymorpha, but very similar protocols can be applied for other yeast species and filamentous fungi. The described methods include cell fractionation procedures and subcellular localization studies using fluorescence microscopy and immunolabeling techniques.
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Affiliation(s)
- Ida van der Klei
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
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Erdmann R, Schliebs W. Peroxisomal matrix protein import: the transient pore model. Nat Rev Mol Cell Biol 2005; 6:738-42. [PMID: 16103872 DOI: 10.1038/nrm1710] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Peroxisomes import folded, even oligomeric, proteins, which distinguishes the peroxisomal translocation machinery from the well-characterized translocons of other organelles. How proteins are transported across the peroxisomal membrane is unclear. Here, we propose a mechanistic model that conceptually divides the import process into three consecutive steps: the formation of a translocation pore by the import receptor, the ubiquitylation of the import receptors, and pore disassembly/ receptor recycling.
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Affiliation(s)
- Ralf Erdmann
- Institute for Physiological Chemistry, Faculty of Medicine, Ruhr-University Bochum, Germany.
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Abstract
Proteins harbouring a peroxisomal targeting signal of type 1 (PTS1) are recognized by the import receptor Pex5p in the cytosol which directs them to a docking and translocation complex at the peroxisomal membrane. We demonstrate the ubiquitination of Pex5p in cells lacking components of the peroxisomal AAA (ATPases associated with various cellular activities) or Pex4p-Pex22p complexes of the peroxisomal protein import machinery and in cells affected in proteasomal degradation. In cells lacking components of the Pex4p-Pex22p complex, mono-ubiquitinated Pex5p represents the major modification, while in cells lacking components of the AAA complex polyubiquitinated forms are most prominent. Ubiquitination of Pex5p is shown to take place exclusively at the peroxisomal membrane after the docking step, and requires the presence of the RING-finger peroxin Pex10p. Mono- and poly-ubiquitination are demonstrated to depend on the ubiquitin-conjugating enzyme Ubc4p, suggesting that the ubiquitinated forms of Pex5p are targeted for proteasomal degradation. Accumulation of ubiquitinated Pex5p in proteasomal mutants demonstrates that the ubiquitination of Pex5p also takes place in strains which are not affected in peroxisomal biogenesis, indicating that the ubiquitination of Pex5p represents a genuine stage in the Pex5p receptor cycle.
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Affiliation(s)
- Harald W. Platta
- Institut für Physiologische Chemie, Abteilung für Systembiochemie, Ruhr-Universität Bochum, Universitätsstrasse 150, D-44780 Bochum, Germany
| | - Wolfgang Girzalsky
- Institut für Physiologische Chemie, Abteilung für Systembiochemie, Ruhr-Universität Bochum, Universitätsstrasse 150, D-44780 Bochum, Germany
| | - Ralf Erdmann
- Institut für Physiologische Chemie, Abteilung für Systembiochemie, Ruhr-Universität Bochum, Universitätsstrasse 150, D-44780 Bochum, Germany
- To whom correspondence should be addressed (email )
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