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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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Gopalswamy M, Zheng C, Gaussmann S, Kooshapur H, Hambruch E, Schliebs W, Erdmann R, Antes I, Sattler M. Distinct conformational and energetic features define the specific recognition of (di)aromatic peptide motifs by PEX14. Biol Chem 2023; 404:179-194. [PMID: 36437542 DOI: 10.1515/hsz-2022-0177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 11/04/2022] [Indexed: 11/29/2022]
Abstract
The cycling import receptor PEX5 and its membrane-located binding partner PEX14 are key constituents of the peroxisomal import machinery. Upon recognition of newly synthesized cargo proteins carrying a peroxisomal targeting signal type 1 (PTS1) in the cytosol, the PEX5/cargo complex docks at the peroxisomal membrane by binding to PEX14. The PEX14 N-terminal domain (NTD) recognizes (di)aromatic peptides, mostly corresponding to Wxxx(F/Y)-motifs, with nano-to micromolar affinity. Human PEX5 possesses eight of these conserved motifs distributed within its 320-residue disordered N-terminal region. Here, we combine biophysical (ITC, NMR, CD), biochemical and computational methods to characterize the recognition of these (di)aromatic peptides motifs and identify key features that are recognized by PEX14. Notably, the eight motifs present in human PEX5 exhibit distinct affinities and energetic contributions for the interaction with the PEX14 NTD. Computational docking and analysis of the interactions of the (di)aromatic motifs identify the specific amino acids features that stabilize a helical conformation of the peptide ligands and mediate interactions with PEX14 NTD. We propose a refined consensus motif ExWΦxE(F/Y)Φ for high affinity binding to the PEX14 NTD and discuss conservation of the (di)aromatic peptide recognition by PEX14 in other species.
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Affiliation(s)
- Mohanraj Gopalswamy
- Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany.,Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Center Munich, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Chen Zheng
- TUM School of Life Sciences, Technical University of Munich, Emil-Erlenmeyer-Forum 8, D-85354 Freising, Germany.,TUM Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, D-85748 Garching, Germany
| | - Stefan Gaussmann
- Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany.,Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Center Munich, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Hamed Kooshapur
- Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany.,Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Center Munich, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Eva Hambruch
- Institute of Biochemistry and Pathobiochemistry, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Iris Antes
- TUM School of Life Sciences, Technical University of Munich, Emil-Erlenmeyer-Forum 8, D-85354 Freising, Germany.,TUM Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, D-85748 Garching, Germany
| | - Michael Sattler
- Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany.,Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Center Munich, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
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3
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Shakya AK, Pratap JV. The coiled-coil domain of glycosomal membrane-associated Leishmania donovani PEX14: cloning, overexpression, purification and preliminary crystallographic analysis. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2020; 76:464-468. [PMID: 33006573 DOI: 10.1107/s2053230x20011127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/12/2020] [Indexed: 12/29/2022]
Abstract
The glycosomal membrane-associated Leishmania donovani protein PEX14, which plays a crucial role in protein import from the cytosol to the glycosomal matrix, consists of three domains: an N-terminal domain where the signalling molecule binds, a transmembrane domain and an 84-residue coiled-coil domain (CC) that is responsible for oligomerization. CCs are versatile domains that participate in a variety of functions including supramolecular assembly, cellular signalling and transport. Recombinant PEX14 CC was cloned, overexpressed, affinity-purified with in-column thrombin cleavage and further purified by size-exclusion chromatography. Crystals that diffracted to 1.98 Å resolution were obtained from a condition consisting of 1.4 M sodium citrate tribasic dihydrate, 0.1 M HEPES buffer pH 7.5. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 143.98, b = 32.62, c = 95.62 Å, β = 94.68°. Structure determination and characterization are in progress.
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Affiliation(s)
- Anil Kumar Shakya
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| | - J Venkatesh Pratap
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
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4
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Jardim A, Hardie DB, Boitz J, Borchers CH. Proteomic Profiling of Leishmania donovani Promastigote Subcellular Organelles. J Proteome Res 2018; 17:1194-1215. [PMID: 29332401 DOI: 10.1021/acs.jproteome.7b00817] [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] [Indexed: 11/28/2022]
Abstract
To facilitate a greater understanding of the biological processes in the medically important Leishmania donovani parasite, a combination of differential and density-gradient ultracentrifugation techniques were used to achieve a comprehensive subcellular fractionation of the promastigote stage. An in-depth label-free proteomic LC-MS/MS analysis of the density gradients resulted in the identification of ∼50% of the Leishmania proteome (3883 proteins detected), which included ∼645 integral membrane proteins and 1737 uncharacterized proteins. Clustering and subcellular localization of proteins was based on a subset of training Leishmania proteins with known subcellular localizations that had been determined using biochemical, confocal microscopy, or immunoelectron microscopy approaches. This subcellular map will be a valuable resource that will help dissect the cell biology and metabolic processes associated with specific organelles of Leishmania and related kinetoplastids.
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Affiliation(s)
- Armando Jardim
- Institute of Parasitology, Macdonald Campus, McGill University , 21111 Lakeshore Road, Saine-Anne-de-Bellevue, Québec H9X 3V9, Canada
| | - Darryl B Hardie
- University of Victoria -Genome British Columbia Proteomics Centre , #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, British Columbia V8Z7X8, Canada
| | - Jan Boitz
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University , Portland, Oregon 97239, United States
| | - Christoph H Borchers
- University of Victoria -Genome British Columbia Proteomics Centre , #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, British Columbia V8Z7X8, Canada.,Department of Biochemistry and Biophysics, University of North Carolina , 120 Mason Farm Road, Campus Box 7260 Third Floor, Genetic Medicine Building, Chapel Hill, North Carolina 27599, United States.,Department of Biochemistry and Microbiology, University of Victoria , Petch Building, Room 270d, 3800 Finnerty Road, Victoria, British Columbia V8P 5C2, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University , 3755 Côte Ste-Catherine Road, Montreal, Quebec H3T 1E2, Canada.,Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University , 3755 Côte Ste-Catherine Road, Montreal, Quebec H3T 1E2, Canada
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5
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The hydrophobic region of the Leishmania peroxin 14: requirements for association with a glycosome mimetic membrane. Biochem J 2018; 475:511-529. [DOI: 10.1042/bcj20170746] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/17/2017] [Accepted: 12/19/2017] [Indexed: 02/07/2023]
Abstract
Protein import into the Leishmania glycosome requires docking of the cargo-loaded peroxin 5 (PEX5) receptor to the peroxin 14 (PEX14) bound to the glycosome surface. To examine the LdPEX14–membrane interaction, we purified L. donovani promastigote glycosomes and determined the phospholipid and fatty acid composition. These membranes contained predominately phosphatidylethanolamine, phosphatidylcholine, and phosphatidylglycerol (PG) modified primarily with C18 and C22 unsaturated fatty acid. Using large unilamellar vesicles (LUVs) with a lipid composition mimicking the glycosomal membrane in combination with sucrose density centrifugation and fluorescence-activated cell sorting technique, we established that the LdPEX14 membrane-binding activity was dependent on a predicted transmembrane helix found within residues 149–179. Monolayer experiments showed that the incorporation of PG and phospholipids with unsaturated fatty acids, which increase membrane fluidity and favor a liquid expanded phase, facilitated the penetration of LdPEX14 into biological membranes. Moreover, we demonstrated that the binding of LdPEX5 receptor or LdPEX5–PTS1 receptor–cargo complex was contingent on the presence of LdPEX14 at the surface of LUVs.
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6
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Watanabe Y, Kawaguchi K, Okuyama N, Sugawara Y, Obita T, Mizuguchi M, Morita M, Imanaka T. Characterization of the interaction betweenTrypanosoma bruceiPex5p and its receptor Pex14p. FEBS Lett 2016; 590:242-50. [DOI: 10.1002/1873-3468.12044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 12/05/2015] [Accepted: 12/07/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Yuichi Watanabe
- Department of Biological Chemistry; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Sugitani Japan
| | - Kosuke Kawaguchi
- Department of Biological Chemistry; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Sugitani Japan
| | - Naoki Okuyama
- Department of Biological Chemistry; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Sugitani Japan
| | - Yuri Sugawara
- Department of Structural Biology; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Sugitani Japan
| | - Takayuki Obita
- Department of Structural Biology; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Sugitani Japan
| | - Mineyuki Mizuguchi
- Department of Structural Biology; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Sugitani Japan
| | - Masashi Morita
- Department of Biological Chemistry; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Sugitani Japan
| | - Tsuneo Imanaka
- Department of Biological Chemistry; Graduate School of Medicine and Pharmaceutical Sciences; University of Toyama; Sugitani Japan
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7
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Hojjat H, Jardim A. The Leishmania donovani peroxin 14 binding domain accommodates a high degeneracy in the pentapeptide motifs present on peroxin 5. Biochim Biophys Acta Gen Subj 2015; 1850:2203-12. [DOI: 10.1016/j.bbagen.2015.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 06/22/2015] [Accepted: 07/21/2015] [Indexed: 12/12/2022]
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8
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Kim PK, Hettema EH. Multiple pathways for protein transport to peroxisomes. J Mol Biol 2015; 427:1176-90. [PMID: 25681696 PMCID: PMC4726662 DOI: 10.1016/j.jmb.2015.02.005] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 02/05/2015] [Accepted: 02/06/2015] [Indexed: 12/15/2022]
Abstract
Peroxisomes are unique among the organelles of the endomembrane system. Unlike other organelles that derive most if not all of their proteins from the ER (endoplasmic reticulum), peroxisomes contain dedicated machineries for import of matrix proteins and insertion of membrane proteins. However, peroxisomes are also able to import a subset of their membrane proteins from the ER. One aspect of peroxisome biology that has remained ill defined is the role the various import pathways play in peroxisome maintenance. In this review, we discuss the available data on matrix and membrane protein import into peroxisomes. Peroxisomal membrane and matrix proteins require distinct factors for their transport. Matrix proteins fold in the cytosol prior to their import. Loaded targeting receptors form part of the matrix protein translocation pore. Many membrane proteins are directly inserted into the peroxisomal membrane. Some peroxisomal membrane proteins are transported via the ER to peroxisomes.
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Affiliation(s)
- P K Kim
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON, Canada M5G 1X8; Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - E H Hettema
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, South Yorkshire S10 2TN, United Kingdom.
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9
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Identification of Leishmania donovani peroxin 14 residues required for binding the peroxin 5 receptor proteins. Biochem J 2015; 465:247-57. [DOI: 10.1042/bj20141133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Trafficking of peroxisomal targeting signal 1 (PTS1) proteins to the Leishmania glycosome is dependent on the docking of the LdPEX5 receptor to LdPEX14 on the glycosomal membrane. A combination of deletion and random mutagenesis was used to identify residues in the LdPEX14 N-terminal region that are critical for mediating the LdPEX5–LdPEX14 interaction. These studies highlighted residues 35–75 on ldpex14 as the core domain required for binding LdPEX5. Single point mutation within this core domain generally did not affect the ldpex5-(203–391)–ldpex14-(1–120) interaction; notable exceptions were substitutions at Phe40, Val46 or Phe57 which completely abolished or increased the apparent Kd value for ldpex5-(203–391) binding 30-fold. Biochemical studies revealed that these point mutations did not alter either the secondary or quaternary structure of LdPEX14 and indicated that the latter residues were critical for stabilizing the LdPEX5–LdPEX14 interaction.
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10
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Choudhry SK, Kawałek A, van der Klei IJ. Peroxisomal quality control mechanisms. Curr Opin Microbiol 2014; 22:30-7. [PMID: 25305535 DOI: 10.1016/j.mib.2014.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/08/2014] [Accepted: 09/12/2014] [Indexed: 10/24/2022]
Abstract
Peroxisomes are ubiquitous organelles that harbor diverse metabolic pathways, which are essential for normal cell performance. Conserved functions of these organelles are hydrogen peroxide metabolism and β-oxidation. Cells employ multiple quality control mechanisms to ensure proper peroxisome function and to protect peroxisomes from damage. These involve the function of molecular chaperones, a peroxisomal Lon protease and autophagic removal of dysfunctional organelles. In addition, multiple mechanisms exist to combat peroxisomal oxidative stress. Here, we outline recent advances in our understanding of peroxisomal quality control, focussing on yeast and filamentous fungi.
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Affiliation(s)
- Sanjeev K Choudhry
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, P.O. Box 11103, 9300CC Groningen, The Netherlands
| | - Adam Kawałek
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, P.O. Box 11103, 9300CC Groningen, The Netherlands
| | - Ida J van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, P.O. Box 11103, 9300CC Groningen, The Netherlands.
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11
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Platta HW, Hagen S, Reidick C, Erdmann R. The peroxisomal receptor dislocation pathway: to the exportomer and beyond. Biochimie 2013; 98:16-28. [PMID: 24345375 DOI: 10.1016/j.biochi.2013.12.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 12/05/2013] [Indexed: 12/29/2022]
Abstract
The biogenesis of peroxisomes is an ubiquitin-dependent process. In particular, the import of matrix proteins into the peroxisomal lumen requires the modification of import receptors with ubiquitin. The matrix proteins are synthesized on free polyribosomes in the cytosol and are recognized by import receptors via a peroxisomal targeting sequence (PTS). Subsequent to the transport of the receptor/cargo-complex to the peroxisomal membrane and the release of the cargo into the peroxisomal lumen, the PTS-receptors are exported back to the cytosol for further rounds of matrix protein import. The exportomer represents the molecular machinery required for the retrotranslocation of the PTS-receptors. It comprises enzymes for the ubiquitination as well as for the ATP-dependent extraction of the PTS-receptors from the peroxisomal membrane. Furthermore, recent evidence indicates a mechanistic interconnection of the ATP-dependent removal of the PTS-receptors with the translocation of the matrix protein into the organellar lumen. Interestingly, the components of the peroxisomal exportomer seem also to be involved in cellular tasks that are distinct from the ubiquitination and dislocation of the peroxisomal PTS-receptors. This includes work that indicates a central function of this machinery in the export of peroxisomal matrix proteins in plants, while a subset of exportomer components is involved in the meiocyte formation in some fungi, the peroxisome-chloroplast contact during photorespiration in plants and possibly even the selective degradation of peroxisomes via pexophagy. In this review, we want to discuss the central role of the exportomer during matrix protein import, but also highlight distinct roles of exportomer constituents in additional cellular processes. This article is part of a Special Issue entitled: Peroxisomes: biogenesis, functions and diseases.
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Affiliation(s)
- Harald W Platta
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany.
| | - Stefanie Hagen
- Systembiochemie, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Christina Reidick
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Ralf Erdmann
- Systembiochemie, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany.
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12
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Hasan S, Platta HW, Erdmann R. Import of proteins into the peroxisomal matrix. Front Physiol 2013; 4:261. [PMID: 24069002 PMCID: PMC3781343 DOI: 10.3389/fphys.2013.00261] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/03/2013] [Indexed: 12/03/2022] Open
Abstract
Peroxisomes constitute a dynamic compartment in all nucleated cells. They fulfill diverse metabolic tasks in response to environmental changes and cellular demands. This adaptation is implemented by modulation of the enzyme content of the organelles, which is accomplished by dynamically operating peroxisomal protein transport machineries. Soluble import receptors recognize their newly synthesized cargo proteins in the cytosol and ferry them to the peroxisomal membrane. Subsequently, the cargo is translocated into the matrix, where the receptor is ubiquitinated and exported back to the cytosol for further rounds of matrix protein import. This review discusses the recent progress in our understanding of the peroxisomal matrix protein import and its regulation by ubiquitination events as well as the current view on the translocation mechanism of folded proteins into peroxisomes. This article is part of a Special Issue entitled: Origin and spatiotemporal dynamics of the peroxisomal endomembrane system.
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Affiliation(s)
- Sohel Hasan
- Systembiochemie, Medizinische Fakultät, Ruhr-Universität Bochum Bochum, Germany
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13
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Paul P, Simm S, Blaumeiser A, Scharf KD, Fragkostefanakis S, Mirus O, Schleiff E. The protein translocation systems in plants - composition and variability on the example of Solanum lycopersicum. BMC Genomics 2013; 14:189. [PMID: 23506162 PMCID: PMC3610429 DOI: 10.1186/1471-2164-14-189] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 02/25/2013] [Indexed: 11/22/2022] Open
Abstract
Background Protein translocation across membranes is a central process in all cells. In the past decades the molecular composition of the translocation systems in the membranes of the endoplasmic reticulum, peroxisomes, mitochondria and chloroplasts have been established based on the analysis of model organisms. Today, these results have to be transferred to other plant species. We bioinformatically determined the inventory of putative translocation factors in tomato (Solanum lycopersicum) by orthologue search and domain architecture analyses. In addition, we investigated the diversity of such systems by comparing our findings to the model organisms Saccharomyces cerevisiae, Arabidopsis thaliana and 12 other plant species. Results The literature search end up in a total of 130 translocation components in yeast and A. thaliana, which are either experimentally confirmed or homologous to experimentally confirmed factors. From our bioinformatic analysis (PGAP and OrthoMCL), we identified (co-)orthologues in plants, which in combination yielded 148 and 143 orthologues in A. thaliana and S. lycopersicum, respectively. Interestingly, we traced 82% overlap in findings from both approaches though we did not find any orthologues for 27% of the factors by either procedure. In turn, 29% of the factors displayed the presence of more than one (co-)orthologue in tomato. Moreover, our analysis revealed that the genomic composition of the translocation machineries in the bryophyte Physcomitrella patens resemble more to higher plants than to single celled green algae. The monocots (Z. mays and O. sativa) follow more or less a similar conservation pattern for encoding the translocon components. In contrast, a diverse pattern was observed in different eudicots. Conclusions The orthologue search shows in most cases a clear conservation of components of the translocation pathways/machineries. Only the Get-dependent integration of tail-anchored proteins seems to be distinct. Further, the complexity of the translocation pathway in terms of existing orthologues seems to vary among plant species. This might be the consequence of palaeoploidisation during evolution in plants; lineage specific whole genome duplications in Arabidopsis thaliana and triplications in Solanum lycopersicum.
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Affiliation(s)
- Puneet Paul
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, 60438, Germany
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14
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Abstract
Peroxisomes are remarkably versatile cell organelles whose size, shape, number, and protein content can vary greatly depending on the organism, the developmental stage of the organism’s life cycle, and the environment in which the organism lives. The main functions usually associated with peroxisomes include the metabolism of lipids and reactive oxygen species. However, in recent years, it has become clear that these organelles may also act as intracellular signaling platforms that mediate developmental decisions by modulating extraperoxisomal concentrations of several second messengers. To fulfill their functions, peroxisomes physically and functionally interact with other cell organelles, including mitochondria and the endoplasmic reticulum. Defects in peroxisome dynamics can lead to organelle dysfunction and have been associated with various human disorders. The purpose of this paper is to thoroughly summarize and discuss the current concepts underlying peroxisome formation, multiplication, and degradation. In addition, this paper will briefly highlight what is known about the interplay between peroxisomes and other cell organelles and explore the physiological and pathological implications of this interorganellar crosstalk.
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Affiliation(s)
- Marc Fransen
- Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, P.O. Box 601, 3000 Leuven, Belgium
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15
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Recent advances in peroxisomal matrix protein import. Curr Opin Cell Biol 2012; 24:484-9. [PMID: 22683191 DOI: 10.1016/j.ceb.2012.05.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Accepted: 05/14/2012] [Indexed: 11/22/2022]
Abstract
Peroxisomes are essential organelles responsible for many metabolic reactions, such as the oxidation of very long chain and branched fatty acids, D-amino acids and polyamines, as well as the production and turnover of hydrogen peroxide. They comprise a class of organelles called microbodies, including glycosomes, glyoxysomes and Woronin bodies. Dysfunction of human peroxisomes causes severe and often fatal peroxisome biogenesis disorders (PBDs). Peroxisomal matrix protein import is mediated by receptors that shuttle between the cytosol and peroxisomal matrix using ubiquitination/deubiquitination reactions and ATP hydrolysis for receptor recycling. We focus on the machinery involved in the peroxisomal matrix protein import cycle, highlighting recent advances in peroxisomal matrix protein import, cargo release and receptor recycling/degradation.
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Abstract
The biogenesis of peroxisomal matrix and membrane proteins is substantially different from the biogenesis of proteins of other subcellular compartments, such as mitochondria and chloroplasts, that are of endosymbiotic origin. Proteins are targeted to the peroxisome matrix through interactions between specific targeting sequences and receptor proteins, followed by protein translocation across the peroxisomal membrane. Recent advances have shed light on the nature of the peroxisomal translocon in matrix protein import and the molecular mechanisms of receptor recycling. Furthermore, the endoplasmic reticulum has been shown to play an important role in peroxisomal membrane protein biogenesis. Defining the molecular events in peroxisome assembly may enhance our understanding of the etiology of human peroxisome biogenesis disorders.
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Affiliation(s)
- Changle Ma
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, CA 92093, USA
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Ito T, Ito D, Ozawa S, Fujimura S, Matsufuji Y, Nakagawa J, Tomizuka N, Hayakawa T, Nakagawa T. Molecular characterization of the PEX14 gene from the methylotrophic yeast Pichia methanolica. J Biosci Bioeng 2011; 111:624-7. [PMID: 21317032 DOI: 10.1016/j.jbiosc.2011.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 01/11/2011] [Accepted: 01/18/2011] [Indexed: 11/28/2022]
Abstract
In this study, we describe the molecular characterization of the PmPEX14 gene encoding the peroxisomal membrane protein from the methylotrophic yeast Pichia methanolica. The pex14Δ strain of P. methanolica lost its ability to grow on methanol and oleate but grew normally on glucose. Disruption of the PmPEX14 caused a decrease in the activities of peroxisomal methanol-metabolizing enzymes and mislocalization of those proteins into the cytosol and vacuole. Taken together, these findings show that PmPex14p has an essential physiological role in methanol metabolism in P. methanolica.
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Affiliation(s)
- Takashi Ito
- Department of Food Science and Technology, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri, Hokkaido 099-2493, Japan
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Galland N, Michels PAM. Comparison of the peroxisomal matrix protein import system of different organisms. Exploration of possibilities for developing inhibitors of the import system of trypanosomatids for anti-parasite chemotherapy. Eur J Cell Biol 2010; 89:621-37. [PMID: 20435370 DOI: 10.1016/j.ejcb.2010.04.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 03/28/2010] [Accepted: 04/06/2010] [Indexed: 10/19/2022] Open
Abstract
In recent decades, research on peroxisome biogenesis has been particularly boosted since the role of these organelles in metabolism became unraveled. Indeed in plants, yeasts and fungi, peroxisomes play an important role in the adaptation of metabolism during developmental processes and/or altered environmental conditions. In mammals their importance is illustrated by the fact that several severe human inherited diseases have been identified as peroxisome biogenesis disorders (PBD). Particularly interesting are the glycosomes - peroxisome-like organelles in trypanosomatids where the major part of the glycolytic pathway is sequestered - because it was demonstrated that proper compartmentalization of matrix proteins inside glycosomes is essential for the parasite. Although the overall process of peroxisome biogenesis seems well conserved between species, careful study of the literature reveals nonetheless many differences at various steps. In this review, we present a comparison of the first two steps of peroxisome biogenesis - receptor loading and docking at the peroxisomal membrane - in yeasts, mammals, plants and trypanosomatids and highlight major differences in the import process between species despite the conservation of (some of) the proteins involved. Some of the unique features of the process as it occurs in trypanosomatids will be discussed with regard to the possibilities for exploiting them for the development of compounds that could specifically disturb interactions between trypanosomatid peroxins. This strategy could eventually lead to the discovery of drugs against the diseases caused by these parasites.
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Affiliation(s)
- Nathalie Galland
- Research Unit for Tropical Diseases, de Duve Institute, Brussels, Belgium
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Survey of the year 2008: applications of isothermal titration calorimetry. J Mol Recognit 2010; 23:395-413. [DOI: 10.1002/jmr.1025] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Su JR, Takeda K, Tamura S, Fujiki Y, Miki K. Monomer-dimer transition of the conserved N-terminal domain of the mammalian peroxisomal matrix protein import receptor, Pex14p. Biochem Biophys Res Commun 2010; 394:217-21. [PMID: 20193661 DOI: 10.1016/j.bbrc.2010.02.160] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 02/24/2010] [Indexed: 11/16/2022]
Abstract
Pex14p is a central component of the peroxisomal matrix protein import machinery. In the recently determined crystal structure, a characteristic face consisting of conserved residues was found on a side of the conserved N-terminal domain of the protein. The face is highly hydrophobic, and is also the binding site for the WXXXF/Y motif of Pex5p. We report herein the dimerization of the domain in the isolated state. The homo-dimers are in equilibrium with the monomers. The homo-dimers are completely dissociated into monomers by complex formation with the WXXXF/Y motif peptide of Pex5p. A putative dimer model shows the interaction between the conserved face and the PXXP motif of another protomer. The model allows us to discuss the mechanism of the oligomeric transition of the full-length Pex14p modulated by the binding of other peroxins.
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Affiliation(s)
- Jian-Rong Su
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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21
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Kumar R, Gupta S, Srivastava R, Sahasrabuddhe AA, Gupta CM. Expression of a PTS2-truncated hexokinase produces glucose toxicity in Leishmania donovani. Mol Biochem Parasitol 2009; 170:41-4. [PMID: 19925831 DOI: 10.1016/j.molbiopara.2009.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 11/06/2009] [Accepted: 11/11/2009] [Indexed: 10/20/2022]
Abstract
Compartmentalization of glycolytic enzymes in glycosomes is vital in trypanosomatid parasites. Retention of these enzymes in the cytosol induces sugar toxicity and accumulation of intermediate metabolites, notably the hexokinase product glucose-6-phosphate. However, the role of hexokinase in sugar mediated toxicity remains unexplored. We have generated Leishmania donovani transfectants expressing a catalytically active cytosolic mutant of hexokinase. In the presence of glucose, these transfectants exhibited toxicity during log and stationary phases of growth. These results suggest that targeting of hexokinase to the glycosome is required to prevent uncontrolled and cytotoxic glucose phosphorylation in L. donovani parasites.
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Affiliation(s)
- Ramesh Kumar
- Parasitology Division, Central Drug Research Institute, C.S.I.R, Lucknow 226001, India
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Nolandt OV, Walther TH, Roth S, Bürck J, Ulrich AS. Structure analysis of the membrane protein TatCd from the Tat system of B. subtilis by circular dichroism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:2238-44. [DOI: 10.1016/j.bbamem.2009.07.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Revised: 06/23/2009] [Accepted: 07/06/2009] [Indexed: 11/16/2022]
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Abstract
Peroxisomes play an important role in lipid metabolic pathways and are implicated in many human disorders. Their biogenesis has been studied over the last two decades using many uni and multi-cellular model systems and many aspects of the mechanisms and proteins involved in peroxisome biogenesis are conserved from yeast to humans. In this manuscript we review the recent progress made in our understanding of the mechanisms by which matrix and membrane proteins are sorted to and assembled into peroxisomes.
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Affiliation(s)
- Changle Ma
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA
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Ma C, Schumann U, Rayapuram N, Subramani S. The peroxisomal matrix import of Pex8p requires only PTS receptors and Pex14p. Mol Biol Cell 2009; 20:3680-9. [PMID: 19570913 DOI: 10.1091/mbc.e09-01-0037] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Pichia pastoris (Pp) Pex8p, the only known intraperoxisomal peroxin at steady state, is targeted to peroxisomes by either the peroxisomal targeting signal (PTS) type 1 or PTS2 pathway. Until recently, all cargoes entering the peroxisome matrix were believed to require the docking and really interesting new gene (RING) subcomplexes, proteins that bridge these two subcomplexes and the PTS receptor-recycling machinery. However, we reported recently that the import of PpPex8p into peroxisomes via the PTS2 pathway is Pex14p dependent but independent of the RING subcomplex (Zhang et al., 2006). In further characterizing the peroxisome membrane-associated translocon, we show that two other components of the docking subcomplex, Pex13p and Pex17p, are dispensable for the import of Pex8p. Moreover, we demonstrate that the import of Pex8p via the PTS1 pathway also does not require the RING subcomplex or intraperoxisomal Pex8p. In receptor-recycling mutants (Deltapex1, Deltapex6, and Deltapex4), Pex8p is largely cytosolic because Pex5p and Pex20p are unstable. However, upon overexpression of the degradation-resistant Pex20p mutant, hemagglutinin (HA)-Pex20p(K19R), in Deltapex4 and Deltapex6 cells, Pex8p enters peroxisome remnants. Our data support the idea that PpPex8p is a special cargo whose translocation into peroxisomes depends only on the PTS receptors and Pex14p and not on intraperoxisomal Pex8p, the RING subcomplex, or the receptor-recycling machinery.
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Affiliation(s)
- Changle Ma
- University of California, San Diego, La Jolla, 92093-0322, USA
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