1
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Fischer S, Bürgi J, Gabay-Maskit S, Maier R, Mastalski T, Yifrach E, Obarska-Kosinska A, Rudowitz M, Erdmann R, Platta HW, Wilmanns M, Schuldiner M, Zalckvar E, Oeljeklaus S, Drepper F, Warscheid B. Phosphorylation of the receptor protein Pex5p modulates import of proteins into peroxisomes. Biol Chem 2023; 404:135-155. [PMID: 36122347 PMCID: PMC9929924 DOI: 10.1515/hsz-2022-0168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/23/2022] [Indexed: 11/15/2022]
Abstract
Peroxisomes are organelles with vital functions in metabolism and their dysfunction is associated with human diseases. To fulfill their multiple roles, peroxisomes import nuclear-encoded matrix proteins, most carrying a peroxisomal targeting signal (PTS) 1. The receptor Pex5p recruits PTS1-proteins for import into peroxisomes; whether and how this process is posttranslationally regulated is unknown. Here, we identify 22 phosphorylation sites of Pex5p. Yeast cells expressing phospho-mimicking Pex5p-S507/523D (Pex5p2D) show decreased import of GFP with a PTS1. We show that the binding affinity between a PTS1-protein and Pex5p2D is reduced. An in vivo analysis of the effect of the phospho-mimicking mutant on PTS1-proteins revealed that import of most, but not all, cargos is affected. The physiological effect of the phosphomimetic mutations correlates with the binding affinity of the corresponding extended PTS1-sequences. Thus, we report a novel Pex5p phosphorylation-dependent mechanism for regulating PTS1-protein import into peroxisomes. In a broader view, this suggests that posttranslational modifications can function in fine-tuning the peroxisomal protein composition and, thus, cellular metabolism.
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Affiliation(s)
- Sven Fischer
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104Freiburg, Germany
| | - Jérôme Bürgi
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, D-22607Hamburg, Germany
- University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246Hamburg, Germany
| | - Shiran Gabay-Maskit
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Renate Maier
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104Freiburg, Germany
| | - Thomas Mastalski
- Biochemistry of Intracellular Transport, Medical Faculty, Ruhr University Bochum, D-44780Bochum, Germany
| | - Eden Yifrach
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Agnieszka Obarska-Kosinska
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, D-22607Hamburg, Germany
- University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246Hamburg, Germany
| | - Markus Rudowitz
- Systems Biochemistry, Medical Faculty, Ruhr-University Bochum, D-44780Bochum, Germany
| | - Ralf Erdmann
- Systems Biochemistry, Medical Faculty, Ruhr-University Bochum, D-44780Bochum, Germany
| | - Harald W. Platta
- Biochemistry of Intracellular Transport, Medical Faculty, Ruhr University Bochum, D-44780Bochum, Germany
| | - Matthias Wilmanns
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, D-22607Hamburg, Germany
- University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246Hamburg, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Silke Oeljeklaus
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104Freiburg, Germany
- Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Am Hubland, D-97074, Würzburg, Germany
| | - Friedel Drepper
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104Freiburg, Germany
| | - Bettina Warscheid
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104Freiburg, Germany
- Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Am Hubland, D-97074, Würzburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, D-79104Freiburg, Germany
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2
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Kelsall IR. Non-lysine ubiquitylation: Doing things differently. Front Mol Biosci 2022; 9:1008175. [PMID: 36200073 PMCID: PMC9527308 DOI: 10.3389/fmolb.2022.1008175] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/01/2022] [Indexed: 11/23/2022] Open
Abstract
The post-translational modification of proteins with ubiquitin plays a central role in nearly all aspects of eukaryotic biology. Historically, studies have focused on the conjugation of ubiquitin to lysine residues in substrates, but it is now clear that ubiquitylation can also occur on cysteine, serine, and threonine residues, as well as on the N-terminal amino group of proteins. Paradigm-shifting reports of non-proteinaceous substrates have further extended the reach of ubiquitylation beyond the proteome to include intracellular lipids and sugars. Additionally, results from bacteria have revealed novel ways to ubiquitylate (and deubiquitylate) substrates without the need for any of the enzymatic components of the canonical ubiquitylation cascade. Focusing mainly upon recent findings, this review aims to outline the current understanding of non-lysine ubiquitylation and speculate upon the molecular mechanisms and physiological importance of this non-canonical modification.
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3
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Galiani S, Reglinski K, Carravilla P, Barbotin A, Urbančič I, Ott J, Sehr J, Sezgin E, Schneider F, Waithe D, Hublitz P, Schliebs W, Erdmann R, Eggeling C. Diffusion and interaction dynamics of the cytosolic peroxisomal import receptor PEX5. BIOPHYSICAL REPORTS 2022; 2:None. [PMID: 36299769 PMCID: PMC9586885 DOI: 10.1016/j.bpr.2022.100055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/24/2022] [Indexed: 11/18/2022]
Abstract
Cellular functions rely on proper actions of organelles such as peroxisomes. These organelles rely on the import of proteins from the cytosol. The peroxisomal import receptor PEX5 takes up target proteins in the cytosol and transports them to the peroxisomal matrix. However, its cytosolic molecular interactions have so far not directly been disclosed. Here, we combined advanced optical microscopy and spectroscopy techniques such as fluorescence correlation spectroscopy and stimulated emission depletion microscopy with biochemical tools to present a detailed characterization of the cytosolic diffusion and interaction dynamics of PEX5. Among other features, we highlight a slow diffusion of PEX5, independent of aggregation or target binding, but associated with cytosolic interaction partners via its N-terminal domain. This sheds new light on the functionality of the receptor in the cytosol as well as highlighting the potential of using complementary microscopy tools to decipher molecular interactions in the cytosol by studying their diffusion dynamics.
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Affiliation(s)
- S. Galiani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - K. Reglinski
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Leibniz-Institute of Photonic Technologies e.V., Jena, Germany
- Institute of Applied Optic and Biophysics, Friedrich-Schiller University Jena, Jena, Germany
- University Hospital Jena, Jena, Germany
| | - P. Carravilla
- Leibniz-Institute of Photonic Technologies e.V., Jena, Germany
- Institute of Applied Optic and Biophysics, Friedrich-Schiller University Jena, Jena, Germany
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain
| | - A. Barbotin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - I. Urbančič
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Laboratory of Biophysics, Condensed Matter Physics Department, Jožef Stefan Institute, Ljubljana, Slovenia
| | - J. Ott
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - J. Sehr
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - E. Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - F. Schneider
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - D. Waithe
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- WIMM Centre for Computational Biology , MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - P. Hublitz
- WIMM Genome Engineering Services, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - W. Schliebs
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - R. Erdmann
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - C. Eggeling
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Leibniz-Institute of Photonic Technologies e.V., Jena, Germany
- Institute of Applied Optic and Biophysics, Friedrich-Schiller University Jena, Jena, Germany
- Jena Center for Soft Matter (JCSM), Jena, Germany
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4
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Pei D, Dalbey RE. Membrane Translocation of Folded Proteins. J Biol Chem 2022; 298:102107. [PMID: 35671825 PMCID: PMC9251779 DOI: 10.1016/j.jbc.2022.102107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 12/01/2022] Open
Abstract
An ever-increasing number of proteins have been shown to translocate across various membranes of bacterial as well as eukaryotic cells in their folded states as a part of physiological and/or pathophysiological processes. Herein we provide an overview of the systems/processes that are established or likely to involve the membrane translocation of folded proteins, such as protein export by the twin-arginine translocation (TAT) system in bacteria and chloroplasts, unconventional protein secretion (UPS) and protein import into the peroxisome in eukaryotes, and the cytosolic entry of proteins (e.g., bacterial toxins) and viruses into eukaryotes. We also discuss the various mechanistic models that have previously been proposed for the membrane translocation of folded proteins including pore/channel formation, local membrane disruption, membrane thinning, and transport by membrane vesicles. Finally, we introduce a newly discovered vesicular transport mechanism, vesicle budding and collapse (VBC), and present evidence that VBC may represent a unifying mechanism that drives some (and potentially all) of folded protein translocation processes.
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Affiliation(s)
- Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210.
| | - Ross E Dalbey
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210.
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5
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Ast J, Bäcker N, Bittner E, Martorana D, Ahmad H, Bölker M, Freitag J. Two Pex5 Proteins With Different Cargo Specificity Are Critical for Peroxisome Function in Ustilago maydis. Front Cell Dev Biol 2022; 10:858084. [PMID: 35646929 PMCID: PMC9133605 DOI: 10.3389/fcell.2022.858084] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
Peroxisomes are dynamic multipurpose organelles with a major function in fatty acid oxidation and breakdown of hydrogen peroxide. Many proteins destined for the peroxisomal matrix contain a C-terminal peroxisomal targeting signal type 1 (PTS1), which is recognized by tetratricopeptide repeat (TPR) proteins of the Pex5 family. Various species express at least two different Pex5 proteins, but how this contributes to protein import and organelle function is not fully understood. Here, we analyzed truncated and chimeric variants of two Pex5 proteins, Pex5a and Pex5b, from the fungus Ustilago maydis. Both proteins are required for optimal growth on oleic acid-containing medium. The N-terminal domain (NTD) of Pex5b is critical for import of all investigated peroxisomal matrix proteins including PTS2 proteins and at least one protein without a canonical PTS. In contrast, the NTD of Pex5a is not sufficient for translocation of peroxisomal matrix proteins. In the presence of Pex5b, however, specific cargo can be imported via this domain of Pex5a. The TPR domains of Pex5a and Pex5b differ in their affinity to variations of the PTS1 motif and thus can mediate import of different subsets of matrix proteins. Together, our data reveal that U. maydis employs versatile targeting modules to control peroxisome function. These findings will promote our understanding of peroxisomal protein import also in other biological systems.
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Affiliation(s)
- Julia Ast
- Department of Biology, Philipps-University Marburg, Marburg, Germany
- Institute of Metabolism and Systems Research (IMSR), and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, United Kingdom
| | - Nils Bäcker
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Elena Bittner
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | | | - Humda Ahmad
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Michael Bölker
- Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Johannes Freitag
- Department of Biology, Philipps-University Marburg, Marburg, Germany
- *Correspondence: Johannes Freitag,
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6
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Pls1 Is a Peroxisomal Matrix Protein with a Role in Regulating Lysine Biosynthesis. Cells 2022; 11:cells11091426. [PMID: 35563734 PMCID: PMC9104712 DOI: 10.3390/cells11091426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/13/2022] [Accepted: 04/16/2022] [Indexed: 12/04/2022] Open
Abstract
Peroxisomes host essential metabolic enzymes and are crucial for human health and survival. Although peroxisomes were first described over 60 years ago, their entire proteome has not yet been identified. As a basis for understanding the variety of peroxisomal functions, we used a high-throughput screen to discover peroxisomal proteins in yeast. To visualize low abundance proteins, we utilized a collection of strains containing a peroxisomal marker in which each protein is expressed from the constitutive and strong TEF2 promoter. Using this approach, we uncovered 18 proteins that were not observed in peroxisomes before and could show their metabolic and targeting factor dependence for peroxisomal localization. We focus on one newly identified and uncharacterized matrix protein, Ynl097c-b, and show that it localizes to peroxisomes upon lysine deprivation and that its localization to peroxisomes depends on the lysine biosynthesis enzyme, Lys1. We demonstrate that Ynl097c-b affects the abundance of Lys1 and the lysine biosynthesis pathway. We have therefore renamed this protein Pls1 for Peroxisomal Lys1 Stabilizing 1. Our work uncovers an additional layer of regulation on the central lysine biosynthesis pathway. More generally it highlights how the discovery of peroxisomal proteins can expand our understanding of cellular metabolism.
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7
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Al‐Hajaya Y, Karpinska B, Foyer CH, Baker A. Nuclear and peroxisomal targeting of catalase. PLANT, CELL & ENVIRONMENT 2022; 45:1096-1108. [PMID: 35040158 PMCID: PMC9305541 DOI: 10.1111/pce.14262] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 06/14/2023]
Abstract
Catalase is a well-known component of the cellular antioxidant network, but there have been conflicting conclusions reached regarding the nature of its peroxisome targeting signal. It has also been reported that catalase can be hijacked to the nucleus by effector proteins of plant pathogens. Using a physiologically relevant system where native untagged catalase variants are expressed in a cat2-1 mutant background, the C terminal most 18 amino acids could be deleted without affecting activity, peroxisomal targeting or ability to complement multiple phenotypes of the cat2-1 mutant. In contrast, converting the native C terminal tripeptide PSI to the canonical PTS1 sequence ARL resulted in lower catalase specific activity. Localisation experiments using split superfolder green fluorescent protein revealed that catalase can be targeted to the nucleus in the absence of any pathogen effectors, and that C terminal tagging in combination with alterations of the native C terminus can interfere with nuclear localisation. These findings provide fundamental new insights into catalase targeting and pave the way for exploration of the mechanism of catalase targeting to the nucleus and its role in non-infected plants.
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Affiliation(s)
- Yousef Al‐Hajaya
- Centre for Plant Sciences and School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Present address:
Department of Laboratory Medical SciencesMutah UniversityKarakJordan
| | - Barbara Karpinska
- Centre for Plant Sciences and School of BiologyUniversity of LeedsLeedsUK
| | - Christine H. Foyer
- Centre for Plant Sciences and School of BiologyUniversity of LeedsLeedsUK
- Present address:
School of Biosciences, College of Life and Environmental SciencesUniversity of BirminghamEdgbastonUK
| | - Alison Baker
- Centre for Plant Sciences and School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
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8
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Yang W, Gutbrod P, Gutbrod K, Peisker H, Song X, Falz AL, Meyer AJ, Dörmann P. 2-Hydroxy-phytanoyl-CoA lyase (AtHPCL) is involved in phytol metabolism in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1290-1304. [PMID: 34902195 DOI: 10.1111/tpj.15632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
During chlorophyll degradation, large amounts of the isoprenoid alcohol phytol are released. The pathway of phytol catabolism has been studied in humans, because chlorophyll is part of the human diet, but little is known for plants. In humans, phytanoyl-CoA derived from phytol is degraded via α-oxidation by phytanoyl-CoA hydroxylase (PAHX) and 2-hydroxy-phytanoyl-CoA lyase (HPCL). Arabidopsis contains two sequences homologous to the human proteins AtPAHX and AtHPCL. Insertional mutants of Arabidopsis (pahx, hpcl) were grown under N deprivation to stimulate chlorophyll breakdown or supplemented with phytol to increase the endogenous amount of phytol. During N deprivation, chlorophyll, phytol, phytenal, upstream metabolites of phytol breakdown, and tocopherol and fatty acid phytyl esters, alternative phytol-derived lipids, accumulated in pahx and hpcl mutants, in line with the scenario that the mutations interfere with phytol degradation. AtHPCL was localized to the peroxisomes. Expression analysis of the AtHPCL sequence in the yeast Δpxp1 or Δmpo1 mutants followed by supplementation with 2-hydroxy-palmitic acid and enzyme assays of peroxisomal proteins from Col-0 and hpcl plants with 2-hydroxy-stearoyl-CoA revealed that AtHPCL harbors 2-hydroxy-acyl-CoA lyase activity. The α-dioxygenases αDOX1 and αDOX2 are involved in α-oxidation of fatty acids and could be involved in an alternative pathway of phytol degradation. However, phytol-related lipids in the αdox1, αdox2, or αdox1 αdox2 mutants were not altered compared with Col-0, indicating that αDOX1 and αDOX2 are not involved in phytol degradation. These results demonstrate that phytol degradation in Arabidopsis involves α-oxidation by AtPAHX and AtHPCL, but that it is independent of αDOX1/αDOX2.
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Affiliation(s)
- Wentao Yang
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Straße 13, 53115, Bonn, Germany
| | - Philipp Gutbrod
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Straße 13, 53115, Bonn, Germany
| | - Katharina Gutbrod
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Straße 13, 53115, Bonn, Germany
| | - Helga Peisker
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Straße 13, 53115, Bonn, Germany
| | - Xiaoning Song
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Straße 13, 53115, Bonn, Germany
| | - Anna-Lena Falz
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
| | - Andreas J Meyer
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
| | - Peter Dörmann
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Straße 13, 53115, Bonn, Germany
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9
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Identification of Six Thiolases and their Effects on Fatty Acid and Ergosterol Biosynthesis in Aspergillus oryzae. Appl Environ Microbiol 2022; 88:e0237221. [PMID: 35138925 DOI: 10.1128/aem.02372-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thiolase plays important roles in lipid metabolism. It can be divided into degradative thiolases (Thioase I) and biosynthetic thiolases (thiolases II), which are involved in fatty acid β-oxidation and acetoacetyl-CoA biosynthesis, respectively. The Saccharomyces cerevisiae (S. cerevisiae) genome harbors only one gene each for thioase I and thiolase II, namely, Pot1 and Erg10, respectively. In this study, six thiolases (named AoErg10A-AoErg10F) were identified in Aspergillus oryzae (A. oryzae) genome using bioinformatics analysis. Quantitative reverse transcription-PCR (qRT-PCR) indicated that the expression of these six thiolases varied at different growth time and under different forms of abiotic stress. Subcellular localization analysis showed that AoErg10A was located in the cytoplasm, AoErg10B and AoErg10C in the mitochondria, and AoErg10D-AoErg10F in the peroxisome. Yeast heterologous complementation assays revealed that AoErg10A, AoErg10D, AoErg10E, AoErg10F and cytoplasmic AoErg10B (AoErg10BΔMTS) recovered the phenotypes of S. cerevisiae erg10 weak and lethal mutants, and that only AoErg10D-F recovered the phenotype of the pot1 mutant that cannot use oleic acid as the carbon source. Overexpression of AoErg10s either affected the growth speed or sporulation of the transgenic strains. In addition, the fatty acid and ergosterol content changed in all the AoErg10-overexpressing strains. This study revealed the function of six thiolases in A. oryzae and their effect on growth, and fatty acid and ergosterol biosynthesis, which may lay the foundation for genetic engineering for lipid metabolism in A. oryzae or other fungi. Importance Thiolase including thioase I and thiolase II, plays important roles in lipid metabolism. A. oryzae, one of the most industrially important filamentous fungi, has been widely used for manufacturing oriental fermented food such as sauce, miso, and sake for a long time. Besides, A. oryzae has a high capability in production of high lipid content and has been used for lipid production. Thus, it is very important to investigate the function of thiolases in A. oryzae. In this study, six thiolase (named AoErg10A-AoErg10F) were identified by bioinformatics analysis. Unlike other reported thiolases in fungi, three of the six thiolases showed dual function of thioase I and thiolase II in S. cerevisiae, indicating the lipid metabolism is more complex in A. oryzae. The reveal of function of these thiolases in A. oryzae can lay the foundation for genetic engineering for lipid metabolism in A. oryzae or other fungi.
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10
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Dindo M, Ambrosini G, Oppici E, Pey AL, O’Toole PJ, Marrison JL, Morrison IEG, Butturini E, Grottelli S, Costantini C, Cellini B. Dimerization Drives Proper Folding of Human Alanine:Glyoxylate Aminotransferase But Is Dispensable for Peroxisomal Targeting. J Pers Med 2021; 11:jpm11040273. [PMID: 33917320 PMCID: PMC8067440 DOI: 10.3390/jpm11040273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 12/15/2022] Open
Abstract
Peroxisomal matrix proteins are transported into peroxisomes in a fully-folded state, but whether multimeric proteins are imported as monomers or oligomers is still disputed. Here, we used alanine:glyoxylate aminotransferase (AGT), a homodimeric pyridoxal 5′-phosphate (PLP)-dependent enzyme, whose deficit causes primary hyperoxaluria type I (PH1), as a model protein and compared the intracellular behavior and peroxisomal import of native dimeric and artificial monomeric forms. Monomerization strongly reduces AGT intracellular stability and increases its aggregation/degradation propensity. In addition, monomers are partly retained in the cytosol. To assess possible differences in import kinetics, we engineered AGT to allow binding of a membrane-permeable dye and followed its intracellular trafficking without interfering with its biochemical properties. By fluorescence recovery after photobleaching, we measured the import rate in live cells. Dimeric and monomeric AGT displayed a similar import rate, suggesting that the oligomeric state per se does not influence import kinetics. However, when dimerization is compromised, monomers are prone to misfolding events that can prevent peroxisomal import, a finding crucial to predicting the consequences of PH1-causing mutations that destabilize the dimer. Treatment with pyridoxine of cells expressing monomeric AGT promotes dimerization and folding, thus, demonstrating the chaperone role of PLP. Our data support a model in which dimerization represents a potential key checkpoint in the cytosol at the crossroad between misfolding and correct targeting, a possible general mechanism for other oligomeric peroxisomal proteins.
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Affiliation(s)
- Mirco Dindo
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (M.D.); (S.G.); (C.C.)
| | - Giulia Ambrosini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (G.A.); (E.O.); (E.B.)
| | - Elisa Oppici
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (G.A.); (E.O.); (E.B.)
| | - Angel L. Pey
- Departamento de Química Física, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain;
| | - Peter J. O’Toole
- Bioscience Technology Facility, Department of Biology, University of York, York YO23 3GE, UK; (P.J.O.); (J.L.M.); (I.E.G.M.)
| | - Joanne L. Marrison
- Bioscience Technology Facility, Department of Biology, University of York, York YO23 3GE, UK; (P.J.O.); (J.L.M.); (I.E.G.M.)
| | - Ian E. G. Morrison
- Bioscience Technology Facility, Department of Biology, University of York, York YO23 3GE, UK; (P.J.O.); (J.L.M.); (I.E.G.M.)
| | - Elena Butturini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (G.A.); (E.O.); (E.B.)
| | - Silvia Grottelli
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (M.D.); (S.G.); (C.C.)
| | - Claudio Costantini
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (M.D.); (S.G.); (C.C.)
| | - Barbara Cellini
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (M.D.); (S.G.); (C.C.)
- Correspondence: ; Tel.: +39-075-585-8339
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11
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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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12
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Kempiński B, Chełstowska A, Poznański J, Król K, Rymer Ł, Frydzińska Z, Girzalsky W, Skoneczna A, Erdmann R, Skoneczny M. The Peroxisomal Targeting Signal 3 (PTS3) of the Budding Yeast Acyl-CoA Oxidase Is a Signal Patch. Front Cell Dev Biol 2020; 8:198. [PMID: 32292783 PMCID: PMC7135854 DOI: 10.3389/fcell.2020.00198] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/09/2020] [Indexed: 11/13/2022] Open
Abstract
The specificity of import of peroxisomal matrix proteins is dependent on the targeting signals encoded within their amino acid sequences. Two known import signals, peroxisomal targeting signal 1 (PTS1), positioned at the C-termini and PTS2 located close to N-termini of these proteins are recognized by the Pex5p and Pex7p receptors, respectively. However, in several yeast species, including Saccharomyces cerevisiae, proteins exist that are efficiently imported into peroxisomes despite having neither PTS1 nor PTS2 and for which no other import signal has been determined. An example of such a protein is S. cerevisiae acyl-CoA oxidase (AOx) encoded by the POX1 gene. While it is known that its import is driven by its interaction with the N-terminal segment of Pex5p, which is separate from its C-terminal PTS1-recognizing tetratricopeptide domain, to date, no AOx polypeptide region has been implicated as critical for this interaction, and thus would constitute the long-sought PTS3 signal. Using random mutagenesis combined with a two-hybrid screen, we identified single amino acid residues within the AOx polypeptide that are crucial for this interaction and for the peroxisomal import of this protein. Interestingly, while scattered throughout the primary sequence, these amino acids come close to each other within two domains of the folded AOx. Although the role of one or both of these regions as the PTS3 signal is not finally proven, our data indicate that the signal guiding AOx into peroxisomal matrix is not a linear sequence but a signal patch.
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Affiliation(s)
- Błażej Kempiński
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Chełstowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamil Król
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Łukasz Rymer
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Zuzanna Frydzińska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Wolfgang Girzalsky
- Medizinische Fakultät, Biochemie und Pathobiochemie/Systembiochemie, Ruhr-Universität Bochum, Bochum, Germany
| | - Adrianna Skoneczna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Ralf Erdmann
- Medizinische Fakultät, Biochemie und Pathobiochemie/Systembiochemie, Ruhr-Universität Bochum, Bochum, Germany
| | - Marek Skoneczny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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13
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Abstract
The past several decades have witnessed tremendous growth in the protein targeting, transport and translocation field. Major advances were made during this time period. Now the molecular details of the targeting factors, receptors and the membrane channels that were envisioned in Blobel's Signal Hypothesis in the 1970s have been revealed by powerful structural methods. It is evident that there is a myriad of cytosolic and membrane associated systems that accurately sort and target newly synthesized proteins to their correct membrane translocases for membrane insertion or protein translocation. Here we will describe the common principles for protein transport in prokaryotes and eukaryotes.
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14
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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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15
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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: 24] [Impact Index Per Article: 4.8] [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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16
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Knebel B, Fahlbusch P, Dille M, Wahlers N, Hartwig S, Jacob S, Kettel U, Schiller M, Herebian D, Koellmer C, Lehr S, Müller-Wieland D, Kotzka J. Fatty Liver Due to Increased de novo Lipogenesis: Alterations in the Hepatic Peroxisomal Proteome. Front Cell Dev Biol 2019; 7:248. [PMID: 31709254 PMCID: PMC6823594 DOI: 10.3389/fcell.2019.00248] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/08/2019] [Indexed: 12/15/2022] Open
Abstract
In non-alcoholic fatty liver disease (NAFLD) caused by ectopic lipid accumulation, lipotoxicity is a crucial molecular risk factor. Mechanisms to eliminate lipid overflow can prevent the liver from functional complications. This may involve increased secretion of lipids or metabolic adaptation to ß-oxidation in lipid-degrading organelles such as mitochondria and peroxisomes. In addition to dietary factors, increased plasma fatty acid levels may be due to increased triglyceride synthesis, lipolysis, as well as de novo lipid synthesis (DNL) in the liver. In the present study, we investigated the impact of fatty liver caused by elevated DNL, in a transgenic mouse model with liver-specific overexpression of human sterol regulatory element-binding protein-1c (alb-SREBP-1c), on hepatic gene expression, on plasma lipids and especially on the proteome of peroxisomes by omics analyses, and we interpreted the results with knowledge-based analyses. In summary, the increased hepatic DNL is accompanied by marginal gene expression changes but massive changes in peroxisomal proteome. Furthermore, plasma phosphatidylcholine (PC) as well as lysoPC species were altered. Based on these observations, it can be speculated that the plasticity of organelles and their functionality may be directly affected by lipid overflow.
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Affiliation(s)
- Birgit Knebel
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Pia Fahlbusch
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Matthias Dille
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Natalie Wahlers
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Sonja Hartwig
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Sylvia Jacob
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Ulrike Kettel
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Martina Schiller
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Diran Herebian
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, University Children’s Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Cornelia Koellmer
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Stefan Lehr
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
| | - Dirk Müller-Wieland
- Department of Internal Medicine I, Clinical Research Centre, University Hospital Aachen, Aachen, Germany
| | - Jorg Kotzka
- Leibniz Center for Diabetes Research, Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, Düsseldorf, Germany
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17
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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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18
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Falter C, Thu NBA, Pokhrel S, Reumann S. New guidelines for fluorophore application in peroxisome targeting analyses in transient plant expression systems. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:884-899. [PMID: 30791204 DOI: 10.1111/jipb.12791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/14/2019] [Indexed: 06/09/2023]
Abstract
Peroxisome research has been revolutionized by proteome studies combined with in vivo subcellular targeting analyses. Yellow and cyan fluorescent protein (YFP and CFP) are the classical fluorophores of plant peroxisome research. In the new transient expression system of Arabidopsis seedlings co-cultivated with Agrobacterium we detected the YFP fusion of one candidate protein in peroxisomes, but only upon co-transformation with the peroxisome marker, CFP-PTS1. The data suggested that the YFP fusion was directed to peroxisomes due to its weak heterodimerization ability with CFP-PTS1, allowing piggy-back import into peroxisomes. Indeed, if co-expressed with monomeric Cerulean-PTS1 (mCer-PTS1), the YFP fusion was no longer matrix localized. We systematically investigated the occurrence and extent of dimerization-based piggy-back import for different fluorophore combinations in five major transient plant expression systems. In Arabidopsis seedlings and tobacco leaves both untagged YFP and monomeric Venus were imported into peroxisomes if co-expressed with CFP-PTS1 but not with mCer-PTS1. By contrast, piggy-back import of cytosolic proteins was not observed in Arabidopsis and tobacco protoplasts or in onion epidermal cells for any fluorophore combination at any time point. Based on these important results we formulate new guidelines for fluorophore usage and experimental design to guarantee reliable identification of novel plant peroxisomal proteins.
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Affiliation(s)
- Christian Falter
- Plant Biochemistry and Infection Biology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
| | - Nguyen Binh Anh Thu
- Plant Biochemistry and Infection Biology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
| | - Saugat Pokhrel
- Plant Biochemistry and Infection Biology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
| | - Sigrun Reumann
- Plant Biochemistry and Infection Biology, Institute of Plant Science and Microbiology, University of Hamburg, Hamburg, Germany
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19
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Romano FB, Blok NB, Rapoport TA. Peroxisome protein import recapitulated in Xenopus egg extracts. J Cell Biol 2019; 218:2021-2034. [PMID: 30971414 PMCID: PMC6548129 DOI: 10.1083/jcb.201901152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/17/2019] [Accepted: 03/28/2019] [Indexed: 12/14/2022] Open
Abstract
Peroxisomes import proteins with a C-terminal SKL sequence by a poorly understood mechanism. Romano et al. use Xenopus egg extracts to study peroxisome import in vitro. The novel assay recapitulates import in vivo and provides mechanistic insights. Peroxisomes import their luminal proteins from the cytosol. Most substrates contain a C-terminal Ser-Lys-Leu (SKL) sequence that is recognized by the receptor Pex5. Pex5 binds to peroxisomes via a docking complex containing Pex14, and recycles back into the cytosol following its mono-ubiquitination at a conserved Cys residue. The mechanism of peroxisome protein import remains incompletely understood. Here, we developed an in vitro import system based on Xenopus egg extracts. Import is dependent on the SKL motif in the substrate and on the presence of Pex5 and Pex14, and is sustained by ATP hydrolysis. A protein lacking an SKL sequence can be coimported, providing strong evidence for import of a folded protein. The conserved cysteine in Pex5 is not essential for import or to clear import sites for subsequent rounds of translocation. This new in vitro assay will be useful for further dissecting the mechanism of peroxisome protein import.
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Affiliation(s)
- Fabian B Romano
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Neil B Blok
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA
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20
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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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21
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Yang J, Pieuchot L, Jedd G. Artificial import substrates reveal an omnivorous peroxisomal importomer. Traffic 2018; 19:786-797. [PMID: 30058098 DOI: 10.1111/tra.12607] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/19/2018] [Accepted: 07/19/2018] [Indexed: 11/30/2022]
Abstract
The peroxisome matrix protein importomer has the remarkable ability to transport oligomeric protein substrates across the bilayer. However, the selectivity and relation between import and overall peroxisome homeostasis remain unclear. Here, we microinject artificial import substrates and employ quantitative microscopy to probe limits and capabilities of the importomer. DNA and polysaccharides are "piggyback" imported when noncovalently bound by a peroxisome targeting signal (PTS)-bearing protein. A dimerization domain that can be tuned to systematically vary the binding dissociation constant (Kd ) shows that a Kd in the millimolar range is sufficient to promote piggyback import. Microinjection of import substrate at high levels results in peroxisome growth and a proportional accumulation of peroxisome membrane proteins (PMPs). However, corresponding PMP mRNAs do not accumulate, suggesting that this response is posttranscriptionally regulated. Together, our data show that the importomer can tolerate diverse macromolecular species. Coupling between matrix import and membrane biogenesis suggests that matrix protein expression levels can be sufficient to regulate peroxisome size.
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Affiliation(s)
- Jing Yang
- Temasek Life Sciences Laboratory, and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Laurent Pieuchot
- CNRS, IS2M UMR 7361, Université de Haute-Alsace, Mulhouse, France
- Université de Strasbourg, Strasbourg, France
| | - Gregory Jedd
- Temasek Life Sciences Laboratory, and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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22
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Rymer Ł, Kempiński B, Chełstowska A, Skoneczny M. The budding yeast Pex5p receptor directs Fox2p and Cta1p into peroxisomes via its N-terminal region near the FxxxW domain. J Cell Sci 2018; 131:jcs.216986. [PMID: 30131444 DOI: 10.1242/jcs.216986] [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: 02/18/2018] [Accepted: 08/07/2018] [Indexed: 01/08/2023] Open
Abstract
The import of most of peroxisomal proteins into the lumen of their target organelle is driven by C-terminal (PTS1) or N-terminal (PTS2) signals recognized by the Pex5p or Pex7p receptors, respectively. However, some proteins in budding yeast, such as acyl-CoA oxidase (AOx) and carnitine acetyltransferase (Cat2p), are imported into peroxisomes via an alternative route that does not rely on known PTS signals and involves the Pex5p receptor N-terminal region. Here, we show that two other budding yeast peroxisomal proteins, a multifunctional enzyme from the β-oxidation pathway (Fox2p) and catalase A (Cta1p), both of which contain PTS1, can be imported independently of this signal. The I264K amino acid substitution in Pex5p adjacent to its FxxxW diaromatic motif, previously shown to abolish the import of AOx and Cat2p into peroxisomes, also affects Fox2p and Cta1p import. Moreover, we demonstrate that Pex9p, a newly discovered paralog of Pex5p that was recently implicated in the import of malate synthases in budding yeast, also exhibits weak receptor activity towards Fox2p and Cta1p. These findings indicate the need to re-evaluate the peroxisomal import paradigm.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Łukasz Rymer
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland
| | - Błażej Kempiński
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland
| | - Anna Chełstowska
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland
| | - Marek Skoneczny
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland
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23
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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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24
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Freitag J, Stehlik T, Stiebler AC, Bölker M. The Obvious and the Hidden: Prediction and Function of Fungal Peroxisomal Matrix Proteins. Subcell Biochem 2018; 89:139-155. [PMID: 30378022 DOI: 10.1007/978-981-13-2233-4_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fungal peroxisomes are characterized by a number of specific biological functions. To understand the physiology and biochemistry of these organelles knowledge of the proteome content is crucial. Here, we address different strategies to predict peroxisomal proteins by bioinformatics approaches. These tools range from simple text searches to network based learning strategies. A complication of this analysis is the existence of cryptic peroxisomal proteins, which are overlooked in conventional bioinformatics queries. These include proteins where targeting information results from transcriptional and posttranscriptional alterations. But also proteins with low efficiency targeting motifs that are predominantly localized in the cytosol, and proteins lacking any canonical targeting information, can play important roles within peroxisomes. Many of these proteins are so far unpredictable. Detection and characterization of these cryptic peroxisomal proteins revealed the presence of novel peroxisomal enzymatic reaction networks in fungi.
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Affiliation(s)
- Johannes Freitag
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Thorsten Stehlik
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Alina C Stiebler
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Michael Bölker
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany.
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25
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Kunze M. Predicting Peroxisomal Targeting Signals to Elucidate the Peroxisomal Proteome of Mammals. Subcell Biochem 2018; 89:157-199. [PMID: 30378023 DOI: 10.1007/978-981-13-2233-4_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peroxisomes harbor a plethora of proteins, but the peroxisomal proteome as the entirety of all peroxisomal proteins is still unknown for mammalian species. Computational algorithms can be used to predict the subcellular localization of proteins based on their amino acid sequence and this method has been amply used to forecast the intracellular fate of individual proteins. However, when applying such algorithms systematically to all proteins of an organism the prediction of its peroxisomal proteome in silico should be possible. Therefore, a reliable detection of peroxisomal targeting signals (PTS ) acting as postal codes for the intracellular distribution of the encoding protein is crucial. Peroxisomal proteins can utilize different routes to reach their destination depending on the type of PTS. Accordingly, independent prediction algorithms have been developed for each type of PTS, but only those for type-1 motifs (PTS1) have so far reached a satisfying predictive performance. This is partially due to the low number of peroxisomal proteins limiting the power of statistical analyses and partially due to specific properties of peroxisomal protein import, which render functional PTS motifs inactive in specific contexts. Moreover, the prediction of the peroxisomal proteome is limited by the high number of proteins encoded in mammalian genomes, which causes numerous false positive predictions even when using reliable algorithms and buries the few yet unidentified peroxisomal proteins. Thus, the application of prediction algorithms to identify all peroxisomal proteins is currently ineffective as stand-alone method, but can display its full potential when combined with other methods.
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Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
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26
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Kalel VC, Erdmann R. Unraveling of the Structure and Function of Peroxisomal Protein Import Machineries. Subcell Biochem 2018; 89:299-321. [PMID: 30378029 DOI: 10.1007/978-981-13-2233-4_13] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peroxisomes are dynamic organelles of eukaryotic cells performing a wide range of functions including fatty acid oxidation, peroxide detoxification and ether-lipid synthesis in mammals. Peroxisomes lack their own DNA and therefore have to import proteins post-translationally. Peroxisomes can import folded, co-factor bound and even oligomeric proteins. The involvement of cycling receptors is a special feature of peroxisomal protein import. Complex machineries of peroxin (PEX) proteins mediate peroxisomal matrix and membrane protein import. Identification of PEX genes was dominated by forward genetic techniques in the early 90s. However, recent developments in proteomic techniques has revolutionized the detailed characterization of peroxisomal protein import. Here, we summarize the current knowledge on peroxisomal protein import with emphasis on the contribution of proteomic approaches to our understanding of the composition and function of the peroxisomal protein import machineries.
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Affiliation(s)
- Vishal C Kalel
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany.
| | - Ralf Erdmann
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany
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27
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Li L, Wang J, Chen H, Chai R, Zhang Z, Mao X, Qiu H, Jiang H, Wang Y, Sun G. Pex14/17, a filamentous fungus-specific peroxin, is required for the import of peroxisomal matrix proteins and full virulence of Magnaporthe oryzae. MOLECULAR PLANT PATHOLOGY 2017; 18:1238-1252. [PMID: 27571711 PMCID: PMC6638247 DOI: 10.1111/mpp.12487] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/11/2016] [Accepted: 08/28/2016] [Indexed: 05/27/2023]
Abstract
Peroxisomes are ubiquitous organelles in eukaryotic cells that fulfil a variety of biochemical functions. The biogenesis of peroxisomes requires a variety of proteins, named peroxins, which are encoded by PEX genes. Pex14/17 is a putative recently identified peroxin, specifically present in filamentous fungal species. Its function in peroxisomal biogenesis is still obscure and its roles in fungal pathogenicity have not yet been documented. Here, we demonstrate the contributions of Pex14/17 in the rice blast fungus Magnaporthe oryzae (Mopex14/17) to peroxisomal biogenesis and fungal pathogenicity by targeting gene replacement strategies. Mopex14/17 has properties of both Pex14 and Pex17 with regard to its protein sequence. Mopex14/17 is distributed at the peroxisomal membrane and is essential for efficient peroxisomal targeting of proteins containing peroxisomal targeting signal 1. MoPEX19 deletion leads to the cytoplasmic distribution of Mopex14/17, indicating that the peroxisomal import of Pex14/17 is dependent on Pex19. The knockout mutants of MoPEX14/17 show reduced fatty acid utilization, reactive oxygen species (ROS) degradation and cell wall integrity. Moreover, Δmopex14/17 mutants show delayed conidial generation and appressorial formation, and a reduction in appressorial turgor accumulation and penetration ability in host plants. These defects result in a significant reduction in the virulence of the mutant. These data indicate that MoPEX14/17 plays a crucial role in peroxisome biogenesis and contributes to fungal development and pathogenicity.
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Affiliation(s)
- Ling Li
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlInstitute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural SciencesHangzhou310021China
- School of Agricultural and Food SciencesZhejiang Agriculture and Forest UniversityHangzhou311300China
| | - Jiaoyu Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlInstitute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural SciencesHangzhou310021China
| | - Haili Chen
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlInstitute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural SciencesHangzhou310021China
| | - Rongyao Chai
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlInstitute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural SciencesHangzhou310021China
| | - Zhen Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlInstitute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural SciencesHangzhou310021China
| | - Xueqin Mao
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlInstitute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural SciencesHangzhou310021China
| | - Haiping Qiu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlInstitute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural SciencesHangzhou310021China
| | - Hua Jiang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlInstitute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural SciencesHangzhou310021China
| | - Yanli Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlInstitute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural SciencesHangzhou310021China
| | - Guochang Sun
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease ControlInstitute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural SciencesHangzhou310021China
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28
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Francisco T, Rodrigues TA, Dias AF, Barros-Barbosa A, Bicho D, Azevedo JE. Protein transport into peroxisomes: Knowns and unknowns. Bioessays 2017; 39. [PMID: 28787099 DOI: 10.1002/bies.201700047] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Peroxisomal matrix proteins are synthesized on cytosolic ribosomes and rapidly transported into the organelle by a complex machinery. The data gathered in recent years suggest that this machinery operates through a syringe-like mechanism, in which the shuttling receptor PEX5 - the "plunger" - pushes a newly synthesized protein all the way through a peroxisomal transmembrane protein complex - the "barrel" - into the matrix of the organelle. Notably, insertion of cargo-loaded receptor into the "barrel" is an ATP-independent process, whereas extraction of the receptor back into the cytosol requires its monoubiquitination and the action of ATP-dependent mechanoenzymes. Here, we review the main data behind this model.
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Affiliation(s)
- 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
| | - 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 F Dias
- 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
| | - Aurora Barros-Barbosa
- 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
| | - Diana Bicho
- 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
| | - 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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29
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Dias AF, Rodrigues TA, Pedrosa AG, Barros-Barbosa A, Francisco T, Azevedo JE. The peroxisomal matrix protein translocon is a large cavity-forming protein assembly into which PEX5 protein enters to release its cargo. J Biol Chem 2017; 292:15287-15300. [PMID: 28765278 DOI: 10.1074/jbc.m117.805044] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 07/26/2017] [Indexed: 12/18/2022] Open
Abstract
A remarkable property of the machinery for import of peroxisomal matrix proteins is that it can accept already folded proteins as substrates. This import involves binding of newly synthesized proteins by cytosolic peroxisomal biogenesis factor 5 (PEX5) followed by insertion of the PEX5-cargo complex into the peroxisomal membrane at the docking/translocation module (DTM). However, how these processes occur remains largely unknown. Here, we used truncated PEX5 molecules to probe the DTM architecture. We found that the DTM can accommodate a larger number of truncated PEX5 molecules comprising amino acid residues 1-197 than full-length PEX5 molecules. A shorter PEX5 version (PEX5(1-125)) still interacted correctly with the DTM; however, this species was largely accessible to exogenously added proteinase K, suggesting that this protease can access the DTM occupied by a small PEX5 protein. Interestingly, the PEX5(1-125)-DTM interaction was inhibited by a polypeptide comprising PEX5 residues 138-639. Apparently, the DTM can recruit soluble PEX5 through interactions with different PEX5 domains, suggesting that the PEX5-DTM interactions are to some degree fuzzy. Finally, we found that the interaction between PEX5 and PEX14, a major DTM component, is stable at pH 11.5. Thus, there is no reason to assume that the hitherto intriguing resistance of DTM-bound PEX5 to alkaline extraction reflects its direct contact with the peroxisomal lipid bilayer. Collectively, these results suggest that the DTM is best described as a large cavity-forming protein assembly into which cytosolic PEX5 can enter to release its cargo.
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Affiliation(s)
- Ana F Dias
- From the Instituto de Investigação e Inovação em Saúde (i3S) and.,the Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal and.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Tony A Rodrigues
- From the Instituto de Investigação e Inovação em Saúde (i3S) and.,the Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal and.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Ana G Pedrosa
- From the Instituto de Investigação e Inovação em Saúde (i3S) and.,the Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal and.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Aurora Barros-Barbosa
- From the Instituto de Investigação e Inovação em Saúde (i3S) and.,the Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal and
| | - Tânia Francisco
- From the Instituto de Investigação e Inovação em Saúde (i3S) and.,the Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal and
| | - Jorge E Azevedo
- From the Instituto de Investigação e Inovação em Saúde (i3S) and .,the Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal and.,Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
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30
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Walton PA, Brees C, Lismont C, Apanasets O, Fransen M. The peroxisomal import receptor PEX5 functions as a stress sensor, retaining catalase in the cytosol in times of oxidative stress. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:1833-1843. [PMID: 28760655 DOI: 10.1016/j.bbamcr.2017.07.013] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 07/03/2017] [Accepted: 07/27/2017] [Indexed: 02/08/2023]
Abstract
Accumulating evidence indicates that peroxisome functioning, catalase localization, and cellular oxidative balance are intimately interconnected. Nevertheless, it remains largely unclear why modest increases in the cellular redox state especially interfere with the subcellular localization of catalase, the most abundant peroxisomal antioxidant enzyme. This study aimed at gaining more insight into this phenomenon. Therefore, we first established a simple and powerful approach to study peroxisomal protein import and protein-protein interactions in living cells in response to changes in redox state. By employing this approach, we confirm and extend previous observations that Cys-11 of human PEX5, the shuttling import receptor for peroxisomal matrix proteins containing a C-terminal peroxisomal targeting signal (PTS1), functions as a redox switch that modulates the protein's activity in response to intracellular oxidative stress. In addition, we show that oxidative stress affects the import of catalase, a non-canonical PTS1-containing protein, more than the import of a reporter protein containing a canonical PTS1. Furthermore, we demonstrate that changes in the local redox state do not affect PEX5-substrate binding and that human PEX5 does not oligomerize in cellulo, not even when the cells are exposed to oxidative stress. Finally, we present evidence that catalase retained in the cytosol can protect against H2O2-mediated redox changes in a manner that peroxisomally targeted catalase does not. Together, these findings lend credit to the idea that inefficient catalase import, when coupled with the role of PEX5 as a redox-regulated import receptor, constitutes a cellular defense mechanism to combat oxidative insults of extra-peroxisomal origin.
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Affiliation(s)
- Paul A Walton
- Laboratory of Lipid Biochemistry and Protein Interactions, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, Box 601, B-3000 Leuven, Belgium; Department of Anatomy and Cell Biology, University of Western Ontario, 474 Medical Sciences Building, London, Ontario ON N6A 3K7, Canada
| | - Chantal Brees
- Laboratory of Lipid Biochemistry and Protein Interactions, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, Box 601, B-3000 Leuven, Belgium
| | - Celien Lismont
- Laboratory of Lipid Biochemistry and Protein Interactions, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, Box 601, B-3000 Leuven, Belgium
| | - Oksana Apanasets
- Laboratory of Lipid Biochemistry and Protein Interactions, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, Box 601, B-3000 Leuven, Belgium
| | - Marc Fransen
- Laboratory of Lipid Biochemistry and Protein Interactions, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, Box 601, B-3000 Leuven, Belgium.
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31
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Beghein E, Gettemans J. Nanobody Technology: A Versatile Toolkit for Microscopic Imaging, Protein-Protein Interaction Analysis, and Protein Function Exploration. Front Immunol 2017; 8:771. [PMID: 28725224 PMCID: PMC5495861 DOI: 10.3389/fimmu.2017.00771] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/16/2017] [Indexed: 01/05/2023] Open
Abstract
Over the last two decades, nanobodies or single-domain antibodies have found their way in research, diagnostics, and therapy. These antigen-binding fragments, derived from Camelid heavy chain only antibodies, possess remarkable characteristics that favor their use over conventional antibodies or fragments thereof, in selected areas of research. In this review, we assess the current status of nanobodies as research tools in diverse aspects of fundamental research. We discuss the use of nanobodies as detection reagents in fluorescence microscopy and focus on recent advances in super-resolution microscopy. Second, application of nanobody technology in investigating protein–protein interactions is reviewed, with emphasis on possible uses in mass spectrometry. Finally, we discuss the potential value of nanobodies in studying protein function, and we focus on their recently reported application in targeted protein degradation. Throughout the review, we highlight state-of-the-art engineering strategies that could expand nanobody versatility and we suggest future applications of the technology in the selected areas of fundamental research.
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Affiliation(s)
- Els Beghein
- Nanobody Laboratory, Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Jan Gettemans
- Nanobody Laboratory, Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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32
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Saryi NAA, Hutchinson JD, Al-Hejjaj MY, Sedelnikova S, Baker P, Hettema EH. Pnc1 piggy-back import into peroxisomes relies on Gpd1 homodimerisation. Sci Rep 2017; 7:42579. [PMID: 28209961 PMCID: PMC5314374 DOI: 10.1038/srep42579] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 12/29/2016] [Indexed: 12/17/2022] Open
Abstract
Peroxisomes are eukaryotic organelles that posttranslationally import proteins via one of two conserved peroxisomal targeting signal (PTS1 or 2) mediated pathways. Oligomeric proteins can be imported via these pathways but evidence is accumulating that at least some PTS1-containing monomers enter peroxisomes before they assemble into oligomers. Some proteins lacking a PTS are imported by piggy-backing onto PTS-containing proteins. One of these proteins is the nicotinamidase Pnc1, that is co-imported with the PTS2-containing enzyme Glycerol-3-phosphate dehydrogenase 1, Gpd1. Here we show that Pnc1 co-import requires Gpd1 to form homodimers. A mutation that interferes with Gpd1 homodimerisation does not prevent Gpd1 import but prevents Pnc1 co-import. A suppressor mutation that restores Gpd1 homodimerisation also restores Pnc1 co-import. In line with this, Pnc1 interacts with Gpd1 in vivo only when Gpd1 can form dimers. Redirection of Gpd1 from the PTS2 import pathway to the PTS1 import pathway supports Gpd1 monomer import but not Gpd1 homodimer import and Pnc1 co-import. Our results support a model whereby Gpd1 may be imported as a monomer or a dimer but only the Gpd1 dimer facilitates co-transport of Pnc1 into peroxisomes.
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Affiliation(s)
- Nadal A Al Saryi
- Department of Molecular Biology and Biotechnology University of Sheffield Firth Court, Western Bank Sheffield S10 2TN United Kingdom
| | - John D Hutchinson
- Department of Molecular Biology and Biotechnology University of Sheffield Firth Court, Western Bank Sheffield S10 2TN United Kingdom
| | - Murtakab Y Al-Hejjaj
- Department of Molecular Biology and Biotechnology University of Sheffield Firth Court, Western Bank Sheffield S10 2TN United Kingdom
| | - Svetlana Sedelnikova
- Department of Molecular Biology and Biotechnology University of Sheffield Firth Court, Western Bank Sheffield S10 2TN United Kingdom
| | - Patrick Baker
- Department of Molecular Biology and Biotechnology University of Sheffield Firth Court, Western Bank Sheffield S10 2TN United Kingdom
| | - Ewald H Hettema
- Department of Molecular Biology and Biotechnology University of Sheffield Firth Court, Western Bank Sheffield S10 2TN United Kingdom
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33
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Affiliation(s)
| | - Maria Daniela D'Agostino
- McGill University Department of Human Genetics and McGill University Health Center, Department of Medical Genetics, Montreal, QC, Canada
| | - Nancy Braverman
- McGill University Department of Human Genetics and Pediatrics, and The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
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34
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Chan A, Schummer A, Fischer S, Schröter T, Cruz-Zaragoza LD, Bender J, Drepper F, Oeljeklaus S, Kunau WH, Girzalsky W, Warscheid B, Erdmann R. Pex17p-dependent assembly of Pex14p/Dyn2p-subcomplexes of the peroxisomal protein import machinery. Eur J Cell Biol 2016; 95:585-597. [PMID: 27823812 DOI: 10.1016/j.ejcb.2016.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/30/2016] [Accepted: 10/10/2016] [Indexed: 01/10/2023] Open
Abstract
Peroxisomal matrix protein import is facilitated by cycling receptors that recognize their cargo proteins in the cytosol by peroxisomal targeting sequences (PTS). In the following, the assembled receptor-cargo complex is targeted to the peroxisomal membrane where it docks to the docking-complex as part of the peroxisomal translocation machinery. The docking-complex is composed of Pex13p, Pex14p and in yeast also Pex17p, whose function is still elusive. In order to characterize the function of Pex17p, we compared the composition and size of peroxisomal receptor-docking complexes from wild-type and pex17Δ cells. Our data demonstrate that the deficiency of Pex17p affects the stoichiometry of the constituents of an isolated 600kDa complex and that pex17Δ cells lack a high molecular weight complex (>900kDa) of unknown function. We identified the dynein light chain protein Dyn2p as an additional core component of the Pex14p/Pex17p-complex. Both, Pex14p and Pex17p interact directly with Dyn2p, but in vivo, Pex17p turned out to be prerequisite for an association of Dyn2p with Pex14p. Finally, like pex17Δ also dyn2Δ cells lack the high molecular weight complex. As dyn2Δ cells also display reduced peroxisomal function, our data indicate that Dyn2p-dependent formation of the high molecular weight Pex14p-complex is required to maintain peroxisomal function on wild-type level.
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Affiliation(s)
- Anna Chan
- Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, System Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Andreas Schummer
- Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Sven Fischer
- Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Thomas Schröter
- Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, System Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Luis Daniel Cruz-Zaragoza
- Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, System Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Julian Bender
- Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Friedel Drepper
- Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Silke Oeljeklaus
- Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Wolf-H Kunau
- Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, System Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Wolfgang Girzalsky
- Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, System Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Bettina Warscheid
- Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, System Biochemistry, Ruhr-University Bochum, Bochum, Germany.
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35
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Beghein E, Van Audenhove I, Zwaenepoel O, Verhelle A, De Ganck A, Gettemans J. A new survivin tracer tracks, delocalizes and captures endogenous survivin at different subcellular locations and in distinct organelles. Sci Rep 2016; 6:31177. [PMID: 27514728 PMCID: PMC4981888 DOI: 10.1038/srep31177] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/13/2016] [Indexed: 01/18/2023] Open
Abstract
Survivin, the smallest member of the inhibitor of apoptosis protein family, plays a central role during mitosis and exerts a cytoprotective function. Survivin is highly expressed in most cancer types and contributes to multiple facets of carcinogenesis. The molecular mechanisms underlying its highly diverse functions need to be extensively explored, which is crucial for rational design of future personalized therapeutics. In this study, we have generated an alpaca survivin nanobody (SVVNb8) that binds with low nanomolar affinity to its target. When expressed as an intrabody in HeLa cells, SVVNb8 faithfully tracks survivin during different phases of mitosis without interfering with survivin function. Furthermore, coupling SVVNb8 with a subcellular delocalization tag efficiently redirects endogenous survivin towards the nucleus, the cytoplasm, peroxisomes and even to the intermembrane space of mitochondria where it presumably interacts with resident mitochondrial survivin. Based on our findings, we believe that SVVNb8 is an excellent instrument to further elucidate survivin biology and topography, and can serve as a model system to investigate mitochondrial and peroxisomal (survivin) protein import.
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Affiliation(s)
- Els Beghein
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Campus Rommelaere, A. Baertsoenkaai 3, Ghent University, Ghent, Belgium
| | - Isabel Van Audenhove
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Campus Rommelaere, A. Baertsoenkaai 3, Ghent University, Ghent, Belgium
| | - Olivier Zwaenepoel
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Campus Rommelaere, A. Baertsoenkaai 3, Ghent University, Ghent, Belgium
| | - Adriaan Verhelle
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Campus Rommelaere, A. Baertsoenkaai 3, Ghent University, Ghent, Belgium
| | - Ariane De Ganck
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Campus Rommelaere, A. Baertsoenkaai 3, Ghent University, Ghent, Belgium
| | - Jan Gettemans
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Campus Rommelaere, A. Baertsoenkaai 3, Ghent University, Ghent, Belgium
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36
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Chen Y, Yu Q, Wang H, Dong Y, Jia C, Zhang B, Xiao C, Zhang B, Xing L, Li M. The malfunction of peroxisome has an impact on the oxidative stress sensitivity in Candida albicans. Fungal Genet Biol 2016; 95:1-12. [PMID: 27473887 DOI: 10.1016/j.fgb.2016.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 07/24/2016] [Accepted: 07/26/2016] [Indexed: 11/28/2022]
Abstract
The peroxisome plays an essential role in eukaryotic cellular metabolism, including β-oxidation of fatty acids and detoxification of hydrogen peroxide. However, its functions in the important fungal pathogen, C. albicans, remain to be investigated. In this study, we identified a homologue of Saccharomyces cerevisiae peroxisomal protein Pex1 in this pathogen, and explored its functions in stress tolerance. Fluorescence observation revealed that C. albicans Pex1 was localized in the peroxisomes, and its loss led to the defect in peroxisome formation. Interestingly, the pex1Δ/Δ mutant had increased tolerance to oxidative stress, which was neither associated with the Cap1 pathway, nor related to the altered distribution of catalase. However, under oxidative stress, the pex1Δ/Δ mutant showed increased expression of autophagy-related genes, with enhanced cytoplasm-to-vacuole transport and degradation of the autophagy markers Atg8 and Lap41. Moreover, the double mutants pex1Δ/Δatg8Δ/Δ and pex1Δ/Δatg1Δ/Δ, both of which were defective in autophagy and peroxisome formation, showed remarkable attenuated tolerance to oxidative stress. These results indicated that autophagy is involved in resistance to oxidative stress in pex1Δ/Δ mutant. Taken together, this study provides evidence that the peroxisomal protein Pex1 regulates oxidative stress tolerance in an autophagy-dependent manner in C. albicans.
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Affiliation(s)
- Yulu Chen
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Honggang Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Yijie Dong
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Chang Jia
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Bing Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Chenpeng Xiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Biao Zhang
- Tianjin University of Traditional Chinese Medicine, Tianjin, PR China
| | - Laijun Xing
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Mingchun Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, PR China.
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Abstract
The blue-light-responsive LOV2 domain of Avena sativa phototropin1 (AsLOV2) has been used to regulate activity and binding of diverse protein targets with light. Here, we used AsLOV2 to photocage a peroxisomal targeting sequence, allowing light regulation of peroxisomal protein import. We generated a protein tag, LOV-PTS1, that can be appended to proteins of interest to direct their import to the peroxisome with light. This method provides a means to inducibly trigger peroxisomal protein trafficking in specific cells at user-defined times.
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Affiliation(s)
- Jessica I. Spiltoir
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Devin Strickland
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Michael Glotzer
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Chandra L. Tucker
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
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38
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Abstract
The import of proteins into peroxisomes possesses many unusual features such as the ability to import folded proteins, and a surprising diversity of targeting signals with differing affinities that can be recognized by the same receptor. As understanding of the structure and function of many components of the protein import machinery has grown, an increasingly complex network of factors affecting each step of the import pathway has emerged. Structural studies have revealed the presence of additional interactions between cargo proteins and the PEX5 receptor that affect import potential, with a subtle network of cargo-induced conformational changes in PEX5 being involved in the import process. Biochemical studies have also indicated an interdependence of receptor-cargo import with release of unloaded receptor from the peroxisome. Here, we provide an update on recent literature concerning mechanisms of protein import into peroxisomes.
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Affiliation(s)
- Alison Baker
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology and Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Thomas Lanyon-Hogg
- Institute of Chemical Biology, Department of Chemistry, Imperial College London, London SW7 2AZ, U.K
| | - Stuart L Warriner
- School of Chemistry, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
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39
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Emmanouilidis L, Gopalswamy M, Passon DM, Wilmanns M, Sattler M. Structural biology of the import pathways of peroxisomal matrix proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:804-13. [DOI: 10.1016/j.bbamcr.2015.09.034] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 09/29/2015] [Accepted: 09/30/2015] [Indexed: 11/28/2022]
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40
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Reumann S, Chowdhary G, Lingner T. Characterization, prediction and evolution of plant peroxisomal targeting signals type 1 (PTS1s). BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1863:790-803. [PMID: 26772785 DOI: 10.1016/j.bbamcr.2016.01.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 01/01/2016] [Accepted: 01/04/2016] [Indexed: 12/22/2022]
Abstract
Our knowledge of the proteome of plant peroxisomes and their functional plasticity is far from being complete, primarily due to major technical challenges in experimental proteome research of the fragile cell organelle. Several unexpected novel plant peroxisome functions, for instance in biotin and phylloquinone biosynthesis, have been uncovered recently. Nevertheless, very few regulatory and membrane proteins of plant peroxisomes have been identified and functionally described up to now. To define the matrix proteome of plant peroxisomes, computational methods have emerged as important powerful tools. Novel prediction approaches of high sensitivity and specificity have been developed for peroxisome targeting signals type 1 (PTS1) and have been validated by in vivo subcellular targeting analyses and thermodynamic binding studies with the cytosolic receptor, PEX5. Accordingly, the algorithms allow the correct prediction of many novel peroxisome-targeted proteins from plant genome sequences and the discovery of additional organelle functions. In this review, we provide an overview of methodologies, capabilities and accuracies of available prediction algorithms for PTS1 carrying proteins. We also summarize and discuss recent quantitative, structural and mechanistic information of the interaction of PEX5 with PTS1 carrying proteins in relation to in vivo import efficiency. With this knowledge, we develop a model of how proteins likely evolved peroxisomal targeting signals in the past and still nowadays, in which order the two import pathways might have evolved in the ancient eukaryotic cell, and how the secondary loss of the PTS2 pathway probably happened in specific organismal groups.
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Affiliation(s)
- S Reumann
- Department of Plant Biochemistry and Infection Biology, Biocentre Klein Flottbek, University of Hamburg, D-22609 Hamburg, Germany; Centre for Organelle Research, University of Stavanger, N-4036 Stavanger, Norway.
| | - G Chowdhary
- Centre for Organelle Research, University of Stavanger, N-4036 Stavanger, Norway; KIIT School of Biotechnology, Campus XI, KIIT University, I-751024 Bhubaneswar, India.
| | - T Lingner
- Department of Bioinformatics, Institute for Microbiology and Genetics, D-37077 Goettingen, Germany.
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41
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Cross LL, Ebeed HT, Baker A. Peroxisome biogenesis, protein targeting mechanisms and PEX gene functions in plants. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:850-62. [DOI: 10.1016/j.bbamcr.2015.09.027] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/15/2015] [Accepted: 09/21/2015] [Indexed: 12/16/2022]
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42
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DeLoache WC, Russ ZN, Dueber JE. Towards repurposing the yeast peroxisome for compartmentalizing heterologous metabolic pathways. Nat Commun 2016; 7:11152. [PMID: 27025684 PMCID: PMC5476825 DOI: 10.1038/ncomms11152] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/23/2016] [Indexed: 11/29/2022] Open
Abstract
Compartmentalization of enzymes into organelles is a promising strategy for limiting metabolic crosstalk and improving pathway efficiency, but improved tools and design rules are needed to make this strategy available to more engineered pathways. Here we focus on the Saccharomyces cerevisiae peroxisome and develop a sensitive high-throughput assay for peroxisomal cargo import. We identify an enhanced peroxisomal targeting signal type 1 (PTS1) for rapidly sequestering non-native cargo proteins. Additionally, we perform the first systematic in vivo measurements of nonspecific metabolite permeability across the peroxisomal membrane using a polymer exclusion assay. Finally, we apply these new insights to compartmentalize a two-enzyme pathway in the peroxisome and characterize the expression regimes where compartmentalization leads to improved product titre. This work builds a foundation for using the peroxisome as a synthetic organelle, highlighting both promise and future challenges on the way to realizing this goal. Compartmentalization of enzymes into cellular organelles is a promising strategy for improving pathway efficiency. Here, the authors use a high-throughput assay to identify enhanced peroxisomal targeting signals in yeast, and study the effects of peroxisomal compartmentalization on the performance of a model pathway.
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Affiliation(s)
- William C DeLoache
- UC Berkeley and UCSF Graduate Program in Bioengineering, University of California, Berkeley (UC Berkeley), Berkeley, California 94720, USA.,Department of Bioengineering, UC Berkeley, Berkeley, California 94720, USA
| | - Zachary N Russ
- UC Berkeley and UCSF Graduate Program in Bioengineering, University of California, Berkeley (UC Berkeley), Berkeley, California 94720, USA.,Department of Bioengineering, UC Berkeley, Berkeley, California 94720, USA
| | - John E Dueber
- Department of Bioengineering, UC Berkeley, Berkeley, California 94720, USA
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43
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Freitas MO, Francisco T, Rodrigues TA, Lismont C, Domingues P, Pinto MP, Grou CP, Fransen M, Azevedo JE. The peroxisomal protein import machinery displays a preference for monomeric substrates. Open Biol 2016; 5:140236. [PMID: 25854684 PMCID: PMC4422123 DOI: 10.1098/rsob.140236] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Peroxisomal matrix proteins are synthesized on cytosolic ribosomes and transported by the shuttling receptor PEX5 to the peroxisomal membrane docking/translocation machinery, where they are translocated into the organelle matrix. Under certain experimental conditions this protein import machinery has the remarkable capacity to accept already oligomerized proteins, a property that has heavily influenced current models on the mechanism of peroxisomal protein import. However, whether or not oligomeric proteins are really the best and most frequent clients of this machinery remain unclear. In this work, we present three lines of evidence suggesting that the peroxisomal import machinery displays a preference for monomeric proteins. First, in agreement with previous findings on catalase, we show that PEX5 binds newly synthesized (monomeric) acyl-CoA oxidase 1 (ACOX1) and urate oxidase (UOX), potently inhibiting their oligomerization. Second, in vitro import experiments suggest that monomeric ACOX1 and UOX are better peroxisomal import substrates than the corresponding oligomeric forms. Finally, we provide data strongly suggesting that although ACOX1 lacking a peroxisomal targeting signal can be imported into peroxisomes when co-expressed with ACOX1 containing its targeting signal, this import pathway is inefficient.
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Affiliation(s)
- Marta O Freitas
- Organelle Biogenesis and Function Group, Instituto de Biologia Celular e Molecular (IBMC), Universidade do Porto, Porto, Portugal
| | - Tânia Francisco
- Organelle Biogenesis and Function Group, Instituto de Biologia Celular e Molecular (IBMC), Universidade do Porto, Porto, Portugal
| | - Tony A Rodrigues
- Organelle Biogenesis and Function Group, Instituto de Biologia Celular e Molecular (IBMC), Universidade do Porto, Porto, Portugal Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Celien Lismont
- Departement Cellulaire en Moleculaire Geneeskunde, KU Leuven-Universiteit Leuven, Leuven, Belgium
| | - Pedro Domingues
- Departamento de Química, Universidade de Aveiro, Aveiro, Portugal
| | - Manuel P Pinto
- Organelle Biogenesis and Function Group, Instituto de Biologia Celular e Molecular (IBMC), Universidade do Porto, Porto, Portugal
| | - Cláudia P Grou
- Organelle Biogenesis and Function Group, Instituto de Biologia Celular e Molecular (IBMC), Universidade do Porto, Porto, Portugal
| | - Marc Fransen
- Departement Cellulaire en Moleculaire Geneeskunde, KU Leuven-Universiteit Leuven, Leuven, Belgium
| | - Jorge E Azevedo
- Organelle Biogenesis and Function Group, Instituto de Biologia Celular e Molecular (IBMC), Universidade do Porto, Porto, Portugal Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
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44
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Kumar Choudhry S, Singh R, Williams CP, van der Klei IJ. Stress exposure results in increased peroxisomal levels of yeast Pnc1 and Gpd1, which are imported via a piggy-backing mechanism. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1863:148-56. [PMID: 26516056 DOI: 10.1016/j.bbamcr.2015.10.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 10/21/2015] [Accepted: 10/23/2015] [Indexed: 11/26/2022]
Abstract
Saccharomyces cerevisiae glycerol phosphate dehydrogenase 1 (Gpd1) and nicotinamidase (Pnc1) are two stress-induced enzymes. Both enzymes are predominantly localised to peroxisomes at normal growth conditions, but were reported to localise to the cytosol and nucleus upon exposure of cells to stress. Import of both proteins into peroxisomes depends on the peroxisomal targeting signal 2 (PTS2) receptor Pex7. Gpd1 contains a PTS2, however, Pnc1 lacks this sequence. Here we show that Pnc1 physically interacts with Gpd1, which is required for piggy-back import of Pnc1 into peroxisomes. Quantitative fluorescence microscopy analyses revealed that the levels of both proteins increased in peroxisomes and in the cytosol upon exposure of cells to stress. However, upon exposure of cells to stress we also observed enhanced cytosolic levels of the control PTS2 protein thiolase, when produced under control of the GPD1 promoter. This suggests that these conditions cause a partial defect in PTS2 protein import, probably because the PTS2 import pathway is easily saturated.
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Affiliation(s)
- Sanjeev Kumar Choudhry
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, P.O. Box 11103, 9700CC Groningen, The Netherlands.
| | - Ritika Singh
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, P.O. Box 11103, 9700CC Groningen, The Netherlands.
| | - Chris P Williams
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, P.O. Box 11103, 9700CC Groningen, The Netherlands.
| | - Ida J van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, P.O. Box 11103, 9700CC Groningen, The Netherlands.
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45
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Montilla-Martinez M, Beck S, Klümper J, Meinecke M, Schliebs W, Wagner R, Erdmann R. Distinct Pores for Peroxisomal Import of PTS1 and PTS2 Proteins. Cell Rep 2015; 13:2126-34. [PMID: 26673321 DOI: 10.1016/j.celrep.2015.11.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 09/10/2015] [Accepted: 11/03/2015] [Indexed: 11/29/2022] Open
Abstract
Two peroxisomal targeting signals, PTS1 and PTS2, recognized by cytosolic receptors Pex5 and cooperating Pex7/Pex18, direct folded proteins to the peroxisomal matrix. A pore consisting of the PTS1 receptor Pex5 and the docking protein Pex14 imports PTS1 proteins. We identified a distinct PTS2-specific pore, which contains the PTS2 co-receptor Pex18 and the Pex14/Pex17-docking complex as major constituents. The estimated maximal pore size of ∼ 4.7 nm is large enough to allow import of folded PTS2 proteins. PTS2 cargo proteins modulate complex gating, open probability, and subconductance states of the pore. While the PTS1 channel is transiently activated by arriving receptor-cargo complexes, the reconstituted PTS2 channel is constitutively present in an open state. However, the cargo-loaded PTS2 channel is largely impermeable to solutes and ions. Our results demonstrate that import of PTS1 and PTS2 proteins does not converge at the peroxisomal membrane as previously anticipated but is performed by distinct pores.
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Affiliation(s)
| | - Sabrina Beck
- Institut für Biochemie und Pathobiochemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Jessica Klümper
- Institut für Biochemie und Pathobiochemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Michael Meinecke
- Institut für Zelluläre Biochemie, Universitätsmedizin Göttingen, 37073 Göttingen, Germany
| | - Wolfgang Schliebs
- Institut für Biochemie und Pathobiochemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Richard Wagner
- Biophysik, Fachbereich Biologie/Chemie, Universität Osnabrück, 49069 Osnabrück, Germany; MOLIFE Research Center, Jacobs University Bremen, 28759 Bremen, Germany.
| | - Ralf Erdmann
- Institut für Biochemie und Pathobiochemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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46
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The first minutes in the life of a peroxisomal matrix protein. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:814-20. [PMID: 26408939 DOI: 10.1016/j.bbamcr.2015.09.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/18/2015] [Accepted: 09/21/2015] [Indexed: 01/30/2023]
Abstract
In the field of intracellular protein sorting, peroxisomes are most famous by their capacity to import oligomeric proteins. The data supporting this remarkable property are abundant and, understandably, have inspired a variety of hypothetical models on how newly synthesized (cytosolic) proteins reach the peroxisome matrix. However, there is also accumulating evidence suggesting that many peroxisomal oligomeric proteins actually arrive at the peroxisome still as monomers. In support of this idea, recent data suggest that PEX5, the shuttling receptor for peroxisomal matrix proteins, is also a chaperone/holdase, binding newly synthesized peroxisomal proteins in the cytosol and blocking their oligomerization. Here we review the data behind these two different perspectives and discuss their mechanistic implications on this protein sorting pathway.
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47
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Effelsberg D, Cruz-Zaragoza LD, Tonillo J, Schliebs W, Erdmann R. Role of Pex21p for Piggyback Import of Gpd1p and Pnc1p into Peroxisomes of Saccharomyces cerevisiae. J Biol Chem 2015; 290:25333-42. [PMID: 26276932 DOI: 10.1074/jbc.m115.653451] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Indexed: 01/30/2023] Open
Abstract
Proteins designated for peroxisomal protein import harbor one of two common peroxisomal targeting signals (PTS). In the yeast Saccharomyces cerevisiae, the oleate-induced PTS2-dependent import of the thiolase Fox3p into peroxisomes is conducted by the soluble import receptor Pex7p in cooperation with the auxiliary Pex18p, one of two supposedly redundant PTS2 co-receptors. Here, we report on a novel function for the co-receptor Pex21p, which cannot be fulfilled by Pex18p. The data establish Pex21p as a general co-receptor in PTS2-dependent protein import, whereas Pex18p is especially important for oleate-induced import of PTS2 proteins. The glycerol-producing PTS2 protein glycerol-3-phosphate dehydrogenase Gpd1p shows a tripartite localization in peroxisomes, in the cytosol, and in the nucleus under osmotic stress conditions. We show the following: (i) Pex21p is required for peroxisomal import of Gpd1p as well as a key enzyme of the NAD(+) salvage pathway, Pnc1p; (ii) Pnc1p, a nicotinamidase without functional PTS2, is co-imported into peroxisomes by piggyback transport via Gpd1p. Moreover, the specific transport of these two enzymes into peroxisomes suggests a novel regulatory role for peroxisomes under various stress conditions.
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Affiliation(s)
- Daniel Effelsberg
- From the Institut für Biochemie und Pathobiochemie, Abteilung Systembiochemie, and
| | | | - Jason Tonillo
- Medizinisches Proteom-Center, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Wolfgang Schliebs
- From the Institut für Biochemie und Pathobiochemie, Abteilung Systembiochemie, and
| | - Ralf Erdmann
- From the Institut für Biochemie und Pathobiochemie, Abteilung Systembiochemie, and
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48
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Mast FD, Rachubinski RA, Aitchison JD. Signaling dynamics and peroxisomes. Curr Opin Cell Biol 2015; 35:131-6. [PMID: 26042681 DOI: 10.1016/j.ceb.2015.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 05/09/2015] [Indexed: 02/08/2023]
Abstract
Peroxisomes are remarkably responsive organelles. Their composition, abundance and even their mechanism of biogenesis are influenced strongly by cell type and the environment. This plasticity underlies peroxisomal functions in metabolism and the detoxification of dangerous reactive oxygen species. However, peroxisomes are integrated into the cellular system as a whole such that they communicate intimately with other organelles, control signaling dynamics as in the case of innate immune responses to infectious disease, and contribute to processes as fundamental as longevity. The increasing evidence for peroxisomes having roles in various cellular and organismal functions, combined with their malleability, suggests complex mechanisms operate to control cellular dynamics and the specificity of cellular responses and functions extending well beyond the peroxisome itself. A deeper understanding of the functions of peroxisomes and the mechanisms that control their plasticity could offer opportunities for exploiting changes in peroxisome abundance to control cellular function.
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Affiliation(s)
- Fred D Mast
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, USA; Institute for Systems Biology, Seattle, USA
| | | | - John D Aitchison
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, USA; Institute for Systems Biology, Seattle, USA.
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49
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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: 99] [Impact Index Per Article: 11.0] [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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Kunze M, Malkani N, Maurer-Stroh S, Wiesinger C, Schmid JA, Berger J. Mechanistic insights into PTS2-mediated peroxisomal protein import: the co-receptor PEX5L drastically increases the interaction strength between the cargo protein and the receptor PEX7. J Biol Chem 2014; 290:4928-4940. [PMID: 25538232 DOI: 10.1074/jbc.m114.601575] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The destination of peroxisomal matrix proteins is encoded by short peptide sequences, which have been characterized as peroxisomal targeting signals (PTS) residing either at the C terminus (PTS1) or close to the N terminus (PTS2). PTS2-carrying proteins interact with their cognate receptor protein PEX7 that mediates their transport to peroxisomes by a concerted action with a co-receptor protein, which in mammals is the PTS1 receptor PEX5L. Using a modified version of the mammalian two-hybrid assay, we demonstrate that the interaction strength between cargo and PEX7 is drastically increased in the presence of the co-receptor PEX5L. In addition, cargo binding is a prerequisite for the interaction between PEX7 and PEX5L and ectopic overexpression of PTS2-carrying cargo protein drastically increases the formation of PEX7-PEX5L complexes in this assay. Consistently, we find that the peroxisomal transfer of PEX7 depends on cargo binding and that ectopic overexpression of cargo protein stimulates this process. Thus, the sequential formation of a highly stable trimeric complex involving cargo protein, PEX7 and PEX5L stabilizes cargo binding and is a prerequisite for PTS2-mediated peroxisomal import.
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Affiliation(s)
- Markus Kunze
- Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria,.
| | - Naila Malkani
- Department of Vascular Biology and Thrombosis Research, Medical University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Singapore 138671; School of Biological Sciences (SBS), Nanyang Technological University (NTU), 8 Medical Drive, Singapore 117597
| | - Christoph Wiesinger
- Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
| | - Johannes A Schmid
- Department of Vascular Biology and Thrombosis Research, Medical University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Johannes Berger
- Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
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