1
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Kashyap I, Deb R, Battineni A, Nagotu S. Acyl CoA oxidase: from its expression, structure, folding, and import to its role in human health and disease. Mol Genet Genomics 2023; 298:1247-1260. [PMID: 37555868 DOI: 10.1007/s00438-023-02059-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/24/2023] [Indexed: 08/10/2023]
Abstract
β-oxidation of fatty acids is an important metabolic pathway and is a shared function between mitochondria and peroxisomes in mammalian cells. On the other hand, peroxisomes are the sole site for the degradation of fatty acids in yeast. The first reaction of this pathway is catalyzed by the enzyme acyl CoA oxidase housed in the matrix of peroxisomes. Studies in various model organisms have reported the conserved function of the protein in fatty acid oxidation. The importance of this enzyme is highlighted by the lethal conditions caused in humans due to its altered function. In this review, we discuss various aspects ranging from gene expression, structure, folding, and import of the protein in both yeast and human cells. Further, we highlight recent findings on the role of the protein in human health and aging, and discuss the identified mutations in the protein associated with debilitating conditions in patients.
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Affiliation(s)
- Isha Kashyap
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Rachayeeta Deb
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Abhigna Battineni
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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2
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Gu Y, Alam S, Oliferenko S. Peroxisomal compartmentalization of amino acid biosynthesis reactions imposes an upper limit on compartment size. Nat Commun 2023; 14:5544. [PMID: 37684233 PMCID: PMC10491753 DOI: 10.1038/s41467-023-41347-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Cellular metabolism relies on just a few redox cofactors. Selective compartmentalization may prevent competition between metabolic reactions requiring the same cofactor. Is such compartmentalization necessary for optimal cell function? Is there an optimal compartment size? Here we probe these fundamental questions using peroxisomal compartmentalization of the last steps of lysine and histidine biosynthesis in the fission yeast Schizosaccharomyces japonicus. We show that compartmentalization of these NAD+ dependent reactions together with a dedicated NADH/NAD+ recycling enzyme supports optimal growth when an increased demand for anabolic reactions taxes cellular redox balance. In turn, compartmentalization constrains the size of individual organelles, with larger peroxisomes accumulating all the required enzymes but unable to support both biosynthetic reactions at the same time. Our reengineering and physiological experiments indicate that compartmentalized biosynthetic reactions are sensitive to the size of the compartment, likely due to scaling-dependent changes within the system, such as enzyme packing density.
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Affiliation(s)
- Ying Gu
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK.
| | - Sara Alam
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK
- Medical Research Council London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK.
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3
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Abstract
Peroxisomes are involved in a multitude of metabolic and catabolic pathways, as well as the innate immune system. Their dysfunction is linked to severe peroxisome-specific diseases, as well as cancer and neurodegenerative diseases. To ensure the ability of peroxisomes to fulfill their many roles in the organism, more than 100 different proteins are post-translationally imported into the peroxisomal membrane and matrix, and their functionality must be closely monitored. In this Review, we briefly discuss the import of peroxisomal membrane proteins, and we emphasize an updated view of both classical and alternative peroxisomal matrix protein import pathways. We highlight different quality control pathways that ensure the degradation of dysfunctional peroxisomal proteins. Finally, we compare peroxisomal matrix protein import with other systems that transport folded proteins across membranes, in particular the twin-arginine translocation (Tat) system and the nuclear pore.
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Affiliation(s)
- Markus Rudowitz
- Systems Biochemistry , Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Ralf Erdmann
- Systems Biochemistry , Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
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4
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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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5
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Rüttermann M, Gatsogiannis C. Good things come to those who bait: the peroxisomal docking complex. Biol Chem 2023; 404:107-119. [PMID: 36117327 DOI: 10.1515/hsz-2022-0161] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/25/2022] [Indexed: 11/15/2022]
Abstract
Peroxisomal integrity and function are highly dependent on its membrane and soluble (matrix) components. Matrix enzymes are imported post-translationally in a folded or even oligomeric state, via a still mysterious protein translocation mechanism. They are guided to peroxisomes via the Peroxisomal Targeting Signal (PTS) sequences which are recognized by specific cytosolic receptors, Pex5, Pex7 and Pex9. Subsequently, cargo-loaded receptors bind to the docking complex in an initial step, followed by channel formation, cargo-release, receptor-recycling and -quality control. The docking complexes of different species share Pex14 as their core component but differ in composition and oligomeric state of Pex14. Here we review and highlight the latest insights on the structure and function of the peroxisomal docking complex. We summarize differences between yeast and mammals and then we integrate this knowledge into our current understanding of the import machinery.
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Affiliation(s)
- Maximilian Rüttermann
- Institute for Medical Physics and Biophysics and Center for Soft Nanoscience, Westfälische Wilhelms Universität Münster, D-48149 Münster, Germany
| | - Christos Gatsogiannis
- Institute for Medical Physics and Biophysics and Center for Soft Nanoscience, Westfälische Wilhelms Universität Münster, D-48149 Münster, Germany
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6
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Yifrach E, Holbrook-Smith D, Bürgi J, Othman A, Eisenstein M, van Roermund CW, Visser W, Tirosh A, Rudowitz M, Bibi C, Galor S, Weill U, Fadel A, Peleg Y, Erdmann R, Waterham HR, Wanders RJA, Wilmanns M, Zamboni N, Schuldiner M, Zalckvar E. Systematic multi-level analysis of an organelle proteome reveals new peroxisomal functions. Mol Syst Biol 2022; 18:e11186. [PMID: 36164978 PMCID: PMC9513677 DOI: 10.15252/msb.202211186] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/18/2022] Open
Abstract
Seventy years following the discovery of peroxisomes, their complete proteome, the peroxi‐ome, remains undefined. Uncovering the peroxi‐ome is crucial for understanding peroxisomal activities and cellular metabolism. We used high‐content microscopy to uncover peroxisomal proteins in the model eukaryote – Saccharomyces cerevisiae. This strategy enabled us to expand the known peroxi‐ome by ~40% and paved the way for performing systematic, whole‐organellar proteome assays. By characterizing the sub‐organellar localization and protein targeting dependencies into the organelle, we unveiled non‐canonical targeting routes. Metabolomic analysis of the peroxi‐ome revealed the role of several newly identified resident enzymes. Importantly, we found a regulatory role of peroxisomes during gluconeogenesis, which is fundamental for understanding cellular metabolism. With the current recognition that peroxisomes play a crucial part in organismal physiology, our approach lays the foundation for deep characterization of peroxisome function in health and disease.
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Affiliation(s)
- Eden Yifrach
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | | | - Jérôme Bürgi
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Hamburg, Germany
| | - Alaa Othman
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Miriam Eisenstein
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Carlo Wt van Roermund
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam University Medical Centers - Location AMC, Amsterdam, The Netherlands
| | - Wouter Visser
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam University Medical Centers - Location AMC, Amsterdam, The Netherlands
| | - Asa Tirosh
- Life Sciences Core Facilities (LSCF), The Weizmann Institute of Science, Rehovot, Israel
| | - Markus Rudowitz
- Department of Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Chen Bibi
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Shahar Galor
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Uri Weill
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Amir Fadel
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Yoav Peleg
- Life Sciences Core Facilities (LSCF), The Weizmann Institute of Science, Rehovot, Israel
| | - Ralf Erdmann
- Department of Systems Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam University Medical Centers - Location AMC, Amsterdam, The Netherlands
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam University Medical Centers - Location AMC, Amsterdam, The Netherlands
| | - Matthias Wilmanns
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Hamburg, Germany.,University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Maya Schuldiner
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
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7
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Insights into the Structure and Function of the Pex1/Pex6 AAA-ATPase in Peroxisome Homeostasis. Cells 2022; 11:cells11132067. [PMID: 35805150 PMCID: PMC9265785 DOI: 10.3390/cells11132067] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/25/2022] [Accepted: 06/26/2022] [Indexed: 02/01/2023] Open
Abstract
The AAA-ATPases Pex1 and Pex6 are required for the formation and maintenance of peroxisomes, membrane-bound organelles that harbor enzymes for specialized metabolism. Together, Pex1 and Pex6 form a heterohexameric AAA-ATPase capable of unfolding substrate proteins via processive threading through a central pore. Here, we review the proposed roles for Pex1/Pex6 in peroxisome biogenesis and degradation, discussing how the unfolding of potential substrates contributes to peroxisome homeostasis. We also consider how advances in cryo-EM, computational structure prediction, and mechanisms of related ATPases are improving our understanding of how Pex1/Pex6 converts ATP hydrolysis into mechanical force. Since mutations in PEX1 and PEX6 cause the majority of known cases of peroxisome biogenesis disorders such as Zellweger syndrome, insights into Pex1/Pex6 structure and function are important for understanding peroxisomes in human health and disease.
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8
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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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9
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Wang M, Li J, Ding Y, Cai S, Li Z, Liu P. PEX5 prevents cardiomyocyte hypertrophy via suppressing the redox-sensitive signaling pathways MAPKs and STAT3. Eur J Pharmacol 2021; 906:174283. [PMID: 34174269 DOI: 10.1016/j.ejphar.2021.174283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023]
Abstract
Peroxisomal biogenesis factor 5 (PEX5) is a member of peroxisome biogenesis protein family which serves as a shuttle receptor for the import of peroxisome matrix protein. The function of PEX5 on cardiomyocyte hypertrophy remained to be elucidated. Our study demonstrated that the protein expression level of PEX5 was declined in primary neonatal rat cardiomyocytes treated with phenylephrine (PE) and hearts from cardiac hypertrophic rats induced by abdominal aortic constriction (AAC). Overexpression of PEX5 alleviated cardiomyocyte hypertrophy induced by PE, while silencing of PEX5 exacerbated cardiomyocyte hypertrophy. PEX5 improved redox imbalance by decreasing cellular reactive oxygen species level and preserving peroxisomal catalase. Moreover, PEX5 knockdown aggravated PE-induced activation of redox-sensitive signaling pathways, including mitogen-activated protein kinase (MAPK) pathway and signal transducer and activator of transcription 3 (STAT3); whereas PEX5 overexpression suppressed activation of MAPK and STAT3. But PEX5 did not affect PE-induced phosphorylation of mammalian target of rapamycin (mTOR). In conclusion, the present study suggests that PEX5 protects cardiomyocyte against hypertrophy via regulating redox homeostasis and inhibiting redox-sensitive signaling pathways MAPK and STAT3.
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Affiliation(s)
- Minghui Wang
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences; National and Local United Engineering Lab of Druggability and New Drugs Evaluation; Guangdong Engineering Laboratory of Druggability and New Drug Evaluation; Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, China
| | - Jingyan Li
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences; National and Local United Engineering Lab of Druggability and New Drugs Evaluation; Guangdong Engineering Laboratory of Druggability and New Drug Evaluation; Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, China; International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Yanqing Ding
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences; National and Local United Engineering Lab of Druggability and New Drugs Evaluation; Guangdong Engineering Laboratory of Druggability and New Drug Evaluation; Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, China
| | - Sidong Cai
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences; National and Local United Engineering Lab of Druggability and New Drugs Evaluation; Guangdong Engineering Laboratory of Druggability and New Drug Evaluation; Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, China
| | - Zhuoming Li
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences; National and Local United Engineering Lab of Druggability and New Drugs Evaluation; Guangdong Engineering Laboratory of Druggability and New Drug Evaluation; Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, China.
| | - Peiqing Liu
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences; National and Local United Engineering Lab of Druggability and New Drugs Evaluation; Guangdong Engineering Laboratory of Druggability and New Drug Evaluation; Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, China.
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10
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Bürgi J, Ekal L, Wilmanns M. Versatile allosteric properties in Pex5-like tetratricopeptide repeat proteins to induce diverse downstream function. Traffic 2021; 22:140-152. [PMID: 33580581 DOI: 10.1111/tra.12785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/30/2021] [Accepted: 02/10/2021] [Indexed: 01/11/2023]
Abstract
Proteins composed of tetratricopeptide repeat (TPR) arrays belong to the α-solenoid tandem-repeat family that have unique properties in terms of their overall conformational flexibility and ability to bind to multiple protein ligands. The peroxisomal matrix protein import receptor Pex5 comprises two TPR triplets that recognize protein cargos with a specific C-terminal Peroxisomal Targeting Signal (PTS) 1 motif. Import of PTS1-containing protein cargos into peroxisomes through a transient pore is mainly driven by allosteric binding, coupling and release mechanisms, without a need for external energy. A very similar TPR architecture is found in the functionally unrelated TRIP8b, a regulator of the hyperpolarization-activated cyclic nucleotide-gated (HCN) ion channel. TRIP8b binds to the HCN ion channel via a C-terminal sequence motif that is nearly identical to the PTS1 motif of Pex5 receptor cargos. Pex5, Pex5-related Pex9, and TRIP8b also share a less conserved N-terminal domain. This domain provides a second protein cargo-binding site and plays a distinct role in allosteric coupling of initial cargo loading by PTS1 motif-mediated interactions and different downstream functional readouts. The data reviewed here highlight the overarching role of molecular allostery in driving the diverse functions of TPR array proteins, which could form a model for other α-solenoid tandem-repeat proteins involved in translocation processes across membranes.
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Affiliation(s)
- Jérôme Bürgi
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Lakhan Ekal
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany.,University Hamburg Clinical Center Hamburg-Eppendorf, Hamburg, Germany
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11
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Uncovering targeting priority to yeast peroxisomes using an in-cell competition assay. Proc Natl Acad Sci U S A 2020; 117:21432-21440. [PMID: 32817524 PMCID: PMC7474679 DOI: 10.1073/pnas.1920078117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Half of eukaryotic proteins reside in organelles to which they are directed by dedicated targeting pathways, each recognizing unique targeting signals. Multiple proteins compete for any targeting pathway and might have different priority of reaching an organelle. However, the proteins with targeting priority, and the mechanisms underlying it, have not been explored. We developed a systematic tool to study targeting priority. We expressed a competitor protein and examined how it affects the localization of all other proteins targeted by the same pathway. We found several proteins with high targeting priority, dissected the mechanism of priority, and suggest that priority is governed by different parameters. This approach can be modified to study targeting priority in various organelles, cell types, and organisms. Approximately half of eukaryotic proteins reside in organelles. To reach their correct destination, such proteins harbor targeting signals recognized by dedicated targeting pathways. It has been shown that differences in targeting signals alter the efficiency in which proteins are recognized and targeted. Since multiple proteins compete for any single pathway, such differences can affect the priority for which a protein is catered. However, to date the entire repertoire of proteins with targeting priority, and the mechanisms underlying it, have not been explored for any pathway. Here we developed a systematic tool to study targeting priority and used the Pex5-mediated targeting to yeast peroxisomes as a model. We titrated Pex5 out by expressing high levels of a Pex5-cargo protein and examined how the localization of each peroxisomal protein is affected. We found that while most known Pex5 cargo proteins were outcompeted, several cargo proteins were not affected, implying that they have high targeting priority. This priority group was dependent on metabolic conditions. We dissected the mechanism of priority for these proteins and suggest that targeting priority is governed by different parameters, including binding affinity of the targeting signal to the cargo factor, the number of binding interfaces to the cargo factor, and more. This approach can be modified to study targeting priority in various organelles, cell types, and organisms.
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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
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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14
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Chang J, Rachubinski RA. Pex20p functions as the receptor for non‐PTS1/non‐PTS2 acyl‐CoA oxidase import into peroxisomes of the yeast
Yarrowia lipolytica. Traffic 2019; 20:504-515. [DOI: 10.1111/tra.12652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/29/2019] [Accepted: 04/29/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Jinlan Chang
- Department of Cell BiologyUniversity of Alberta Edmonton Alberta Canada
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15
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Knoblach B, Rachubinski RA. Reconstitution of human peroxisomal β-oxidation in yeast. FEMS Yeast Res 2018; 18:5075582. [PMID: 30124827 DOI: 10.1093/femsyr/foy092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/14/2018] [Indexed: 11/14/2022] Open
Abstract
We report the permanent introduction of the human peroxisomal β-oxidation enzymatic machinery required for straight chain degradation of fatty acids into the yeast, Saccharomyces cerevisiae. Peroxisomal β-oxidation encompasses four sequential reactions that are confined to three enzymes. The genes encoding human acyl-CoA oxidase 1, peroxisomal multifunctional enzyme type 2 and 3-ketoacyl-CoA thiolase were introduced into the genomic loci of their yeast gene equivalents. The human β-oxidation genes were individually tagged with sequence coding for GFP and expression of the protein chimeras as well as their targeting to peroxisomes was confirmed. Functional complementation of the β-oxidation pathway was assessed by growth on media containing fatty acids of different chain lengths. Yeast cells exhibited distinctive substrate specificities depending on whether they expressed the human or their endogenous β-oxidation machinery. The genetic engineering of yeast to contain a 'humanized' organelle is a first step for the in vivo study of human peroxisome disorders in a model organism.
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Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, MSB 5-14, Edmonton, Alberta T6G 2H7, Canada
| | - Richard A Rachubinski
- Department of Cell Biology, University of Alberta, Edmonton, MSB 5-14, Edmonton, Alberta T6G 2H7, Canada
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16
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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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17
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Akşit A, van der Klei IJ. Yeast peroxisomes: How are they formed and how do they grow? Int J Biochem Cell Biol 2018; 105:24-34. [PMID: 30268746 DOI: 10.1016/j.biocel.2018.09.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 01/01/2023]
Abstract
Peroxisomes are single membrane enclosed cell organelles, which are present in almost all eukaryotic cells. In addition to the common peroxisomal pathways such as β-oxidation of fatty acids and decomposition of H2O2, these organelles fulfil a range of metabolic and non-metabolic functions. Peroxisomes are very important since various human disorders exist that are caused by a defect in peroxisome function. Here we describe our current knowledge on the molecular mechanisms of peroxisome biogenesis in yeast, including peroxisomal protein sorting, organelle dynamics and peroxisomal membrane contact sites.
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Affiliation(s)
- Arman Akşit
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands
| | - Ida J van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands.
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18
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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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19
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Functional Analyses of a Putative, Membrane-Bound, Peroxisomal Protein Import Mechanism from the Apicomplexan Protozoan Toxoplasma gondii. Genes (Basel) 2018; 9:genes9090434. [PMID: 30158461 PMCID: PMC6162456 DOI: 10.3390/genes9090434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/17/2018] [Accepted: 08/21/2018] [Indexed: 01/28/2023] Open
Abstract
Peroxisomes are central to eukaryotic metabolism, including the oxidation of fatty acids—which subsequently provide an important source of metabolic energy—and in the biosynthesis of cholesterol and plasmalogens. However, the presence and nature of peroxisomes in the parasitic apicomplexan protozoa remains controversial. A survey of the available genomes revealed that genes encoding peroxisome biogenesis factors, so-called peroxins (Pex), are only present in a subset of these parasites, the coccidia. The basic principle of peroxisomal protein import is evolutionarily conserved, proteins harbouring a peroxisomal-targeting signal 1 (PTS1) interact in the cytosol with the shuttling receptor Pex5 and are then imported into the peroxisome via the membrane-bound protein complex formed by Pex13 and Pex14. Surprisingly, whilst Pex5 is clearly identifiable, Pex13 and, perhaps, Pex14 are apparently absent from the coccidian genomes. To investigate the functionality of the PTS1 import mechanism in these parasites, expression of Pex5 from the model coccidian Toxoplasma gondii was shown to rescue the import defect of Pex5-deleted Saccharomyces cerevisiae. In support of these data, green fluorescent protein (GFP) bearing the enhanced (e)PTS1 known to efficiently localise to peroxisomes in yeast, localised to peroxisome-like bodies when expressed in Toxoplasma. Furthermore, the PTS1-binding domain of Pex5 and a PTS1 ligand from the putatively peroxisome-localised Toxoplasma sterol carrier protein (SCP2) were shown to interact in vitro. Taken together, these data demonstrate that the Pex5–PTS1 interaction is functional in the coccidia and indicate that a nonconventional peroxisomal import mechanism may operate in the absence of Pex13 and Pex14.
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20
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Thomas AS, Krikken AM, de Boer R, Williams C. Hansenula polymorpha Aat2p is targeted to peroxisomes via a novel Pex20p-dependent pathway. FEBS Lett 2018; 592:2466-2475. [PMID: 29924881 PMCID: PMC6099311 DOI: 10.1002/1873-3468.13168] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/25/2018] [Accepted: 06/11/2018] [Indexed: 12/29/2022]
Abstract
Saccharomyces cerevisiae Aat2p contains a peroxisomal targeting signal type‐1 and localizes to peroxisomes in oleate‐grown cells, but not in glucose‐grown cells. Here, we have investigated Aat2p from the yeast Hansenula polymorpha, which lacks a recognizable peroxisomal targeting signal. Aat2p tagged with GFP at its C terminus displays a dual cytosol‐peroxisome localization in ethanol‐grown cells. The partial peroxisomal localization of Aat2p persisted in the absence of the classical cycling receptors Pex5p and Pex7p but Aat2p targeting to peroxisomes was reduced in cells deleted for the matrix protein import factors PEX1, PEX2 and PEX13. Furthermore, we demonstrate that Aat2p targeting to peroxisomes requires Pex20p. Together, our data identify a Pex20p‐dependent pathway for targeting Aat2p to peroxisomes.
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Affiliation(s)
- Ann S Thomas
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Arjen M Krikken
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Rinse de Boer
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Chris Williams
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
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21
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Suaste-Olmos F, Zirión-Martínez C, Takano-Rojas H, Peraza-Reyes L. Meiotic development initiation in the fungus Podospora anserina requires the peroxisome receptor export machinery. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:572-586. [DOI: 10.1016/j.bbamcr.2018.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 12/29/2017] [Accepted: 01/03/2018] [Indexed: 01/19/2023]
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22
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Mutation in the peroxin-coding gene PEX22 contributing to high malate production in Saccharomyces cerevisiae. J Biosci Bioeng 2018; 125:211-217. [DOI: 10.1016/j.jbiosc.2017.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/10/2017] [Accepted: 08/21/2017] [Indexed: 11/22/2022]
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23
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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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24
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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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25
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Wang W, Subramani S. Role of PEX5 ubiquitination in maintaining peroxisome dynamics and homeostasis. Cell Cycle 2017; 16:2037-2045. [PMID: 28933989 PMCID: PMC5731411 DOI: 10.1080/15384101.2017.1376149] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 08/24/2017] [Accepted: 09/01/2017] [Indexed: 12/15/2022] Open
Abstract
Peroxisomes are essential and dynamic organelles that allow cells to rapidly adapt and cope with changing environments and/or physiological conditions by modulation of both peroxisome biogenesis and turnover. Peroxisome biogenesis involves the assembly of peroxisome membranes and the import of peroxisomal matrix proteins. The latter depends on the receptor, PEX5, which recognizes peroxisomal matrix proteins in the cytosol directly or indirectly, and transports them to the peroxisomal lumen. In this review, we discuss the role of PEX5 ubiquitination in both peroxisome biogenesis and turnover, specifically in PEX5 receptor recycling, stability and abundance, as well as its role in pexophagy (autophagic degradation of peroxisomes).
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Affiliation(s)
- Wei Wang
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Suresh Subramani
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
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26
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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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27
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Kong F, Liang Y, Légeret B, Beyly-Adriano A, Blangy S, Haslam RP, Napier JA, Beisson F, Peltier G, Li-Beisson Y. Chlamydomonas carries out fatty acid β-oxidation in ancestral peroxisomes using a bona fide acyl-CoA oxidase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:358-371. [PMID: 28142200 DOI: 10.1111/tpj.13498] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/25/2017] [Accepted: 01/27/2017] [Indexed: 05/03/2023]
Abstract
Peroxisomes are thought to have played a key role in the evolution of metabolic networks of photosynthetic organisms by connecting oxidative and biosynthetic routes operating in different compartments. While the various oxidative pathways operating in the peroxisomes of higher plants are fairly well characterized, the reactions present in the primitive peroxisomes (microbodies) of algae are poorly understood. Screening of a Chlamydomonas insertional mutant library identified a strain strongly impaired in oil remobilization and defective in Cre05.g232002 (CrACX2), a gene encoding a member of the acyl-CoA oxidase/dehydrogenase superfamily. The purified recombinant CrACX2 expressed in Escherichia coli catalyzed the oxidation of fatty acyl-CoAs into trans-2-enoyl-CoA and produced H2 O2 . This result demonstrated that CrACX2 is a genuine acyl-CoA oxidase, which is responsible for the first step of the peroxisomal fatty acid (FA) β-oxidation spiral. A fluorescent protein-tagging study pointed to a peroxisomal location of CrACX2. The importance of peroxisomal FA β-oxidation in algal physiology was shown by the impact of the mutation on FA turnover during day/night cycles. Moreover, under nitrogen depletion the mutant accumulated 20% more oil than the wild type, illustrating the potential of β-oxidation mutants for algal biotechnology. This study provides experimental evidence that a plant-type FA β-oxidation involving H2 O2 -producing acyl-CoA oxidation activity has already evolved in the microbodies of the unicellular green alga Chlamydomonas reinhardtii.
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Affiliation(s)
- Fantao Kong
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Yuanxue Liang
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Bertrand Légeret
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Audrey Beyly-Adriano
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Stéphanie Blangy
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Richard P Haslam
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Johnathan A Napier
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Fred Beisson
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Gilles Peltier
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Yonghua Li-Beisson
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
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Effelsberg D, Cruz-Zaragoza LD, Schliebs W, Erdmann R. Pex9p is a new yeast peroxisomal import receptor for PTS1-containing proteins. J Cell Sci 2016; 129:4057-4066. [PMID: 27678487 DOI: 10.1242/jcs.195271] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 07/27/2016] [Indexed: 11/20/2022] Open
Abstract
Peroxisomal proteins carrying a type 1 peroxisomal targeting signal (PTS1) are recognized by the well-conserved cycling import receptor Pex5p. The yeast YMR018W gene encodes a Pex5p paralog and newly identified peroxin that is involved in peroxisomal import of a subset of matrix proteins. The new peroxin was designated Pex9p, and it interacts with the docking protein Pex14p and a subclass of PTS1-containing peroxisomal matrix enzymes. Unlike Pex5p, Pex9p is not expressed in glucose- or ethanol-grown cells, but it is strongly induced by oleate. Under these conditions, Pex9p acts as a cytosolic and membrane-bound peroxisome import receptor for both malate synthase isoenzymes, Mls1p and Mls2p. The inducible Pex9p-dependent import pathway provides a mechanism for the oleate-inducible peroxisomal targeting of malate synthases. The existence of two distinct PTS1 receptors, in addition to two PTS2-dependent import routes, contributes to the adaptive metabolic capacity of peroxisomes in response to environmental changes and underlines the role of peroxisomes as multi-purpose organelles. The identification of different import routes into peroxisomes contributes to the molecular understanding of how regulated protein targeting can alter the function of organelles according to cellular needs.
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Affiliation(s)
- Daniel Effelsberg
- Abteilung Systembiochemie, Institut für Biochemie und Pathobiochemie, Abteilung Systembiochemie, Ruhr-Universität Bochum, Bochum D-44780, Germany
| | - Luis Daniel Cruz-Zaragoza
- Abteilung Systembiochemie, Institut für Biochemie und Pathobiochemie, Abteilung Systembiochemie, Ruhr-Universität Bochum, Bochum D-44780, Germany
| | - Wolfgang Schliebs
- Abteilung Systembiochemie, Institut für Biochemie und Pathobiochemie, Abteilung Systembiochemie, Ruhr-Universität Bochum, Bochum D-44780, Germany
| | - Ralf Erdmann
- Abteilung Systembiochemie, Institut für Biochemie und Pathobiochemie, Abteilung Systembiochemie, Ruhr-Universität Bochum, Bochum D-44780, Germany
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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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Lauersen KJ, Willamme R, Coosemans N, Joris M, Kruse O, Remacle C. Peroxisomal microbodies are at the crossroads of acetate assimilation in the green microalga Chlamydomonas reinhardtii. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.03.026] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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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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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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Kunze M, Berger J. The similarity between N-terminal targeting signals for protein import into different organelles and its evolutionary relevance. Front Physiol 2015; 6:259. [PMID: 26441678 PMCID: PMC4585086 DOI: 10.3389/fphys.2015.00259] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/04/2015] [Indexed: 12/04/2022] Open
Abstract
The proper distribution of proteins between the cytosol and various membrane-bound compartments is crucial for the functionality of eukaryotic cells. This requires the cooperation between protein transport machineries that translocate diverse proteins from the cytosol into these compartments and targeting signal(s) encoded within the primary sequence of these proteins that define their cellular destination. The mechanisms exerting protein translocation differ remarkably between the compartments, but the predominant targeting signals for mitochondria, chloroplasts and the ER share the N-terminal position, an α-helical structural element and the removal from the core protein by intraorganellar cleavage. Interestingly, similar properties have been described for the peroxisomal targeting signal type 2 mediating the import of a fraction of soluble peroxisomal proteins, whereas other peroxisomal matrix proteins encode the type 1 targeting signal residing at the extreme C-terminus. The structural similarity of N-terminal targeting signals poses a challenge to the specificity of protein transport, but allows the generation of ambiguous targeting signals that mediate dual targeting of proteins into different compartments. Dual targeting might represent an advantage for adaptation processes that involve a redistribution of proteins, because it circumvents the hierarchy of targeting signals. Thus, the co-existence of two equally functional import pathways into peroxisomes might reflect a balance between evolutionary constant and flexible transport routes.
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Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna Vienna, Austria
| | - Johannes Berger
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna Vienna, Austria
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Platta HW, Brinkmeier R, Reidick C, Galiani S, Clausen MP, Eggeling C. Regulation of peroxisomal matrix protein import by ubiquitination. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:838-49. [PMID: 26367801 DOI: 10.1016/j.bbamcr.2015.09.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/09/2015] [Accepted: 09/10/2015] [Indexed: 02/02/2023]
Abstract
Peroxisomes are organelles that play an important role in many cellular tasks. The functionality of peroxisomes depends on the proper import of their matrix proteins. Peroxisomal matrix proteins are imported posttranslationally in a folded, sometimes even oligomeric state. They harbor a peroxisomal targeting sequence (PTS), which is recognized by dynamic PTS-receptors in the cytosol. The PTS-receptors ferry the cargo to the peroxisomal membrane, where they become part of a transient import pore and then release the cargo into the peroxisomal lumen. Subsequentially, the PTS-receptors are ubiquitinated in order to mark them for the export-machinery, which releases them back to the cytosol. Upon deubiquitination, the PTS-receptors can facilitate further rounds of cargo import. Because the ubiquitination of the receptors is an essential step in the import cycle, it also represents a central regulatory element that governs peroxisomal dynamics. In this review we want to give an introduction to the functional role played by ubiquitination during peroxisomal protein import and highlight the mechanistic concepts that have emerged based on data derived from different species since the discovery of the first ubiquitinated peroxin 15years ago. Moreover, we discuss future tasks and the potential of using advanced technologies for investigating further details of peroxisomal protein transport.
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Affiliation(s)
- Harald W Platta
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Rebecca Brinkmeier
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Christina Reidick
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Silvia Galiani
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - Mathias P Clausen
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom.
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Cysteine-specific ubiquitination protects the peroxisomal import receptor Pex5p against proteasomal degradation. Biosci Rep 2015; 35:BSR20150103. [PMID: 26182377 PMCID: PMC4613714 DOI: 10.1042/bsr20150103] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 05/01/2015] [Indexed: 11/22/2022] Open
Abstract
Peroxisomal import receptors cycle between the peroxisomal membrane and the cytosol. A monoubiquitinated cysteine is required for efficient recycling of the peroxisomal import receptor Pex5p and prevents the protein from polyubiquitination, which leads to a rapid degradation of the protein. Peroxisomal matrix protein import is mediated by dynamic import receptors, which cycle between the peroxisomal membrane and the cytosol. Proteins with a type 1 peroxisomal targeting signal (PTS1) are bound by the import receptor Pex5p in the cytosol and guided to the peroxisomal membrane. After cargo translocation into the peroxisomal matrix, the receptor is released from the membrane back to the cytosol in an ATP-dependent manner by the AAA-type ATPases Pex1p and Pex6p. These mechanoenzymes recognize ubiquitinated Pex5p-species as substrates for membrane extraction. The PTS1-receptor is either polyubiquitinated via peptide bonds at two certain lysines and results in proteasomal degradation or monoubiquitinated via a thioester-bond at a conserved cysteine, which enables the recycling of Pex5p and further rounds of matrix protein import. To investigate the physiological relevance of the conserved N-terminal cysteine of Pex5p, the known target amino acids for ubiquitination were substituted by site-directed mutagenesis. In contrast with Pex5pC6A, Pex5pC6K turned out to be functional in PTS1 import and utilization of oleic acid, independent of the lysines at position 18 and 24. In contrast with wild-type Pex5p, Pex5pC6K displays an ubiquitination pattern, similar to the polyubiquitination pattern of Pex4p or Pex22p mutant strains. Moreover, Pex5pC6K displays a significantly reduced steady-state level when the deubiquitinating enzyme Ubp15p is missing. Thus, our results indicate that not the cysteine residue but the position of ubiquitination is important for Pex5p function. The presence of the cysteine prevents polyubiquitination and rapid degradation of Pex5p.
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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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A PEX7-centered perspective on the peroxisomal targeting signal type 2-mediated protein import pathway. Mol Cell Biol 2014; 34:2917-28. [PMID: 24865970 DOI: 10.1128/mcb.01727-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Peroxisomal matrix proteins are synthesized on cytosolic ribosomes and transported to the organelle by shuttling receptors. Matrix proteins containing a type 1 signal are carried to the peroxisome by PEX5, whereas those harboring a type 2 signal are transported by a PEX5-PEX7 complex. The pathway followed by PEX5 during the protein transport cycle has been characterized in detail. In contrast, not much is known regarding PEX7. In this work, we show that PEX7 is targeted to the peroxisome in a PEX5- and cargo-dependent manner, where it becomes resistant to exogenously added proteases. Entry of PEX7 and its cargo into the peroxisome occurs upstream of the first cytosolic ATP-dependent step of the PEX5-mediated import pathway, i.e., before monoubiquitination of PEX5. PEX7 passing through the peroxisome becomes partially, if not completely, exposed to the peroxisome matrix milieu, suggesting that cargo release occurs at the trans side of the peroxisomal membrane. Finally, we found that export of peroxisomal PEX7 back into the cytosol requires export of PEX5 but, strikingly, the two export events are not strictly coupled, indicating that the two proteins leave the peroxisome separately.
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38
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Gudipati V, Koch K, Lienhart WD, Macheroux P. The flavoproteome of the yeast Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:535-44. [PMID: 24373875 PMCID: PMC3991850 DOI: 10.1016/j.bbapap.2013.12.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 12/18/2013] [Accepted: 12/21/2013] [Indexed: 01/29/2023]
Abstract
Genome analysis of the yeast Saccharomyces cerevisiae identified 68 genes encoding flavin-dependent proteins (1.1% of protein encoding genes) to which 47 distinct biochemical functions were assigned. The majority of flavoproteins operate in mitochondria where they participate in redox processes revolving around the transfer of electrons to the electron transport chain. In addition, we found that flavoenzymes play a central role in various aspects of iron metabolism, such as iron uptake, the biogenesis of iron–sulfur clusters and insertion of the heme cofactor into apocytochromes. Another important group of flavoenzymes is directly (Dus1-4p and Mto1p) or indirectly (Tyw1p) involved in reactions leading to tRNA-modifications. Despite the wealth of genetic information available for S. cerevisiae, we were surprised that many flavoproteins are poorly characterized biochemically. For example, the role of the yeast flavodoxins Pst2p, Rfs1p and Ycp4p with regard to their electron donor and acceptor is presently unknown. Similarly, the function of the heterodimeric Aim45p/Cir1p, which is homologous to the electron-transferring flavoproteins of higher eukaryotes, in electron transfer processes occurring in the mitochondrial matrix remains to be elucidated. This lack of information extends to the five membrane proteins involved in riboflavin or FAD transport as well as FMN and FAD homeostasis within the yeast cell. Nevertheless, several yeast flavoproteins, were identified as convenient model systems both in terms of their mechanism of action as well as structurally to improve our understanding of diseases caused by dysfunctional human flavoprotein orthologs. Overview of flavin-dependent proteins in S. cerevisiae. The role of yeast flavoproteins in iron metabolism. Biosynthesis and transport of flavins. Yeast as a model organism for investigating human diseases linked to flavoproteins.
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Affiliation(s)
- Venugopal Gudipati
- Graz University of Technology, Institute of Biochemistry, Petersgasse 12, A-8010 Graz, Austria
| | - Karin Koch
- Graz University of Technology, Institute of Biochemistry, Petersgasse 12, A-8010 Graz, Austria
| | - Wolf-Dieter Lienhart
- Graz University of Technology, Institute of Biochemistry, Petersgasse 12, A-8010 Graz, Austria
| | - Peter Macheroux
- Graz University of Technology, Institute of Biochemistry, Petersgasse 12, A-8010 Graz, Austria.
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Ast J, Stiebler AC, Freitag J, Bölker M. Dual targeting of peroxisomal proteins. Front Physiol 2013; 4:297. [PMID: 24151469 PMCID: PMC3798809 DOI: 10.3389/fphys.2013.00297] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 09/28/2013] [Indexed: 01/08/2023] Open
Abstract
Cellular compartmentalization into organelles serves to separate biological processes within the environment of a single cell. While some metabolic reactions are specific to a single organelle, others occur in more than one cellular compartment. Specific targeting of proteins to compartments inside of eukaryotic cells is mediated by defined sequence motifs. To achieve multiple targeting to different compartments cells use a variety of strategies. Here, we focus on mechanisms leading to dual targeting of peroxisomal proteins. In many instances, isoforms of peroxisomal proteins with distinct intracellular localization are encoded by separate genes. But also single genes can give rise to differentially localized proteins. Different isoforms can be generated by use of alternative transcriptional start sites, by differential splicing or ribosomal read-through of stop codons. In all these cases different peptide variants are produced, of which only one carries a peroxisomal targeting signal. Alternatively, peroxisomal proteins contain additional signals that compete for intracellular targeting. Dual localization of proteins residing in both the cytoplasm and in peroxisomes may also result from use of inefficient targeting signals. The recent observation that some bona fide cytoplasmic enzymes were also found in peroxisomes indicates that dual targeting of proteins to both the cytoplasm and the peroxisome might be more widespread. Although current knowledge of proteins exhibiting only partial peroxisomal targeting is far from being complete, we speculate that the metabolic capacity of peroxisomes might be larger than previously assumed.
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Affiliation(s)
- Julia Ast
- Department of Biology, Philipps University Marburg Marburg, Germany
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40
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Hasan S, Platta HW, Erdmann R. Import of proteins into the peroxisomal matrix. Front Physiol 2013; 4:261. [PMID: 24069002 PMCID: PMC3781343 DOI: 10.3389/fphys.2013.00261] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/03/2013] [Indexed: 12/03/2022] Open
Abstract
Peroxisomes constitute a dynamic compartment in all nucleated cells. They fulfill diverse metabolic tasks in response to environmental changes and cellular demands. This adaptation is implemented by modulation of the enzyme content of the organelles, which is accomplished by dynamically operating peroxisomal protein transport machineries. Soluble import receptors recognize their newly synthesized cargo proteins in the cytosol and ferry them to the peroxisomal membrane. Subsequently, the cargo is translocated into the matrix, where the receptor is ubiquitinated and exported back to the cytosol for further rounds of matrix protein import. This review discusses the recent progress in our understanding of the peroxisomal matrix protein import and its regulation by ubiquitination events as well as the current view on the translocation mechanism of folded proteins into peroxisomes. This article is part of a Special Issue entitled: Origin and spatiotemporal dynamics of the peroxisomal endomembrane system.
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Affiliation(s)
- Sohel Hasan
- Systembiochemie, Medizinische Fakultät, Ruhr-Universität Bochum Bochum, Germany
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41
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Francisco T, Rodrigues TA, Freitas MO, Grou CP, Carvalho AF, Sá-Miranda C, Pinto MP, Azevedo JE. A cargo-centered perspective on the PEX5 receptor-mediated peroxisomal protein import pathway. J Biol Chem 2013; 288:29151-9. [PMID: 23963456 DOI: 10.1074/jbc.m113.487140] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Peroxisomal matrix proteins are synthesized on cytosolic ribosomes and post-translationally targeted to the organelle by PEX5, the peroxisomal shuttling receptor. The pathway followed by PEX5 during this process is known with reasonable detail. After recognizing cargo proteins in the cytosol, the receptor interacts with the peroxisomal docking/translocation machinery, where it gets inserted; PEX5 is then monoubiquitinated, extracted back to the cytosol and, finally, deubiquitinated. However, despite this information, the exact step of this pathway where cargo proteins are translocated across the organelle membrane is still ill-defined. In this work, we used an in vitro import system to characterize the translocation mechanism of a matrix protein possessing a type 1 targeting signal. Our results suggest that translocation of proteins across the organelle membrane occurs downstream of a reversible docking step and upstream of the first cytosolic ATP-dependent step (i.e. before ubiquitination of PEX5), concomitantly with the insertion of the receptor into the docking/translocation machinery.
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42
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A tuberous sclerosis complex signalling node at the peroxisome regulates mTORC1 and autophagy in response to ROS. Nat Cell Biol 2013; 15:1186-96. [PMID: 23955302 PMCID: PMC3789865 DOI: 10.1038/ncb2822] [Citation(s) in RCA: 197] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 07/10/2013] [Indexed: 12/12/2022]
Abstract
Subcellular localization is emerging as an important mechanism for mTORC1 regulation. We report that the tuberous sclerosis complex (TSC) signaling node, TSC1, TSC2 and Rheb, localizes to peroxisomes, where it regulates mTORC1 in response to reactive oxygen species (ROS). TSC1 and TSC2 were bound by PEX19 and PEX5, respectively, and peroxisome-localized TSC functioned as a Rheb GAP to suppress mTORC1 and induce autophagy. Naturally occurring pathogenic mutations in TSC2 decreased PEX5 binding, abrogated peroxisome localization, Rheb GAP activity, and suppression of mTORC1 by ROS. Cells lacking peroxisomes were deficient in mTORC1 repression by ROS and peroxisome-localization deficient TSC2 mutants caused polarity defects and formation of multiple axons in neurons. These data identify a role for TSC in responding to ROS at the peroxisome, and identify the peroxisome as a signaling organelle involved in regulation of mTORC1.
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Francisco T, Rodrigues TA, Pinto MP, Carvalho AF, Azevedo JE, Grou CP. Ubiquitin in the peroxisomal protein import pathway. Biochimie 2013; 98:29-35. [PMID: 23954799 DOI: 10.1016/j.biochi.2013.08.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 08/05/2013] [Indexed: 10/26/2022]
Abstract
PEX5 is the shuttling receptor for newly synthesized peroxisomal matrix proteins. Alone, or with the help of an adaptor protein, this receptor binds peroxisomal matrix proteins in the cytosol and transports them to the peroxisomal membrane docking/translocation module (DTM). The interaction between cargo-loaded PEX5 and the DTM ultimately results in its insertion into the DTM with the concomitant translocation of the cargo protein across the organelle membrane. PEX5 is not consumed in this event; rather it is dislocated back into the cytosol so that it can promote additional rounds of protein transportation. Remarkably, the data collected in recent years indicate that dislocation is preceded by monoubiquitination of PEX5 at a conserved cysteine residue. This mandatory modification is not the only type of ubiquitination occurring at the DTM. Indeed, several findings suggest that defective receptors jamming the DTM are polyubiquitinated and targeted to the proteasome for degradation.
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Affiliation(s)
- Tânia Francisco
- Organelle Biogenesis and Function Group, Instituto de Biologia Celular e Molecular (IBMC), Universidade do Porto, R. do Campo Alegre, 823, 4150-180 Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, R. de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Tony A Rodrigues
- Organelle Biogenesis and Function Group, Instituto de Biologia Celular e Molecular (IBMC), Universidade do Porto, R. do Campo Alegre, 823, 4150-180 Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, R. de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Manuel P Pinto
- Organelle Biogenesis and Function Group, Instituto de Biologia Celular e Molecular (IBMC), Universidade do Porto, R. do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Andreia F Carvalho
- Organelle Biogenesis and Function Group, Instituto de Biologia Celular e Molecular (IBMC), Universidade do Porto, R. do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Jorge E Azevedo
- Organelle Biogenesis and Function Group, Instituto de Biologia Celular e Molecular (IBMC), Universidade do Porto, R. do Campo Alegre, 823, 4150-180 Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, R. de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| | - Cláudia P Grou
- Organelle Biogenesis and Function Group, Instituto de Biologia Celular e Molecular (IBMC), Universidade do Porto, R. do Campo Alegre, 823, 4150-180 Porto, Portugal.
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Lipid droplets and peroxisomes: key players in cellular lipid homeostasis or a matter of fat--store 'em up or burn 'em down. Genetics 2013; 193:1-50. [PMID: 23275493 PMCID: PMC3527239 DOI: 10.1534/genetics.112.143362] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Lipid droplets (LDs) and peroxisomes are central players in cellular lipid homeostasis: some of their main functions are to control the metabolic flux and availability of fatty acids (LDs and peroxisomes) as well as of sterols (LDs). Both fatty acids and sterols serve multiple functions in the cell—as membrane stabilizers affecting membrane fluidity, as crucial structural elements of membrane-forming phospholipids and sphingolipids, as protein modifiers and signaling molecules, and last but not least, as a rich carbon and energy source. In addition, peroxisomes harbor enzymes of the malic acid shunt, which is indispensable to regenerate oxaloacetate for gluconeogenesis, thus allowing yeast cells to generate sugars from fatty acids or nonfermentable carbon sources. Therefore, failure of LD and peroxisome biogenesis and function are likely to lead to deregulated lipid fluxes and disrupted energy homeostasis with detrimental consequences for the cell. These pathological consequences of LD and peroxisome failure have indeed sparked great biomedical interest in understanding the biogenesis of these organelles, their functional roles in lipid homeostasis, interaction with cellular metabolism and other organelles, as well as their regulation, turnover, and inheritance. These questions are particularly burning in view of the pandemic development of lipid-associated disorders worldwide.
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Farnesyl diphosphate synthase, the target for nitrogen-containing bisphosphonate drugs, is a peroxisomal enzyme in the model system Dictyostelium discoideum. Biochem J 2012; 447:353-61. [PMID: 22849378 PMCID: PMC3465988 DOI: 10.1042/bj20120750] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
NBP (nitrogen-containing bisphosphonate) drugs protect against excessive osteoclast-mediated bone resorption. After binding to bone mineral, they are taken up selectively by the osteoclasts and inhibit the essential enzyme FDPS (farnesyl diphosphate synthase). NBPs inhibit also growth of amoebae of Dictyostelium discoideum in which their target is again FDPS. A fusion protein between FDPS and GFP (green fluorescent protein) was found, in D. discoideum, to localize to peroxisomes and to confer resistance to the NBP alendronate. GFP was also directed to peroxisomes by a fragment of FDPS comprising amino acids 1–22. This contains a sequence of nine amino acids that closely resembles the nonapeptide PTS2 (peroxisomal targeting signal type 2): there is only a single amino acid mismatch between the two sequences. Mutation analysis confirmed that the atypical PTS2 directs FDPS into peroxisomes. Furthermore, expression of the D. discoideum FDPS–GFP fusion protein in strains of Saccharomyces cerevisiae defective in peroxisomal protein import demonstrated that import of FDPS into peroxisomes was blocked in a strain lacking the PTS2-dependent import pathway. The peroxisomal location of FDPS in D. discoideum indicates that NBPs have to cross the peroxisomal membrane before they can bind to their target.
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Abstract
Peroxisomes are remarkably versatile cell organelles whose size, shape, number, and protein content can vary greatly depending on the organism, the developmental stage of the organism’s life cycle, and the environment in which the organism lives. The main functions usually associated with peroxisomes include the metabolism of lipids and reactive oxygen species. However, in recent years, it has become clear that these organelles may also act as intracellular signaling platforms that mediate developmental decisions by modulating extraperoxisomal concentrations of several second messengers. To fulfill their functions, peroxisomes physically and functionally interact with other cell organelles, including mitochondria and the endoplasmic reticulum. Defects in peroxisome dynamics can lead to organelle dysfunction and have been associated with various human disorders. The purpose of this paper is to thoroughly summarize and discuss the current concepts underlying peroxisome formation, multiplication, and degradation. In addition, this paper will briefly highlight what is known about the interplay between peroxisomes and other cell organelles and explore the physiological and pathological implications of this interorganellar crosstalk.
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Affiliation(s)
- Marc Fransen
- Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, P.O. Box 601, 3000 Leuven, Belgium
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Pieuchot L, Jedd G. Peroxisome Assembly and Functional Diversity in Eukaryotic Microorganisms. Annu Rev Microbiol 2012; 66:237-63. [DOI: 10.1146/annurev-micro-092611-150126] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Laurent Pieuchot
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 117604 Singapore; ,
| | - Gregory Jedd
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 117604 Singapore; ,
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D-amino acid-induced expression of D-amino acid oxidase in the yeast Schizosaccharomyces pombe. Curr Microbiol 2012; 65:764-9. [PMID: 22986818 DOI: 10.1007/s00284-012-0227-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 08/10/2012] [Indexed: 10/27/2022]
Abstract
We investigated D-amino acid oxidase (DAO) induction in the popular model yeast Schizosaccharomyces pombe. The product of the putative DAO gene of the yeast expressed in E. coli displayed oxidase activity to neutral and basic D-amino acids, but not to an L-amino acid or acidic D-amino acids, showing that the putative DAO gene encodes catalytically active DAO. DAO activity was weakly detected in yeast cells grown on a culture medium without D-amino acid, and was approximately doubled by adding D-alanine. The elimination of ammonium chloride from culture medium induced activity by up to eight-fold. L-Alanine also induced the activity, but only by about half of that induced by D-alanine. The induction by D-alanine reached a maximum level at 2 h cultivation; it remained roughly constant until cell growth reached a stationary phase. The best inducer was D-alanine, followed by D-proline and then D-serine. Not effective were N-carbamoyl-D,L-alanine (a better inducer of DAO than D-alanine in the yeast Trigonopsis variabilis), and both basic and acidic D-amino acids. These results showed that S. pombe DAO could be a suitable model for analyzing the regulation of DAO expression in eukaryotic organisms.
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Ohdate T, Inoue Y. Involvement of glutathione peroxidase 1 in growth and peroxisome formation in Saccharomyces cerevisiae in oleic acid medium. Biochim Biophys Acta Mol Cell Biol Lipids 2012; 1821:1295-305. [DOI: 10.1016/j.bbalip.2012.05.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 05/04/2012] [Accepted: 05/18/2012] [Indexed: 10/28/2022]
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Molecular basis of peroxisomal biogenesis disorders caused by defects in peroxisomal matrix protein import. Biochim Biophys Acta Mol Basis Dis 2012; 1822:1326-36. [PMID: 22617146 DOI: 10.1016/j.bbadis.2012.05.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 03/26/2012] [Accepted: 05/09/2012] [Indexed: 12/28/2022]
Abstract
Peroxisomal biogenesis disorders (PBDs) represent a spectrum of autosomal recessive metabolic disorders that are collectively characterized by abnormal peroxisome assembly and impaired peroxisomal function. The importance of this ubiquitous organelle for human health is highlighted by the fact that PBDs are multisystemic disorders that often cause death in early infancy. Peroxisomes contribute to central metabolic pathways. Most enzymes in the peroxisomal matrix are linked to lipid metabolism and detoxification of reactive oxygen species. Proper assembly of peroxisomes and thus also import of their enzymes relies on specific peroxisomal biogenesis factors, so called peroxins with PEX being the gene acronym. To date, 13 PEX genes are known to cause PBDs when mutated. Studies of the cellular and molecular defects in cells derived from PBD patients have significantly contributed to the understanding of the functional role of the corresponding peroxins in peroxisome assembly. In this review, we discuss recent data derived from both human cell culture as well as model organisms like yeasts and present an overview on the molecular mechanism underlying peroxisomal biogenesis disorders with emphasis on disorders caused by defects in the peroxisomal matrix protein import machinery.
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