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Wang J, Kunze M, Villoria-González A, Weinhofer I, Berger J. Peroxisomal Localization of a Truncated HMG-CoA Reductase under Low Cholesterol Conditions. Biomolecules 2024; 14:244. [PMID: 38397481 PMCID: PMC10886633 DOI: 10.3390/biom14020244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
3-hydroxy-3-methylglutaryl-CoA reductase (HMG-CoA reductase, HMGCR) is one of the rate-limiting enzymes in the mevalonate pathway required for cholesterol biosynthesis. It is an integral membrane protein of the endoplasmic reticulum (ER) but has occasionally been described in peroxisomes. By co-immunofluorescence microscopy using different HMGCR antibodies, we present evidence for a dual localization of HMGCR in the ER and peroxisomes in differentiated human monocytic THP-1 cells, primary human monocyte-derived macrophages and human primary skin fibroblasts under conditions of low cholesterol and statin treatment. Using density gradient centrifugation and Western blot analysis, we observed a truncated HMGCR variant of 76 kDa in the peroxisomal fractions, while a full-length HMGCR of 96 kDa was contained in fractions of the ER. In contrast to primary human control fibroblasts, peroxisomal HMGCR was not found in fibroblasts from patients suffering from type-1 rhizomelic chondrodysplasia punctata, who lack functional PEX7 and, thus, cannot import peroxisomal matrix proteins harboring a type-2 peroxisomal targeting signal (PTS2). Moreover, in the N-terminal region of the soluble 76 kDa C-terminal catalytic domain, we identified a PTS2-like motif, which was functional in a reporter context. We propose that under sterol-depleted conditions, part of the soluble HMGCR domain, which is released from the ER by proteolytic processing for further turnover, remains sufficiently long in the cytosol for peroxisomal import via a PTS2/PEX7-dependent mechanism. Altogether, our findings describe a dual localization of HMGCR under combined lipid depletion and statin treatment, adding another puzzle piece to the complex regulation of HMGCR.
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Affiliation(s)
| | | | | | | | - Johannes Berger
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, 1090 Vienna, Austria
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2
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Martinek J, Cifrová P, Vosolsobě S, García-González J, Malínská K, Mauerová Z, Jelínková B, Krtková J, Sikorová L, Leaves I, Sparkes I, Schwarzerová K. ARP2/3 complex associates with peroxisomes to participate in pexophagy in plants. NATURE PLANTS 2023; 9:1874-1889. [PMID: 37845336 DOI: 10.1038/s41477-023-01542-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/11/2023] [Indexed: 10/18/2023]
Abstract
Actin-related protein (ARP2/3) complex is a heteroheptameric protein complex, evolutionary conserved in all eukaryotic organisms. Its conserved role is based on the induction of actin polymerization at the interface between membranes and the cytoplasm. Plant ARP2/3 has been reported to participate in actin reorganization at the plasma membrane during polarized growth of trichomes and at the plasma membrane-endoplasmic reticulum contact sites. Here we demonstrate that individual plant subunits of ARP2/3 fused to fluorescent proteins form motile spot-like structures in the cytoplasm that are associated with peroxisomes in Arabidopsis and tobacco. ARP2/3 is found at the peroxisome periphery and contains the assembled ARP2/3 complex and the WAVE/SCAR complex subunit NAP1. This ARP2/3-positive peroxisomal domain colocalizes with the autophagosome and, under conditions that affect the autophagy, colocalization between ARP2/3 and the autophagosome increases. ARP2/3 subunits co-immunoprecipitate with ATG8f and peroxisome-associated ARP2/3 interact in vivo with the ATG8f marker. Since mutants lacking functional ARP2/3 complex have more peroxisomes than wild type, we suggest that ARP2/3 has a novel role in the process of peroxisome degradation by autophagy, called pexophagy.
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Affiliation(s)
- Jan Martinek
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petra Cifrová
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Stanislav Vosolsobě
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Judith García-González
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Kateřina Malínská
- Imaging Facility of Institute of Experimental Botany AS CR, Prague, Czech Republic
| | - Zdeňka Mauerová
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Barbora Jelínková
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jana Krtková
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lenka Sikorová
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ian Leaves
- Biosciences, CLES, Exeter University, Exeter, UK
| | - Imogen Sparkes
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Kateřina Schwarzerová
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic.
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3
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Turkolmez S, Chornyi S, Alhajouj S, IJlst L, Waterham HR, Mitchell PJ, Hettema EH, van Roermund CWT. Peroxisomal NAD(H) Homeostasis in the Yeast Debaryomyces hansenii Depends on Two Redox Shuttles and the NAD + Carrier, Pmp47. Biomolecules 2023; 13:1294. [PMID: 37759694 PMCID: PMC10526880 DOI: 10.3390/biom13091294] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Debaryomyces hansenii is considered an unconventional yeast with a strong biotechnological potential, which can produce and store high amounts of lipids. However, relatively little is known about its lipid metabolism, and genetic tools for this yeast have been limited. The aim of this study was to explore the fatty acid β-oxidation pathway in D. hansenii. To this end, we employed recently developed methods to generate multiple gene deletions and tag open reading frames with GFP in their chromosomal context in this yeast. We found that, similar as in other yeasts, the β-oxidation of fatty acids in D. hansenii was restricted to peroxisomes. We report a series of experiments in D. hansenii and the well-studied yeast Saccharomyces cerevisiae that show that the homeostasis of NAD+ in D. hansenii peroxisomes is dependent upon the peroxisomal membrane protein Pmp47 and two peroxisomal dehydrogenases, Mdh3 and Gpd1, which both export reducing equivalents produced during β-oxidation to the cytosol. Pmp47 is the first identified NAD+ carrier in yeast peroxisomes.
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Affiliation(s)
- Selva Turkolmez
- School of Bioscience, University of Sheffield, Sheffield S10 2TN, UK
| | - Serhii Chornyi
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Sondos Alhajouj
- School of Bioscience, University of Sheffield, Sheffield S10 2TN, UK
| | - Lodewijk IJlst
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Hans R. Waterham
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development, Amsterdam, The Netherlands
| | - Phil J. Mitchell
- School of Bioscience, University of Sheffield, Sheffield S10 2TN, UK
| | - Ewald H. Hettema
- School of Bioscience, University of Sheffield, Sheffield S10 2TN, UK
| | - Carlo W. T. van Roermund
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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4
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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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5
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Záhonová K, Low RS, Warren CJ, Cantoni D, Herman EK, Yiangou L, Ribeiro CA, Phanprasert Y, Brown IR, Rueckert S, Baker NL, Tachezy J, Betts EL, Gentekaki E, van der Giezen M, Clark CG, Jackson AP, Dacks JB, Tsaousis AD. Evolutionary analysis of cellular reduction and anaerobicity in the hyper-prevalent gut microbe Blastocystis. Curr Biol 2023:S0960-9822(23)00620-6. [PMID: 37267944 DOI: 10.1016/j.cub.2023.05.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 03/22/2023] [Accepted: 05/11/2023] [Indexed: 06/04/2023]
Abstract
Blastocystis is the most prevalent microbial eukaryote in the human and animal gut, yet its role as commensal or parasite is still under debate. Blastocystis has clearly undergone evolutionary adaptation to the gut environment and possesses minimal cellular compartmentalization, reduced anaerobic mitochondria, no flagella, and no reported peroxisomes. To address this poorly understood evolutionary transition, we have taken a multi-disciplinary approach to characterize Proteromonas lacertae, the closest canonical stramenopile relative of Blastocystis. Genomic data reveal an abundance of unique genes in P. lacertae but also reductive evolution of the genomic complement in Blastocystis. Comparative genomic analysis sheds light on flagellar evolution, including 37 new candidate components implicated with mastigonemes, the stramenopile morphological hallmark. The P. lacertae membrane-trafficking system (MTS) complement is only slightly more canonical than that of Blastocystis, but notably, we identified that both organisms encode the complete enigmatic endocytic TSET complex, a first for the entire stramenopile lineage. Investigation also details the modulation of mitochondrial composition and metabolism in both P. lacertae and Blastocystis. Unexpectedly, we identify in P. lacertae the most reduced peroxisome-derived organelle reported to date, which leads us to speculate on a mechanism of constraint guiding the dynamics of peroxisome-mitochondrion reductive evolution on the path to anaerobiosis. Overall, these analyses provide a launching point to investigate organellar evolution and reveal in detail the evolutionary path that Blastocystis has taken from a canonical flagellated protist to the hyper-divergent and hyper-prevalent animal and human gut microbe.
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Affiliation(s)
- Kristína Záhonová
- Division of Infectious Diseases, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton T6G 2G3, Canada; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, České Budějovice (Budweis) 370 05, Czech Republic; Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, Vestec 252 50, Czech Republic; Life Science Research Centre, Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, Ostrava 710 00, Czech Republic
| | - Ross S Low
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Christopher J Warren
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Diego Cantoni
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Emily K Herman
- Division of Infectious Diseases, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton T6G 2G3, Canada; Department of Agricultural, Food, and Nutritional Science, Faculty of Agricultural, Life, and Environmental Sciences, University of Alberta, 2-31 General Services Building, Edmonton, AB T6G 2H1, Canada
| | - Lyto Yiangou
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Cláudia A Ribeiro
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Yasinee Phanprasert
- Division of Infectious Diseases, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton T6G 2G3, Canada; School of Science, Mae Fah Luang Universit, 333 Moo 1, T. Tasud, Muang District, Chiang Rai 57100, Thailand
| | - Ian R Brown
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Sonja Rueckert
- School of Applied Sciences, Sighthill Campus, Room 3.B.36, Edinburgh EH11 4BN, Scotland; Faculty of Biology, AG Eukaryotische Mikrobiologie, Universitätsstrasse 5, S05 R04 H83, Essen 45141, Germany
| | - Nicola L Baker
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, Vestec 252 50, Czech Republic
| | - Emma L Betts
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK; School of Applied Sciences, Sighthill Campus, Room 3.B.36, Edinburgh EH11 4BN, Scotland
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang Universit, 333 Moo 1, T. Tasud, Muang District, Chiang Rai 57100, Thailand; Gut Microbiome Research Group, Mae Fah Luang University, 333 Moo 1, T. Tasud, Muang District, Chiang Rai 57100, Thailand
| | - Mark van der Giezen
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger Richard Johnsens Gate 4, 4021 Stavanger, Norway; Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - C Graham Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Andrew P Jackson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton T6G 2G3, Canada; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, České Budějovice (Budweis) 370 05, Czech Republic; Centre for Life's Origin and Evolution, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.
| | - Anastasios D Tsaousis
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK.
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Hoernstein SNW, Özdemir B, van Gessel N, Miniera AA, Rogalla von Bieberstein B, Nilges L, Schweikert Farinha J, Komoll R, Glauz S, Weckerle T, Scherzinger F, Rodriguez-Franco M, Müller-Schüssele SJ, Reski R. A deeply conserved protease, acylamino acid-releasing enzyme (AARE), acts in ageing in Physcomitrella and Arabidopsis. Commun Biol 2023; 6:61. [PMID: 36650210 PMCID: PMC9845386 DOI: 10.1038/s42003-023-04428-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023] Open
Abstract
Reactive oxygen species (ROS) are constant by-products of aerobic life. In excess, ROS lead to cytotoxic protein aggregates, which are a hallmark of ageing in animals and linked to age-related pathologies in humans. Acylamino acid-releasing enzymes (AARE) are bifunctional serine proteases, acting on oxidized proteins. AARE are found in all domains of life, albeit under different names, such as acylpeptide hydrolase (APEH/ACPH), acylaminoacyl peptidase (AAP), or oxidized protein hydrolase (OPH). In humans, AARE malfunction is associated with age-related pathologies, while their function in plants is less clear. Here, we provide a detailed analysis of AARE genes in the plant lineage and an in-depth analysis of AARE localization and function in the moss Physcomitrella and the angiosperm Arabidopsis. AARE loss-of-function mutants have not been described for any organism so far. We generated and analysed such mutants and describe a connection between AARE function, aggregation of oxidized proteins and plant ageing, including accelerated developmental progression and reduced life span. Our findings complement similar findings in animals and humans, and suggest a unified concept of ageing may exist in different life forms.
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Affiliation(s)
- Sebastian N W Hoernstein
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
| | - Buğra Özdemir
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
- Euro-BioImaging Bio-Hub, EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
| | - Alessandra A Miniera
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
| | - Bruno Rogalla von Bieberstein
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
- Department of Anesthesiology, University Hospital Würzburg, Oberduerrbacher Strasse 6, 97072, Würzburg, Germany
| | - Lars Nilges
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
| | - Joana Schweikert Farinha
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Ramona Komoll
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
- Heraeus Medical GmbH, Philipp-Reis-Straße 8-13, 61273, Wehrheim, Germany
| | - Stella Glauz
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
| | - Tim Weckerle
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
- Zymo Research Europe GmbH, Muelhauser Strasse 9, 79110, Freiburg, Germany
| | - Friedrich Scherzinger
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
- Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
| | - Marta Rodriguez-Franco
- Cell Biology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
| | - Stefanie J Müller-Schüssele
- Molecular Botany, Department of Biology, Technical University of Kaiserslautern, Erwin-Schrödinger-Strasse 70, 67663, Kaiserslautern, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany.
- Signalling Research Centres BIOSS and CIBSS, Schaenzlestrasse 18, 79104, Freiburg, Germany.
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7
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Kunze M. Computational Evaluation of Peroxisomal Targeting Signals in Metazoa. Methods Mol Biol 2023; 2643:391-404. [PMID: 36952201 DOI: 10.1007/978-1-0716-3048-8_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Most soluble proteins enclosed in peroxisomes encode either type-1 or type-2 peroxisomal targeting signals (PTS1 or PTS2), which act as postal codes and define the proteins' intracellular destination. Thus, various computational programs have been developed to evaluate the probability of specific peptide sequences for being a functional PTS or to scan the primary sequence of proteins for such signals. Among these prediction algorithms the PTS1-predictor ( https://mendel.imp.ac.at/pts1/ ) has been amply used, but the research logic of this and other PTS1 prediction tools is occasionally misjudged giving rise to characteristic pitfalls. Here, a proper utilization of the PTS1-predictor is introduced together with a framework of additional tests to increase the validity of the interpretation of results. Moreover, a list of possible causes for a mismatch between results of such predictions and experimental outcomes is provided. However, the foundational arguments apply to other prediction tools for PTS1 motifs as well.
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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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8
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Deori NM, Nagotu S. Peroxisome biogenesis and inter-organelle communication: an indispensable role for Pex11 and Pex30 family proteins in yeast. Curr Genet 2022; 68:537-550. [PMID: 36242632 DOI: 10.1007/s00294-022-01254-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/26/2022]
Abstract
Peroxisomes are highly dynamic organelles present in most eukaryotic cells. They also play an important role in human health and the optimum functioning of cells. An extensive repertoire of proteins is associated with the biogenesis and function of these organelles. Two protein families that are involved in regulating peroxisome number in a cell directly or indirectly are Pex11 and Pex30. Interestingly, these proteins are also reported to regulate the contact sites between peroxisomes and other cell organelles such as mitochondria, endoplasmic reticulum and lipid droplets. In this manuscript, we review our current knowledge of the role of these proteins in peroxisome biogenesis in various yeast species. Further, we also discuss in detail the role of these protein families in the regulation of inter-organelle contacts in yeast.
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Affiliation(s)
- Nayan Moni Deori
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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9
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Andrade-Alviárez D, Bonive-Boscan AD, Cáceres AJ, Quiñones W, Gualdrón-López M, Ginger ML, Michels PAM. Delineating transitions during the evolution of specialised peroxisomes: Glycosome formation in kinetoplastid and diplonemid protists. Front Cell Dev Biol 2022; 10:979269. [PMID: 36172271 PMCID: PMC9512073 DOI: 10.3389/fcell.2022.979269] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/17/2022] [Indexed: 12/01/2022] Open
Abstract
One peculiarity of protists belonging to classes Kinetoplastea and Diplonemea within the phylum Euglenozoa is compartmentalisation of most glycolytic enzymes within peroxisomes that are hence called glycosomes. This pathway is not sequestered in peroxisomes of the third Euglenozoan class, Euglenida. Previous analysis of well-studied kinetoplastids, the ‘TriTryps’ parasites Trypanosoma brucei, Trypanosoma cruzi and Leishmania spp., identified within glycosomes other metabolic processes usually not present in peroxisomes. In addition, trypanosomatid peroxins, i.e. proteins involved in biogenesis of these organelles, are divergent from human and yeast orthologues. In recent years, genomes, transcriptomes and proteomes for a variety of euglenozoans have become available. Here, we track the possible evolution of glycosomes by querying these databases, as well as the genome of Naegleria gruberi, a non-euglenozoan, which belongs to the same protist supergroup Discoba. We searched for orthologues of TriTryps proteins involved in glycosomal metabolism and biogenesis. Predicted cellular location(s) of each metabolic enzyme identified was inferred from presence or absence of peroxisomal-targeting signals. Combined with a survey of relevant literature, we refine extensively our previously postulated hypothesis about glycosome evolution. The data agree glycolysis was compartmentalised in a common ancestor of the kinetoplastids and diplonemids, yet additionally indicates most other processes found in glycosomes of extant trypanosomatids, but not in peroxisomes of other eukaryotes were either sequestered in this ancestor or shortly after separation of the two lineages. In contrast, peroxin divergence is evident in all euglenozoans. Following their gain of pathway complexity, subsequent evolution of peroxisome/glycosome function is complex. We hypothesize compartmentalisation in glycosomes of glycolytic enzymes, their cofactors and subsequently other metabolic enzymes provided selective advantage to kinetoplastids and diplonemids during their evolution in changing marine environments. We contend two specific properties derived from the ancestral peroxisomes were key: existence of nonselective pores for small solutes and the possibility of high turnover by pexophagy. Critically, such pores and pexophagy are characterised in extant trypanosomatids. Increasing amenability of free-living kinetoplastids and recently isolated diplonemids to experimental study means our hypothesis and interpretation of bioinformatic data are suited to experimental interrogation.
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Affiliation(s)
- Diego Andrade-Alviárez
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Alejandro D. Bonive-Boscan
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Ana J. Cáceres
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Wilfredo Quiñones
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | | | - Michael L. Ginger
- School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Paul A. M. Michels
- Centre for Immunity, Infection and Evolution and Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
- *Correspondence: Paul A. M. Michels,
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10
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Kato N, McCuiston C, Szuska KA, Lauersen KJ, Nelson G, Strain A. Chlamydomonas reinhardtii Alternates Peroxisomal Contents in Response to Trophic Conditions. Cells 2022; 11:cells11172724. [PMID: 36078132 PMCID: PMC9454557 DOI: 10.3390/cells11172724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Chlamydomonas reinhardtii is a model green microalga capable of heterotrophic growth on acetic acid but not fatty acids, despite containing a full complement of genes for β-oxidation. Recent reports indicate that the alga preferentially sequesters, rather than breaks down, lipid acyl chains as a means to rebuild its membranes rapidly. Here, we assemble a list of potential Chlamydomonas peroxins (PEXs) required for peroxisomal biogenesis to suggest that C. reinhardtii has a complete set of peroxisome biogenesis factors. To determine involvements of the peroxisomes in the metabolism of exogenously added fatty acids, we examined transgenic C. reinhardtii expressing fluorescent proteins fused to N- or C-terminal peptide of peroxisomal proteins, concomitantly with fluorescently labeled palmitic acid under different trophic conditions. We used confocal microscopy to track the populations of the peroxisomes in illuminated and dark conditions, with and without acetic acid as a carbon source. In the cells, four major populations of compartments were identified, containing: (1) a glyoxylate cycle enzyme marker and a protein containing peroxisomal targeting signal 1 (PTS1) tripeptide but lacking the fatty acid marker, (2) the fatty acid marker alone, (3) the glyoxylate cycle enzyme marker alone, and (4) the PTS1 marker alone. Less than 5% of the compartments contained both fatty acid and peroxisomal markers. Statistical analysis on optically sectioned images found that C. reinhardtii simultaneously carries diverse populations of the peroxisomes in the cell and modulates peroxisomal contents based on light conditions. On the other hand, the ratio of the compartment containing both fatty acid and peroxisomal markers did not change significantly regardless of the culture conditions. The result indicates that β-oxidation may be only a minor occurrence in the peroxisomal population in C. reinhardtii, which supports the idea that lipid biosynthesis and not β-oxidation is the primary metabolic preference of fatty acids in the alga.
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Affiliation(s)
- Naohiro Kato
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
- Correspondence:
| | - Clayton McCuiston
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Kimberly A. Szuska
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Kyle J. Lauersen
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Gabela Nelson
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Alexis Strain
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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11
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Tarafdar S, Chowdhary G. Translating the Arabidopsis thaliana Peroxisome Proteome Insights to Solanum lycopersicum: Consensus Versus Diversity. Front Cell Dev Biol 2022; 10:909604. [PMID: 35912119 PMCID: PMC9328179 DOI: 10.3389/fcell.2022.909604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022] Open
Abstract
Peroxisomes are small, single-membrane specialized organelles present in all eukaryotic organisms. The peroxisome is one of the nodal centers of reactive oxygen species homeostasis in plants, which are generated in a high amount due to various stress conditions. Over the past decade, there has been extensive study on peroxisomal proteins and their signaling pathways in the model plant Arabidopsis thaliana, and a lot has been deciphered. However, not much impetus has been given to studying the peroxisome proteome of economically important crops. Owing to the significance of peroxisomes in the physiology of plants during normal and stress conditions, understating its proteome is of much importance. Hence, in this paper, we have made a snapshot of putative peroxisomal matrix proteins in the economically important vegetable crop tomato (Solanum lycopersicum, (L.) family Solanaceae). First, a reference peroxisomal matrix proteome map was generated for Arabidopsis thaliana using the available proteomic and localization studies, and proteins were categorized into various groups as per their annotations. This was used to create the putative peroxisomal matrix proteome map for S. lycopersicum. The putative peroxisome proteome in S. lycopersicum retains the basic framework: the bulk of proteins had peroxisomal targeting signal (PTS) type 1, a minor group had PTS2, and the catalase family retained its characteristic internal PTS. Apart from these, a considerable number of S. lycopersicum orthologs did not contain any "obvious" PTS. The number of PTS2 isoforms was found to be reduced in S. lycopersicum. We further investigated the PTS1s in the case of both the plant species and generated a pattern for canonical and non-canonical PTS1s. The number of canonical PTS1 proteins was comparatively lesser in S. lycopersicum. The non-canonical PTS1s were found to be comparable in both the plant species; however, S. lycopersicum showed greater diversity in the composition of the signal tripeptide. Finally, we have tried to address the lacunas and probable strategies to fill those gaps.
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Affiliation(s)
| | - Gopal Chowdhary
- Plant Molecular Biology Laboratory, School of Biotechnology, KIIT, Bhubaneswar, India
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12
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Vasilev J, Mix AK, Heimerl T, Maier UG, Moog D. Inferred Subcellular Localization of Peroxisomal Matrix Proteins of Guillardia theta Suggests an Important Role of Peroxisomes in Cryptophytes. FRONTIERS IN PLANT SCIENCE 2022; 13:889662. [PMID: 35783940 PMCID: PMC9244630 DOI: 10.3389/fpls.2022.889662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Peroxisomes participate in several important metabolic processes in eukaryotic cells, such as the detoxification of reactive oxygen species (ROS) or the degradation of fatty acids by β-oxidation. Recently, the presence of peroxisomes in the cryptophyte Guillardia theta and other "chromalveolates" was revealed by identifying proteins for peroxisomal biogenesis. Here, we investigated the subcellular localization of candidate proteins of G. theta in the diatom Phaeodactylum tricornutum, either possessing a putative peroxisomal targeting signal type 1 (PTS1) sequence or factors lacking a peroxisomal targeting signal but known to be involved in β-oxidation. Our results indicate important contributions of the peroxisomes of G. theta to the carbohydrate, ether phospholipid, nucleotide, vitamin K, ROS, amino acid, and amine metabolisms. Moreover, our results suggest that in contrast to many other organisms, the peroxisomes of G. theta are not involved in the β-oxidation of fatty acids, which exclusively seems to occur in the cryptophyte's mitochondria.
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Affiliation(s)
- Jana Vasilev
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Ann-Kathrin Mix
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Uwe G. Maier
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Daniel Moog
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
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13
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Pei D, Dalbey RE. Membrane Translocation of Folded Proteins. J Biol Chem 2022; 298:102107. [PMID: 35671825 PMCID: PMC9251779 DOI: 10.1016/j.jbc.2022.102107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 12/01/2022] Open
Abstract
An ever-increasing number of proteins have been shown to translocate across various membranes of bacterial as well as eukaryotic cells in their folded states as a part of physiological and/or pathophysiological processes. Herein we provide an overview of the systems/processes that are established or likely to involve the membrane translocation of folded proteins, such as protein export by the twin-arginine translocation (TAT) system in bacteria and chloroplasts, unconventional protein secretion (UPS) and protein import into the peroxisome in eukaryotes, and the cytosolic entry of proteins (e.g., bacterial toxins) and viruses into eukaryotes. We also discuss the various mechanistic models that have previously been proposed for the membrane translocation of folded proteins including pore/channel formation, local membrane disruption, membrane thinning, and transport by membrane vesicles. Finally, we introduce a newly discovered vesicular transport mechanism, vesicle budding and collapse (VBC), and present evidence that VBC may represent a unifying mechanism that drives some (and potentially all) of folded protein translocation processes.
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Affiliation(s)
- Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210.
| | - Ross E Dalbey
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12(th) Avenue, Columbus, OH 43210.
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Yang W, Gutbrod P, Gutbrod K, Peisker H, Song X, Falz AL, Meyer AJ, Dörmann P. 2-Hydroxy-phytanoyl-CoA lyase (AtHPCL) is involved in phytol metabolism in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1290-1304. [PMID: 34902195 DOI: 10.1111/tpj.15632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
During chlorophyll degradation, large amounts of the isoprenoid alcohol phytol are released. The pathway of phytol catabolism has been studied in humans, because chlorophyll is part of the human diet, but little is known for plants. In humans, phytanoyl-CoA derived from phytol is degraded via α-oxidation by phytanoyl-CoA hydroxylase (PAHX) and 2-hydroxy-phytanoyl-CoA lyase (HPCL). Arabidopsis contains two sequences homologous to the human proteins AtPAHX and AtHPCL. Insertional mutants of Arabidopsis (pahx, hpcl) were grown under N deprivation to stimulate chlorophyll breakdown or supplemented with phytol to increase the endogenous amount of phytol. During N deprivation, chlorophyll, phytol, phytenal, upstream metabolites of phytol breakdown, and tocopherol and fatty acid phytyl esters, alternative phytol-derived lipids, accumulated in pahx and hpcl mutants, in line with the scenario that the mutations interfere with phytol degradation. AtHPCL was localized to the peroxisomes. Expression analysis of the AtHPCL sequence in the yeast Δpxp1 or Δmpo1 mutants followed by supplementation with 2-hydroxy-palmitic acid and enzyme assays of peroxisomal proteins from Col-0 and hpcl plants with 2-hydroxy-stearoyl-CoA revealed that AtHPCL harbors 2-hydroxy-acyl-CoA lyase activity. The α-dioxygenases αDOX1 and αDOX2 are involved in α-oxidation of fatty acids and could be involved in an alternative pathway of phytol degradation. However, phytol-related lipids in the αdox1, αdox2, or αdox1 αdox2 mutants were not altered compared with Col-0, indicating that αDOX1 and αDOX2 are not involved in phytol degradation. These results demonstrate that phytol degradation in Arabidopsis involves α-oxidation by AtPAHX and AtHPCL, but that it is independent of αDOX1/αDOX2.
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Affiliation(s)
- Wentao Yang
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Straße 13, 53115, Bonn, Germany
| | - Philipp Gutbrod
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Straße 13, 53115, Bonn, Germany
| | - Katharina Gutbrod
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Straße 13, 53115, Bonn, Germany
| | - Helga Peisker
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Straße 13, 53115, Bonn, Germany
| | - Xiaoning Song
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Straße 13, 53115, Bonn, Germany
| | - Anna-Lena Falz
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
| | - Andreas J Meyer
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
| | - Peter Dörmann
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Straße 13, 53115, Bonn, Germany
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15
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Neofunctionalization of Glycolytic Enzymes: An Evolutionary Route to Plant Parasitism in the Oomycete Phytophthora nicotianae. Microorganisms 2022; 10:microorganisms10020281. [PMID: 35208735 PMCID: PMC8879444 DOI: 10.3390/microorganisms10020281] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/12/2022] [Accepted: 01/23/2022] [Indexed: 02/04/2023] Open
Abstract
Oomycetes, of the genus Phytophthora, comprise of some of the most devastating plant pathogens. Parasitism of Phytophthora results from evolution from an autotrophic ancestor and adaptation to a wide range of environments, involving metabolic adaptation. Sequence mining showed that Phytophthora spp. display an unusual repertoire of glycolytic enzymes, made of multigene families and enzyme replacements. To investigate the impact of these gene duplications on the biology of Phytophthora and, eventually, identify novel functions associated to gene expansion, we focused our study on the first glycolytic step on P. nicotianae, a broad host range pathogen. We reveal that this step is committed by a set of three glucokinase types that differ by their structure, enzymatic properties, and evolutionary histories. In addition, they are expressed differentially during the P. nicotianae life cycle, including plant infection. Last, we show that there is a strong association between the expression of a glucokinase member in planta and extent of plant infection. Together, these results suggest that metabolic adaptation is a component of the processes underlying evolution of parasitism in Phytophthora, which may possibly involve the neofunctionalization of metabolic enzymes.
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16
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Pex7 selectively imports PTS2 target proteins to peroxisomes and is required for anthracnose disease development in Colletotrichum scovillei. Fungal Genet Biol 2021; 157:103636. [PMID: 34742890 DOI: 10.1016/j.fgb.2021.103636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 11/22/2022]
Abstract
Pex7 is a shuttling receptor that imports matrix proteins with a type 2 peroxisomal targeting signal (PTS2) to peroxisomes. The Pex7-mediated PTS2 protein import contributes to crucial metabolic processes such as the fatty acid β-oxidation and glucose metabolism in a number of fungi, but cellular roles of Pex7 between the import of PTS2 target proteins and metabolic processes have not been fully understood. In this study, we investigated the functional roles of CsPex7, a homolog of the yeast Pex7, by targeted gene deletion in the pepper anthracnose fungus Colletotrichum scovillei. CsPex7 was required for carbon source utilization, scavenging of reactive oxygen species, conidial production, and disease development in C. scovillei. The expression of fluorescently tagged PTS2 signal of hexokinases and 3-ketoacyl-CoA thiolases showed that peroxisomal localization of the hexokinase CsGlk1 PTS2 is dependent on CsPex7, but those of the 3-ketoacyl-CoA thiolases are independent on CsPex7. In addition, GFP-tagged CsPex7 proteins were intensely localized to the peroxisomes on glucose-containing media, indicating a role of CsPex7 in glucose utilization. Collectively, these findings indicate that CsPex7 selectively recognizes specific PTS2 signal for import of PTS2-containing proteins to peroxisomes, thereby mediating peroxisomal targeting efficiency of PTS2-containing proteins in C. scovillei. On pepper fruits, the ΔCspex7 mutant exhibited significantly reduced virulence, in which excessive accumulation of hydrogen peroxide was observed in the pepper cells. We think the reduced virulence results from the abnormality in hydrogen peroxide metabolism of the ΔCspex7 mutant. Our findings provide insight into the cellular roles of CsPex7 in PTS2 protein import system.
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17
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BiFC Method Based on Intraorganellar Protein Crowding Detects Oleate-Dependent Peroxisomal Targeting of Pichia pastoris Malate Dehydrogenase. Int J Mol Sci 2021; 22:ijms22094890. [PMID: 34063066 PMCID: PMC8124512 DOI: 10.3390/ijms22094890] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/24/2021] [Accepted: 04/29/2021] [Indexed: 12/15/2022] Open
Abstract
The maintenance of intracellular NAD+/NADH homeostasis across multiple, subcellular compartments requires the presence of NADH-shuttling proteins, which circumvent the lack of permeability of organelle membranes to these cofactors. Very little is known regarding these proteins in the methylotrophic yeast, Pichia pastoris. During the study of the subcellular locations of these shuttling proteins, which often have dual subcellular locations, it became necessary to develop new ways to detect the weak peroxisomal locations of some of these proteins. We have developed a novel variation of the traditional Bimolecular Fluorescence Complementation (BiFC), called divergent BiFC, to detect intraorganellar colocalization of two noninteracting proteins based on their proximity-based protein crowding within a small subcellular compartment, rather than on the traditional protein–protein interactions expected for BiFC. This method is used to demonstrate the partially peroxisomal location of one such P. pastoris NADH-shuttling protein, malate dehydrogenase B, only when cells are grown in oleate, but not when grown in methanol or glucose. We discuss the mode of NADH shuttling in P. pastoris and the physiological basis of the medium-dependent compartmentalization of PpMdhB.
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18
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Lubbers RJM, Dilokpimol A, Visser J, de Vries RP. Aspergillus niger uses the peroxisomal CoA-dependent β-oxidative genes to degrade the hydroxycinnamic acids caffeic acid, ferulic acid, and p-coumaric acid. Appl Microbiol Biotechnol 2021; 105:4199-4211. [PMID: 33950281 PMCID: PMC8140964 DOI: 10.1007/s00253-021-11311-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/05/2021] [Accepted: 04/20/2021] [Indexed: 11/28/2022]
Abstract
Abstract Aromatic compounds are important molecules which are widely applied in many industries and are mainly produced from nonrenewable sources. Renewable sources such as plant biomass are interesting alternatives for the production of aromatic compounds. Ferulic acid and p-coumaric acid, a precursor for vanillin and p-vinyl phenol, respectively, can be released from plant biomass by the fungus Aspergillus niger. The degradation of hydroxycinnamic acids such as caffeic acid, ferulic acid, and p-coumaric acid has been observed in many fungi. In A. niger, multiple metabolic pathways were suggested for the degradation of hydroxycinnamic acids. However, no genes were identified for these hydroxycinnamic acid metabolic pathways. In this study, several pathway genes were identified using whole-genome transcriptomic data of A. niger grown on different hydroxycinnamic acids. The genes are involved in the CoA-dependent β-oxidative pathway in fungi. This pathway is well known for the degradation of fatty acids, but not for hydroxycinnamic acids. However, in plants, it has been shown that hydroxycinnamic acids are degraded through this pathway. We identified genes encoding hydroxycinnamate-CoA synthase (hcsA), multifunctional β-oxidation hydratase/dehydrogenase (foxA), 3-ketoacyl CoA thiolase (katA), and four thioesterases (theA-D) of A. niger, which were highly induced by all three tested hydroxycinnamic acids. Deletion mutants revealed that these genes were indeed involved in the degradation of several hydroxycinnamic acids. In addition, foxA and theB are also involved in the degradation of fatty acids. HcsA, FoxA, and KatA contained a peroxisomal targeting signal and are therefore predicted to be localized in peroxisomes. Key points • Metabolism of hydroxycinnamic acid was investigated in Aspergillus niger • Using transcriptome data, multiple CoA-dependent β-oxidative genes were identified. • Both foxA and theB are involved in hydroxycinnamate but also fatty acid metabolism. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11311-0.
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Affiliation(s)
- R J M Lubbers
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - A Dilokpimol
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - J Visser
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - R P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.
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19
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Kechasov D, de Grahl I, Endries P, Reumann S. Evolutionary Maintenance of the PTS2 Protein Import Pathway in the Stramenopile Alga Nannochloropsis. Front Cell Dev Biol 2020; 8:593922. [PMID: 33330478 PMCID: PMC7710942 DOI: 10.3389/fcell.2020.593922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/13/2020] [Indexed: 12/18/2022] Open
Abstract
The stramenopile alga Nannochloropsis evolved by secondary endosymbiosis of a red alga by a heterotrophic host cell and emerged as a promising organism for biotechnological applications, such as the production of polyunsaturated fatty acids and biodiesel. Peroxisomes play major roles in fatty acid metabolism but experimental analyses of peroxisome biogenesis and metabolism in Nannochloropsis are not reported yet. In fungi, animals, and land plants, soluble proteins of peroxisomes are targeted to the matrix by one of two peroxisome targeting signals (type 1, PTS1, or type 2, PTS2), which are generally conserved across kingdoms and allow the prediction of peroxisomal matrix proteins from nuclear genome sequences. Because diatoms lost the PTS2 pathway secondarily, we investigated its presence in the stramenopile sister group of diatoms, the Eustigmatophyceae, represented by Nannochloropsis. We detected a full-length gene of a putative PEX7 ortholog coding for the cytosolic receptor of PTS2 proteins and demonstrated its expression in Nannochloropsis gaditana. The search for predicted PTS2 cargo proteins in N. gaditana yielded several candidates. In vivo subcellular targeting analyses of representative fusion proteins in different plant expression systems demonstrated that two predicted PTS2 domains were indeed functional and sufficient to direct a reporter protein to peroxisomes. Peroxisome targeting of the predicted PTS2 cargo proteins was further confirmed in Nannochloropsis oceanica by confocal and transmission electron microscopy. Taken together, the results demonstrate for the first time that one group of stramenopile algae maintained the import pathway for PTS2 cargo proteins. To comprehensively map and model the metabolic capabilities of Nannochloropsis peroxisomes, in silico predictions needs to encompass both the PTS1 and the PTS2 matrix proteome.
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Affiliation(s)
- Dmitry Kechasov
- Centre for Organelle Research, University of Stavanger, Stavanger, Norway
| | - Imke de Grahl
- Plant Biochemistry and Infection Biology, Institute for Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Pierre Endries
- Plant Biochemistry and Infection Biology, Institute for Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Sigrun Reumann
- Centre for Organelle Research, University of Stavanger, Stavanger, Norway
- Plant Biochemistry and Infection Biology, Institute for Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
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20
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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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21
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Kunze M. The type-2 peroxisomal targeting signal. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1867:118609. [PMID: 31751594 DOI: 10.1016/j.bbamcr.2019.118609] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/08/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022]
Abstract
The type-2 peroxisomal targeting signal (PTS2) is one of two peptide motifs destining soluble proteins for peroxisomes. This signal acts as amphiphilic α-helix exposing the side chains of all conserved residues to the same side. PTS2 motifs are recognized by a bipartite protein complex consisting of the receptor PEX7 and a co-receptor. Cargo-loaded receptor complexes are translocated across the peroxisomal membrane by a transient pore and inside peroxisomes, cargo proteins are released and processed in many, but not all species. The components of the bipartite receptor are re-exported into the cytosol by a ubiquitin-mediated and ATP-driven export mechanism. Structurally, PTS2 motifs resemble other N-terminal targeting signals, whereas the functional relation to the second peroxisomal targeting signal (PTS1) is unclear. Although only a few PTS2-carrying proteins are known in humans, subjects lacking a functional import mechanism for these proteins suffer from the severe inherited disease rhizomelic chondrodysplasia punctata.
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Affiliation(s)
- Markus Kunze
- Medical University of Vienna, Center for Brain Research, Department of Pathobiology of the Nervous System, Spitalgasse 4, 1090 Vienna, Austria.
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22
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Kong X, Zhang H, Wang X, van der Lee T, Waalwijk C, van Diepeningen A, Brankovics B, Xu J, Xu J, Chen W, Feng J. FgPex3, a Peroxisome Biogenesis Factor, Is Involved in Regulating Vegetative Growth, Conidiation, Sexual Development, and Virulence in Fusarium graminearum. Front Microbiol 2019; 10:2088. [PMID: 31616386 PMCID: PMC6764106 DOI: 10.3389/fmicb.2019.02088] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/23/2019] [Indexed: 12/28/2022] Open
Abstract
Peroxisomes are involved in a wide range of important cellular functions. Here, the role of the peroxisomal membrane protein PEX3 in the plant-pathogen and mycotoxin producer Fusarium graminearum was studied using knock-out and complemented strains. To fluorescently label peroxisomes’ punctate structures, GFP and RFP fusions with the PTS1 and PTS2 localization signal were transformed into the wild type PH-1 and ΔFgPex3 knock-out strains. The GFP and RFP transformants in the ΔFgPex3 background showed a diffuse fluorescence pattern across the cytoplasm suggesting the absence of mature peroxisomes. The ΔFgPex3 strain showed a minor, non-significant reduction in growth on various sugar carbon sources. In contrast, deletion of FgPex3 affected fatty acid β-oxidation in F. graminearum and significantly reduced the utilization of fatty acids. Furthermore, the ΔFgPex3 mutant was sensitive to osmotic stressors as well as to cell wall-damaging agents. Reactive oxygen species (ROS) levels in the mutant had increased significantly, which may be linked to the reduced longevity of cultured strains. The mutant also showed reduced production of conidiospores, while sexual reproduction was completely impaired. The pathogenicity of ΔFgPex3, especially during the process of systemic infection, was strongly reduced on both tomato and on wheat, while to production of deoxynivalenol (DON), an important factor for virulence, appeared to be unaffected.
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Affiliation(s)
- Xiangjiu Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Hao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Xiaoliang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Theo van der Lee
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Cees Waalwijk
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Anne van Diepeningen
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Balazs Brankovics
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Jin Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Jingsheng Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Jie Feng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
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Acosta H, Burchmore R, Naula C, Gualdrón-López M, Quintero-Troconis E, Cáceres AJ, Michels PAM, Concepción JL, Quiñones W. Proteomic analysis of glycosomes from Trypanosoma cruzi epimastigotes. Mol Biochem Parasitol 2019; 229:62-74. [PMID: 30831156 PMCID: PMC7082770 DOI: 10.1016/j.molbiopara.2019.02.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/25/2019] [Accepted: 02/27/2019] [Indexed: 12/20/2022]
Abstract
In Trypanosoma cruzi, the causal agent of Chagas disease, the first seven steps of glycolysis are compartmentalized in glycosomes, which are authentic but specialized peroxisomes. Besides glycolysis, activity of enzymes of other metabolic processes have been reported to be present in glycosomes, such as β-oxidation of fatty acids, purine salvage, pentose-phosphate pathway, gluconeogenesis and biosynthesis of ether-lipids, isoprenoids, sterols and pyrimidines. In this study, we have purified glycosomes from T. cruzi epimastigotes, collected the soluble and membrane fractions of these organelles, and separated peripheral and integral membrane proteins by Na2CO3 treatment and osmotic shock. Proteomic analysis was performed on each of these fractions, allowing us to confirm the presence of enzymes involved in various metabolic pathways as well as identify new components of this parasite's glycosomes.
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Affiliation(s)
- Héctor Acosta
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, 5101, Venezuela
| | - Richard Burchmore
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Christina Naula
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Melisa Gualdrón-López
- Instituto Salud Global, Hospital Clinic-Universitat de Barcelona, and Institute for Health Sciences Trias i Pujol, Barcelona, Spain
| | - Ender Quintero-Troconis
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, 5101, Venezuela
| | - Ana J Cáceres
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, 5101, Venezuela
| | - Paul A M Michels
- Centre for Immunity, Infection and Evolution and Centre for Translational and Chemical Biology, The University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Juan Luis Concepción
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, 5101, Venezuela
| | - Wilfredo Quiñones
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, 5101, Venezuela.
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24
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Su T, Li W, Wang P, Ma C. Dynamics of Peroxisome Homeostasis and Its Role in Stress Response and Signaling in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:705. [PMID: 31214223 PMCID: PMC6557986 DOI: 10.3389/fpls.2019.00705] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 05/13/2019] [Indexed: 05/19/2023]
Abstract
Peroxisomes play vital roles in plant growth, development, and environmental stress response. During plant development and in response to environmental stresses, the number and morphology of peroxisomes are dynamically regulated to maintain peroxisome homeostasis in cells. To execute their various functions in the cell, peroxisomes associate and communicate with other organelles. Under stress conditions, reactive oxygen species (ROS) produced in peroxisomes and other organelles activate signal transduction pathways, in a process known as retrograde signaling, to synergistically regulate defense systems. In this review, we focus on the recent advances in the plant peroxisome field to provide an overview of peroxisome biogenesis, degradation, crosstalk with other organelles, and their role in response to environmental stresses.
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25
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Niwa H, Miyauchi-Nanri Y, Okumoto K, Mukai S, Noi K, Ogura T, Fujiki Y. A newly isolated Pex7-binding, atypical PTS2 protein P7BP2 is a novel dynein-type AAA+ protein. J Biochem 2018; 164:437-447. [PMID: 30204880 DOI: 10.1093/jb/mvy073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/10/2018] [Indexed: 12/19/2022] Open
Abstract
A newly isolated binding protein of peroxisomal targeting signal type 2 (PTS2) receptor Pex7, termed P7BP2, is transported into peroxisomes by binding to the longer isoform of Pex5p, Pex5pL, via Pex7p. The binding to Pex7p and peroxisomal localization of P7BP2 depends on the cleavable PTS2 in the N-terminal region, suggesting that P7BP2 is a new PTS2 protein. By search on human database, three AAA+ domains are found in the N-terminal half of P7BP2. Protein sequence alignment and motif search reveal that in the C-terminal region P7BP2 contains additional structural domains featuring weak but sufficient homology to AAA+ domain. P7BP2 behaves as a monomer in gel-filtration chromatography and the single molecule observed under atomic force microscope shapes a disc-like ring. Collectively, these results suggest that P7BP2 is a novel dynein-type AAA+ family protein, of which domains are arranged into a pseudo-hexameric ring structure.
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Affiliation(s)
- Hajime Niwa
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Japan
| | - Yasuhiro Miyauchi-Nanri
- Department of Biology, Faculty of Sciences, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, Japan
| | - Kanji Okumoto
- Department of Biology, Faculty of Sciences, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, Japan
| | - Satoru Mukai
- Department of Biology, Faculty of Sciences, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, Japan
| | - Kentaro Noi
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama, Japan
| | - Teru Ogura
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama, Japan
| | - Yukio Fujiki
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Japan
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26
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Kalel VC, Mäser P, Sattler M, Erdmann R, Popowicz GM. Come, sweet death: targeting glycosomal protein import for antitrypanosomal drug development. Curr Opin Microbiol 2018; 46:116-122. [PMID: 30481613 DOI: 10.1016/j.mib.2018.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/09/2018] [Indexed: 01/18/2023]
Abstract
Glycosomes evolved as specialized system for glycolysis in trypanosomatids. These organelle rely on protein import to maintain function. A machinery of peroxin (PEX) proteins is responsible for recognition and transport of glycosomal proteins to the organelle. Disruption of PEX-based import system was expected to be a strategy against trypanosomatids. Recently, a proof of this hypothesis has been presented. Here, we review current information about trypanosomatids' glycosomal transport components as targets for new trypanocidal therapies.
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Affiliation(s)
- Vishal C Kalel
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr University Bochum, 44780 Bochum, Germany
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland; University of Basel, 4001 Basel, Switzerland
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr University Bochum, 44780 Bochum, Germany
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany.
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27
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Wanders RJA, Vaz FM, Ferdinandusse S, Kemp S, Ebberink MS, Waterham HR. Laboratory Diagnosis of Peroxisomal Disorders in the -Omics Era and the Continued Importance of Biomarkers and Biochemical Studies. JOURNAL OF INBORN ERRORS OF METABOLISM AND SCREENING 2018. [DOI: 10.1177/2326409818810285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Ronald J. A. Wanders
- Laboratory Genetic Metabolic Diseases, Departments of Clinical Chemistry and Pediatrics, EmmaChildren’s Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Frédéric M. Vaz
- Laboratory Genetic Metabolic Diseases, Departments of Clinical Chemistry and Pediatrics, EmmaChildren’s Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Departments of Clinical Chemistry and Pediatrics, EmmaChildren’s Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Stephan Kemp
- Laboratory Genetic Metabolic Diseases, Departments of Clinical Chemistry and Pediatrics, EmmaChildren’s Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Merel S. Ebberink
- Laboratory Genetic Metabolic Diseases, Departments of Clinical Chemistry and Pediatrics, EmmaChildren’s Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Hans R. Waterham
- Laboratory Genetic Metabolic Diseases, Departments of Clinical Chemistry and Pediatrics, EmmaChildren’s Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
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28
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Fujikawa Y, Suekawa M, Endo S, Fukami Y, Mano S, Nishimura M, Esaka M. Effect of mutation of C-terminal and heme binding region of Arabidopsis catalase on the import to peroxisomes. Biosci Biotechnol Biochem 2018; 83:322-325. [PMID: 30295129 DOI: 10.1080/09168451.2018.1530094] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We evaluated the import of Arabidopsis catalase to peroxisomes under homogenous transient expression. The amino acids at -11 to -4 from the C-terminus are necessary for catalase import. The results are in agreement with the previous work under stable expression. We first demonstrate that heme-binding sites are important for peroxisomal import, suggesting the importance of catalase folding. Abbreviations: AtCat: Arabidopsis catalase; PTS: peroxisomal targeting signal; PEX: Peroxin.
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Affiliation(s)
- Yukichi Fujikawa
- a Graduate School of Biosphere Sciences , Hiroshima University , Higashi-Hiroshima , Japan
| | - Marina Suekawa
- a Graduate School of Biosphere Sciences , Hiroshima University , Higashi-Hiroshima , Japan
| | - Satoshi Endo
- a Graduate School of Biosphere Sciences , Hiroshima University , Higashi-Hiroshima , Japan
| | - Youjirou Fukami
- a Graduate School of Biosphere Sciences , Hiroshima University , Higashi-Hiroshima , Japan
| | - Shoji Mano
- b Department of Cell Biology , National Institute for Basic Biology , Okazaki , Japan.,c Department of Basic Biology , School of Life Science, SOKENDAI (The Graduate University for Advanced Studies) , Okazaki , Japan
| | - Mikio Nishimura
- d Department of Biology, Faculty of Science and Engineering , Konan University , Kobe , Japan
| | - Muneharu Esaka
- a Graduate School of Biosphere Sciences , Hiroshima University , Higashi-Hiroshima , Japan
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29
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Yang J, Pieuchot L, Jedd G. Artificial import substrates reveal an omnivorous peroxisomal importomer. Traffic 2018; 19:786-797. [PMID: 30058098 DOI: 10.1111/tra.12607] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/19/2018] [Accepted: 07/19/2018] [Indexed: 11/30/2022]
Abstract
The peroxisome matrix protein importomer has the remarkable ability to transport oligomeric protein substrates across the bilayer. However, the selectivity and relation between import and overall peroxisome homeostasis remain unclear. Here, we microinject artificial import substrates and employ quantitative microscopy to probe limits and capabilities of the importomer. DNA and polysaccharides are "piggyback" imported when noncovalently bound by a peroxisome targeting signal (PTS)-bearing protein. A dimerization domain that can be tuned to systematically vary the binding dissociation constant (Kd ) shows that a Kd in the millimolar range is sufficient to promote piggyback import. Microinjection of import substrate at high levels results in peroxisome growth and a proportional accumulation of peroxisome membrane proteins (PMPs). However, corresponding PMP mRNAs do not accumulate, suggesting that this response is posttranscriptionally regulated. Together, our data show that the importomer can tolerate diverse macromolecular species. Coupling between matrix import and membrane biogenesis suggests that matrix protein expression levels can be sufficient to regulate peroxisome size.
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Affiliation(s)
- Jing Yang
- Temasek Life Sciences Laboratory, and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Laurent Pieuchot
- CNRS, IS2M UMR 7361, Université de Haute-Alsace, Mulhouse, France
- Université de Strasbourg, Strasbourg, France
| | - Gregory Jedd
- Temasek Life Sciences Laboratory, and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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30
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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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31
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Chen Y, Zheng S, Ju Z, Zhang C, Tang G, Wang J, Wen Z, Chen W, Ma Z. Contribution of peroxisomal docking machinery to mycotoxin biosynthesis, pathogenicity and pexophagy in the plant pathogenic fungusFusarium graminearum. Environ Microbiol 2018; 20:3224-3245. [DOI: 10.1111/1462-2920.14291] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 05/17/2018] [Accepted: 05/19/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Yun Chen
- State Key Laboratory of Rice Biology; Zhejiang University; 866 Yuhangtang Road, Hangzhou 310058 China
- Institute of Biotechnology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects; Zhejiang University; 866 Yuhangtang Road, Hangzhou 310058 China
| | - Shiyu Zheng
- State Key Laboratory of Rice Biology; Zhejiang University; 866 Yuhangtang Road, Hangzhou 310058 China
- Institute of Biotechnology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects; Zhejiang University; 866 Yuhangtang Road, Hangzhou 310058 China
| | - Zhenzhen Ju
- State Key Laboratory of Rice Biology; Zhejiang University; 866 Yuhangtang Road, Hangzhou 310058 China
- Institute of Biotechnology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects; Zhejiang University; 866 Yuhangtang Road, Hangzhou 310058 China
| | - Chengqi Zhang
- State Key Laboratory of Rice Biology; Zhejiang University; 866 Yuhangtang Road, Hangzhou 310058 China
| | - Guangfei Tang
- State Key Laboratory of Rice Biology; Zhejiang University; 866 Yuhangtang Road, Hangzhou 310058 China
- Institute of Biotechnology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects; Zhejiang University; 866 Yuhangtang Road, Hangzhou 310058 China
| | - Jing Wang
- State Key Laboratory of Rice Biology; Zhejiang University; 866 Yuhangtang Road, Hangzhou 310058 China
- Institute of Biotechnology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects; Zhejiang University; 866 Yuhangtang Road, Hangzhou 310058 China
| | - Ziyue Wen
- State Key Laboratory of Rice Biology; Zhejiang University; 866 Yuhangtang Road, Hangzhou 310058 China
- Institute of Biotechnology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects; Zhejiang University; 866 Yuhangtang Road, Hangzhou 310058 China
| | - Wei Chen
- State Key Laboratory of Rice Biology; Zhejiang University; 866 Yuhangtang Road, Hangzhou 310058 China
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology; Zhejiang University; 866 Yuhangtang Road, Hangzhou 310058 China
- Institute of Biotechnology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects; Zhejiang University; 866 Yuhangtang Road, Hangzhou 310058 China
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32
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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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33
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Wanders RJA. Peroxisomal disorders: Improved laboratory diagnosis, new defects and the complicated route to treatment. Mol Cell Probes 2018; 40:60-69. [PMID: 29438773 DOI: 10.1016/j.mcp.2018.02.001] [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: 09/14/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 12/15/2022]
Abstract
Peroxisomes catalyze a number of essential metabolic functions of which fatty acid alpha- and beta-oxidation, ether phospholipid biosynthesis, glyoxylate detoxification and bile acid synthesis are the most important. The key role of peroxisomes in humans is exemplified by the existence of a group of peroxisomal disorders, caused by mutations in > 30 different genes which code for proteins with a role in either peroxisome biogenesis or one of the metabolic pathways in peroxisomes. Technological advances in laboratory methods at the metabolite-, enzyme-, and molecular level have not only allowed the identification of new peroxisomal disorders but also new phenotypes associated with already identified genetic defects thus extending the clinical spectrum. Unfortunately, progress in the field of pathogenesis and treatment has lagged behind although there are certainly new and hopeful developments with respect to X-linked adrenoleukodystrophy and hyperoxaluria type 1.
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Affiliation(s)
- Ronald J A Wanders
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; Department of Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
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34
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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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35
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Abstract
Our knowledge of the proteome of plant peroxisomes is far from being complete, and the functional complexity and plasticity of this cell organelle are amazingly high particularly in plants, as exemplified by the model species Arabidopsis thaliana. Plant-specific peroxisome functions that have been uncovered only recently include, for instance, the participation of peroxisomes in phylloquinone and biotin biosynthesis. Experimental proteome studies have been proved very successful in defining the proteome of Arabidopsis peroxisomes but this approach also faces significant challenges and limitations. Complementary to experimental approaches, computational methods have emerged as important powerful tools to define the proteome of soluble matrix proteins of plant peroxisomes. Compared to other cell organelles such as mitochondria, plastids and the ER, the simultaneous operation of two major import pathways for soluble proteins in peroxisomes is rather atypical. Novel machine learning prediction approaches have been developed for peroxisome targeting signals type 1 (PTS1) and revealed high sensitivity and specificity, as validated by in vivo subcellular targeting analyses in diverse transient plant expression systems. Accordingly, the algorithms allow the correct prediction of many novel peroxisome-targeted proteins from plant genome sequences and the discovery of additional organelle functions. In contrast, the prediction of PTS2 proteins largely remains restricted to genome searches by conserved patterns contrary to more advanced machine learning methods. Here, we summarize and discuss the capabilities and accuracies of available prediction algorithms for PTS1 and PTS2 carrying proteins.
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Affiliation(s)
- Sigrun Reumann
- Department of Plant Biochemistry and Infection Biology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany.
| | - Gopal Chowdhary
- KIIT School of Biotechnology, Campus XI, KIIT University, Bhubaneswar, 751024, India
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36
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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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Kalel VC, Erdmann R. Unraveling of the Structure and Function of Peroxisomal Protein Import Machineries. Subcell Biochem 2018; 89:299-321. [PMID: 30378029 DOI: 10.1007/978-981-13-2233-4_13] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peroxisomes are dynamic organelles of eukaryotic cells performing a wide range of functions including fatty acid oxidation, peroxide detoxification and ether-lipid synthesis in mammals. Peroxisomes lack their own DNA and therefore have to import proteins post-translationally. Peroxisomes can import folded, co-factor bound and even oligomeric proteins. The involvement of cycling receptors is a special feature of peroxisomal protein import. Complex machineries of peroxin (PEX) proteins mediate peroxisomal matrix and membrane protein import. Identification of PEX genes was dominated by forward genetic techniques in the early 90s. However, recent developments in proteomic techniques has revolutionized the detailed characterization of peroxisomal protein import. Here, we summarize the current knowledge on peroxisomal protein import with emphasis on the contribution of proteomic approaches to our understanding of the composition and function of the peroxisomal protein import machineries.
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Affiliation(s)
- Vishal C Kalel
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany.
| | - Ralf Erdmann
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany
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Schwerter DP, Grimm I, Platta HW, Erdmann R. ATP-driven processes of peroxisomal matrix protein import. Biol Chem 2017; 398:607-624. [PMID: 27977397 DOI: 10.1515/hsz-2016-0293] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/11/2016] [Indexed: 12/13/2022]
Abstract
In peroxisomal matrix protein import two processes directly depend on the binding and hydrolysis of ATP, both taking place at the late steps of the peroxisomal import cycle. First, ATP hydrolysis is required to initiate a ubiquitin-transfer cascade to modify the import (co-)receptors. These receptors display a dual localization in the cytosol and at the peroxisomal membrane, whereas only the membrane bound fraction receives the ubiquitin modification. The second ATP-dependent process of the import cycle is carried out by the two AAA+-proteins Pex1p and Pex6p. These ATPases form a heterohexameric complex, which is recruited to the peroxisomal import machinery by the membrane anchor protein Pex15p. The Pex1p/Pex6p complex recognizes the ubiquitinated import receptors, pulls them out of the membrane and releases them into the cytosol. There the deubiquitinated receptors are provided for further rounds of import. ATP binding and hydrolysis are required for Pex1p/Pex6p complex formation and receptor export. In this review, we summarize the current knowledge on the peroxisomal import cascade. In particular, we will focus on the ATP-dependent processes, which are so far best understood in the model organism Saccharomyces cerevisiae.
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Affiliation(s)
- Daniel P Schwerter
- Abteilung für Systembiochemie, Institut für Biochemie und Pathobiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum
| | - Immanuel Grimm
- Abteilung für Systembiochemie, Institut für Biochemie und Pathobiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum
| | - Harald W Platta
- Biochemie Intrazellulärer Transportprozesse, Medizinische Fakultät der Ruhr-Universität Bochum, D-44780 Bochum
| | - Ralf Erdmann
- Abteilung für Systembiochemie, Institut für Biochemie und Pathobiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum
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Saryi NAA, Hutchinson JD, Al-Hejjaj MY, Sedelnikova S, Baker P, Hettema EH. Pnc1 piggy-back import into peroxisomes relies on Gpd1 homodimerisation. Sci Rep 2017; 7:42579. [PMID: 28209961 PMCID: PMC5314374 DOI: 10.1038/srep42579] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 12/29/2016] [Indexed: 12/17/2022] Open
Abstract
Peroxisomes are eukaryotic organelles that posttranslationally import proteins via one of two conserved peroxisomal targeting signal (PTS1 or 2) mediated pathways. Oligomeric proteins can be imported via these pathways but evidence is accumulating that at least some PTS1-containing monomers enter peroxisomes before they assemble into oligomers. Some proteins lacking a PTS are imported by piggy-backing onto PTS-containing proteins. One of these proteins is the nicotinamidase Pnc1, that is co-imported with the PTS2-containing enzyme Glycerol-3-phosphate dehydrogenase 1, Gpd1. Here we show that Pnc1 co-import requires Gpd1 to form homodimers. A mutation that interferes with Gpd1 homodimerisation does not prevent Gpd1 import but prevents Pnc1 co-import. A suppressor mutation that restores Gpd1 homodimerisation also restores Pnc1 co-import. In line with this, Pnc1 interacts with Gpd1 in vivo only when Gpd1 can form dimers. Redirection of Gpd1 from the PTS2 import pathway to the PTS1 import pathway supports Gpd1 monomer import but not Gpd1 homodimer import and Pnc1 co-import. Our results support a model whereby Gpd1 may be imported as a monomer or a dimer but only the Gpd1 dimer facilitates co-transport of Pnc1 into peroxisomes.
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Affiliation(s)
- Nadal A Al Saryi
- Department of Molecular Biology and Biotechnology University of Sheffield Firth Court, Western Bank Sheffield S10 2TN United Kingdom
| | - John D Hutchinson
- Department of Molecular Biology and Biotechnology University of Sheffield Firth Court, Western Bank Sheffield S10 2TN United Kingdom
| | - Murtakab Y Al-Hejjaj
- Department of Molecular Biology and Biotechnology University of Sheffield Firth Court, Western Bank Sheffield S10 2TN United Kingdom
| | - Svetlana Sedelnikova
- Department of Molecular Biology and Biotechnology University of Sheffield Firth Court, Western Bank Sheffield S10 2TN United Kingdom
| | - Patrick Baker
- Department of Molecular Biology and Biotechnology University of Sheffield Firth Court, Western Bank Sheffield S10 2TN United Kingdom
| | - Ewald H Hettema
- Department of Molecular Biology and Biotechnology University of Sheffield Firth Court, Western Bank Sheffield S10 2TN United Kingdom
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Chen N, Teng XL, Xiao XG. Subcellular Localization of a Plant Catalase-Phenol Oxidase, AcCATPO, from Amaranthus and Identification of a Non-canonical Peroxisome Targeting Signal. FRONTIERS IN PLANT SCIENCE 2017; 8:1345. [PMID: 28824680 PMCID: PMC5539789 DOI: 10.3389/fpls.2017.01345] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/18/2017] [Indexed: 05/03/2023]
Abstract
AcCATPO is a plant catalase-phenol oxidase recently identified from red amaranth. Its physiological function remains unexplored. As the starting step of functional analysis, here we report its subcellular localization and a non-canonical targeting signal. Commonly used bioinformatics programs predicted a peroxisomal localization for AcCATPO, but failed in identification of canonical peroxisomal targeting signals (PTS). The C-terminal GFP tagging led the fusion protein AcCATPO-GFP to the cytosol and the nucleus, but N-terminal tagging directed the GFP-AcCATPO to peroxisomes and nuclei, in transgenic tobacco. Deleting the tripeptide (PTM) at the extreme C-terminus almost ruled out the peroxisomal localization of GFP-AcCATPOΔ3, and removing the C-terminal decapeptide completely excluded peroxisomes as the residence of GFP-AcCATPOΔ10. Furthermore, this decapeptide as a targeting signal could import GFP-10aa to the peroxisome exclusively. Taken together, these results demonstrate that AcCATPO is localized to the peroxisome and the nucleus, and its peroxisomal localization is attributed to a non-canonical PTS1, the C-terminal decapeptide which contains an internal SRL motif and a conserved tripeptide P-S/T-I/M at the extreme of C-terminus. This work may further the study as to the physiological function of AcCATPO, especially clarify its involvement in betalain biosynthesis, and provide a clue to elucidate more non-canonic PTS.
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Affiliation(s)
| | - Maria Daniela D'Agostino
- McGill University Department of Human Genetics and McGill University Health Center, Department of Medical Genetics, Montreal, QC, Canada
| | - Nancy Braverman
- McGill University Department of Human Genetics and Pediatrics, and The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
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Peroxisomal protein import pores. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:821-7. [DOI: 10.1016/j.bbamcr.2015.10.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/14/2015] [Accepted: 10/16/2015] [Indexed: 02/06/2023]
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Baron MN, Klinger CM, Rachubinski RA, Simmonds AJ. A Systematic Cell-Based Analysis of Localization of PredictedDrosophilaPeroxisomal Proteins. Traffic 2016; 17:536-53. [DOI: 10.1111/tra.12384] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/29/2016] [Accepted: 01/29/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Matthew N. Baron
- Department of Cell Biology; University of Alberta; Medical Sciences Building 5-14 Edmonton AB T6G 2H7 Canada
| | - Christen M. Klinger
- Department of Cell Biology; University of Alberta; Medical Sciences Building 5-14 Edmonton AB T6G 2H7 Canada
| | - Richard A. Rachubinski
- Department of Cell Biology; University of Alberta; Medical Sciences Building 5-14 Edmonton AB T6G 2H7 Canada
| | - Andrew J. Simmonds
- Department of Cell Biology; University of Alberta; Medical Sciences Building 5-14 Edmonton AB T6G 2H7 Canada
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Jamdhade MD, Pawar H, Chavan S, Sathe G, Umasankar PK, Mahale KN, Dixit T, Madugundu AK, Prasad TSK, Gowda H, Pandey A, Patole MS. Comprehensive proteomics analysis of glycosomes from Leishmania donovani. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:157-70. [PMID: 25748437 DOI: 10.1089/omi.2014.0163] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Leishmania donovani is a kinetoplastid protozoan that causes a severe and fatal disease kala-azar, or visceral leishmaniasis. L. donovani infects human host after the phlebotomine sandfly takes a blood meal and resides within the phagolysosome of infected macrophages. Previous studies on host-parasite interactions have not focused on Leishmania organelles and the role that they play in the survival of this parasite within macrophages. Leishmania possess glycosomes that are unique and specialized subcellular microbody organelles. Glycosomes are known to harbor most peroxisomal enzymes and, in addition, they also possess nine glycolytic enzymes. In the present study, we have carried out proteomic profiling using high resolution mass spectrometry of a sucrose density gradient-enriched glycosomal fraction isolated from L. donovani promastigotes. This study resulted in the identification of 4022 unique peptides, leading to the identification of 1355 unique proteins from a preparation enriched in L. donovani glycosomes. Based on protein annotation, 566 (41.8%) were identified as hypothetical proteins with no known function. A majority of the identified proteins are involved in metabolic processes such as carbohydrate, lipid, and nucleic acid metabolism. Our present proteomic analysis is the most comprehensive study to date to map the proteome of L. donovani glycosomes.
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Grimm I, Erdmann R, Girzalsky W. Role of AAA(+)-proteins in peroxisome biogenesis and function. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:828-37. [PMID: 26453804 DOI: 10.1016/j.bbamcr.2015.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 09/30/2015] [Accepted: 10/03/2015] [Indexed: 11/16/2022]
Abstract
Mutations in the PEX1 gene, which encodes a protein required for peroxisome biogenesis, are the most common cause of the Zellweger spectrum diseases. The recognition that Pex1p shares a conserved ATP-binding domain with p97 and NSF led to the discovery of the extended family of AAA+-type ATPases. So far, four AAA+-type ATPases are related to peroxisome function. Pex6p functions together with Pex1p in peroxisome biogenesis, ATAD1/Msp1p plays a role in membrane protein targeting and a member of the Lon-family of proteases is associated with peroxisomal quality control. This review summarizes the current knowledge on the AAA+-proteins involved in peroxisome biogenesis and function.
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Affiliation(s)
- Immanuel Grimm
- Abteilung für Systembiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Ralf Erdmann
- Abteilung für Systembiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, D-44780 Bochum, Germany.
| | - Wolfgang Girzalsky
- Abteilung für Systembiochemie, Medizinische Fakultät der Ruhr-Universität Bochum, D-44780 Bochum, Germany.
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46
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The Design and Structure of Outer Membrane Receptors from Peroxisomes, Mitochondria, and Chloroplasts. Structure 2015; 23:1783-1800. [DOI: 10.1016/j.str.2015.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/20/2015] [Accepted: 08/10/2015] [Indexed: 01/03/2023]
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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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48
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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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Kim PK, Hettema EH. Multiple pathways for protein transport to peroxisomes. J Mol Biol 2015; 427:1176-90. [PMID: 25681696 PMCID: PMC4726662 DOI: 10.1016/j.jmb.2015.02.005] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 02/05/2015] [Accepted: 02/06/2015] [Indexed: 12/15/2022]
Abstract
Peroxisomes are unique among the organelles of the endomembrane system. Unlike other organelles that derive most if not all of their proteins from the ER (endoplasmic reticulum), peroxisomes contain dedicated machineries for import of matrix proteins and insertion of membrane proteins. However, peroxisomes are also able to import a subset of their membrane proteins from the ER. One aspect of peroxisome biology that has remained ill defined is the role the various import pathways play in peroxisome maintenance. In this review, we discuss the available data on matrix and membrane protein import into peroxisomes. Peroxisomal membrane and matrix proteins require distinct factors for their transport. Matrix proteins fold in the cytosol prior to their import. Loaded targeting receptors form part of the matrix protein translocation pore. Many membrane proteins are directly inserted into the peroxisomal membrane. Some peroxisomal membrane proteins are transported via the ER to peroxisomes.
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Affiliation(s)
- P K Kim
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON, Canada M5G 1X8; Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - E H Hettema
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, South Yorkshire S10 2TN, United Kingdom.
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Kunze M, Malkani N, Maurer-Stroh S, Wiesinger C, Schmid JA, Berger J. Mechanistic insights into PTS2-mediated peroxisomal protein import: the co-receptor PEX5L drastically increases the interaction strength between the cargo protein and the receptor PEX7. J Biol Chem 2014; 290:4928-4940. [PMID: 25538232 DOI: 10.1074/jbc.m114.601575] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The destination of peroxisomal matrix proteins is encoded by short peptide sequences, which have been characterized as peroxisomal targeting signals (PTS) residing either at the C terminus (PTS1) or close to the N terminus (PTS2). PTS2-carrying proteins interact with their cognate receptor protein PEX7 that mediates their transport to peroxisomes by a concerted action with a co-receptor protein, which in mammals is the PTS1 receptor PEX5L. Using a modified version of the mammalian two-hybrid assay, we demonstrate that the interaction strength between cargo and PEX7 is drastically increased in the presence of the co-receptor PEX5L. In addition, cargo binding is a prerequisite for the interaction between PEX7 and PEX5L and ectopic overexpression of PTS2-carrying cargo protein drastically increases the formation of PEX7-PEX5L complexes in this assay. Consistently, we find that the peroxisomal transfer of PEX7 depends on cargo binding and that ectopic overexpression of cargo protein stimulates this process. Thus, the sequential formation of a highly stable trimeric complex involving cargo protein, PEX7 and PEX5L stabilizes cargo binding and is a prerequisite for PTS2-mediated peroxisomal import.
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Affiliation(s)
- Markus Kunze
- Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria,.
| | - Naila Malkani
- Department of Vascular Biology and Thrombosis Research, Medical University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Singapore 138671; School of Biological Sciences (SBS), Nanyang Technological University (NTU), 8 Medical Drive, Singapore 117597
| | - Christoph Wiesinger
- Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
| | - Johannes A Schmid
- Department of Vascular Biology and Thrombosis Research, Medical University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Johannes Berger
- Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
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