1
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Chen R, Lu K, Yang L, Jiang J, Li L. Peroxin MoPex22 Regulates the Import of Peroxisomal Matrix Proteins and Appressorium-Mediated Plant Infection in Magnaporthe oryzae. J Fungi (Basel) 2024; 10:143. [PMID: 38392815 PMCID: PMC10890347 DOI: 10.3390/jof10020143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Magnaporthe oryzae, the pathogen responsible for rice blast disease, utilizes specialized infection structures known as appressoria to breach the leaf cuticle and establish intracellular, infectious hyphae. Our study demonstrates that the peroxin MoPex22 is crucial for appressorium function, specifically for the development of primary penetration hyphae. The ∆Mopex22 mutant exhibited slow growth, reduced aerial hyphae, and almost complete loss of virulence. Specifically, despite the mutant's capability to form appressoria, it showed abnormalities during appressorium development, including reduced turgor, increased permeability of the appressorium wall, failure to form septin rings, and significantly decreased ability to penetrate host cells. Additionally, there was a delay in the degradation of lipid droplets during conidial germination and appressorium development. Consistent with these findings, the ΔMopex22 mutant showed an inefficient utilization of long-chain fatty acids and defects in cell wall integrity. Moreover, our findings indicate that MoPex22 acts as an anchor for MoPex4, facilitating the localization of MoPex4 to peroxisomes. Together with MoPex4, it affects the function of MoPex5, thus regulating the import of peroxisomal matrix proteins. Overall, these results highlight the essential role of MoPex22 in regulating the transport of peroxisomal matrix proteins, which affect fatty acid metabolism, glycerol accumulation, cell wall integrity, growth, appressorium development, and the pathogenicity of M. oryzae. This study provides valuable insights into the significance of peroxin functions in fungal biology and appressorium-mediated plant infection.
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Affiliation(s)
- Rangrang Chen
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Kailun Lu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Lina Yang
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Jihong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
| | - Lianwei Li
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China
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2
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Jiang H, Nair V, Sun Y, Ding C. The diverse roles of peroxisomes in the interplay between viruses and mammalian cells. Antiviral Res 2024; 221:105780. [PMID: 38092324 DOI: 10.1016/j.antiviral.2023.105780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/26/2023]
Abstract
Peroxisomes are ubiquitous organelles found in eukaryotic cells that play a critical role in the oxidative metabolism of lipids and detoxification of reactive oxygen species (ROS). Recently, the role of peroxisomes in viral infections has been extensively studied. Although several studies have reported that peroxisomes exert antiviral activity, evidence indicates that viruses have also evolved diverse strategies to evade peroxisomal antiviral signals. In this review, we summarize the multiple roles of peroxisomes in the interplay between viruses and mammalian cells. Focus is given on the peroxisomal regulation of innate immune response, lipid metabolism, ROS production, and viral regulation of peroxisomal biosynthesis and degradation. Understanding the interactions between peroxisomes and viruses provides novel insights for the development of new antiviral strategies.
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Affiliation(s)
- Hui Jiang
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai, China
| | - Venugopal Nair
- Avian Oncogenic Viruses Group, UK-China Centre of Excellence in Avian Disease Research, The Pirbright Institute, Pirbright, Guildford, Surrey, United Kingdom
| | - Yingjie Sun
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai, China.
| | - Chan Ding
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu Province, China.
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3
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Pedrosa AG, Reglinski K, Lismont C, Kors S, Costello J, Rodrigues TA, Marques M, Linka N, Argyriou C, Weinhofer I, Kocherlakota S, Riccio V, Ferreira V, Di Cara F, Ferreira AR, Francisco T, Azevedo JE, Ribeiro D. Peroxisomes : novel findings and future directions. Histochem Cell Biol 2023; 159:379-387. [PMID: 37160800 PMCID: PMC10170047 DOI: 10.1007/s00418-023-02201-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2023] [Indexed: 05/11/2023]
Affiliation(s)
- Ana G Pedrosa
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Katharina Reglinski
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, UK
- Leibniz-Institute of Photonic Technologies, Albert-Einstein Strasse 9, 07745, Jena, Germany
- Institute of Applied Optic and Biophysics, Friedrich-Schiller University Jena, Max-Wien-Platz 1, 07743, Jena, Germany
- University Hospital Jena, Bachstraße 18, Jena, Germany
| | - Celien Lismont
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Suzan Kors
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
| | - Joseph Costello
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, UK
| | - Tony A Rodrigues
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Mariana Marques
- Institute of Biomedicine - iBiMED & Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Nicole Linka
- Institute of Plant Biochemistry, Heinrich Heine University, Düsseldorf, Germany
| | | | - Isabelle Weinhofer
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | | | - Victoria Riccio
- Cell Biology Department, Hospital for Sick Children, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Vanessa Ferreira
- Institute of Biomedicine - iBiMED & Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Francesca Di Cara
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Department of Pediatrics, Nova Scotia Health Authority IWK, Halifax, NS, Canada
| | - Ana Rita Ferreira
- Institute of Biomedicine - iBiMED & Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Tânia Francisco
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Jorge E Azevedo
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
- Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal.
| | - Daniela Ribeiro
- Institute of Biomedicine - iBiMED & Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.
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4
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Nuebel E, Morgan JT, Fogarty S, Winter JM, Lettlova S, Berg JA, Chen YC, Kidwell CU, Maschek JA, Clowers KJ, Argyriou C, Chen L, Wittig I, Cox JE, Roh-Johnson M, Braverman N, Bonkowsky J, Gygi SP, Rutter J. The biochemical basis of mitochondrial dysfunction in Zellweger Spectrum Disorder. EMBO Rep 2021; 22:e51991. [PMID: 34351705 DOI: 10.15252/embr.202051991] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 06/21/2021] [Accepted: 07/12/2021] [Indexed: 01/09/2023] Open
Abstract
Peroxisomal biogenesis disorders (PBDs) are genetic disorders of peroxisome biogenesis and metabolism that are characterized by profound developmental and neurological phenotypes. The most severe class of PBDs-Zellweger spectrum disorder (ZSD)-is caused by mutations in peroxin genes that result in both non-functional peroxisomes and mitochondrial dysfunction. It is unclear, however, how defective peroxisomes contribute to mitochondrial impairment. In order to understand the molecular basis of this inter-organellar relationship, we investigated the fate of peroxisomal mRNAs and proteins in ZSD model systems. We found that peroxins were still expressed and a subset of them accumulated on the mitochondrial membrane, which resulted in gross mitochondrial abnormalities and impaired mitochondrial metabolic function. We showed that overexpression of ATAD1, a mitochondrial quality control factor, was sufficient to rescue several aspects of mitochondrial function in human ZSD fibroblasts. Together, these data suggest that aberrant peroxisomal protein localization is necessary and sufficient for the devastating mitochondrial morphological and metabolic phenotypes in ZSDs.
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Affiliation(s)
- Esther Nuebel
- Howard Hughes Medical Institute, Salt Lake City, UT, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.,Department of Biomedical Sciences, Noorda College of Osteopathic Medicine, Provo, USA
| | - Jeffrey T Morgan
- Howard Hughes Medical Institute, Salt Lake City, UT, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Sarah Fogarty
- Howard Hughes Medical Institute, Salt Lake City, UT, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Jacob M Winter
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Sandra Lettlova
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Jordan A Berg
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Yu-Chan Chen
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Chelsea U Kidwell
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - J Alan Maschek
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.,Diabetes & Metabolism Research Center, University of Utah, Salt Lake City, UT, USA.,Metabolomics, Proteomics and Mass Spectrometry Core Research Facilities, University of Utah, Salt Lake City, UT, USA
| | - Katie J Clowers
- Department of Cell Biology, Harvard University School of Medicine, Boston, MA, USA
| | | | - Lingxiao Chen
- Department of Pathology, McGill University, Montreal, ON, Canada
| | - Ilka Wittig
- Functional Proteomics, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - James E Cox
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.,Diabetes & Metabolism Research Center, University of Utah, Salt Lake City, UT, USA.,Metabolomics, Proteomics and Mass Spectrometry Core Research Facilities, University of Utah, Salt Lake City, UT, USA
| | - Minna Roh-Johnson
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Nancy Braverman
- Department of Human Genetics, McGill University, Montreal, ON, Canada.,Department of Pediatrics, Research Institute of the McGill University Health Centre, Montreal, ON, Canada
| | - Joshua Bonkowsky
- Primary Children's Hospital, University of Utah, Salt Lake City, UT, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard University School of Medicine, Boston, MA, USA
| | - Jared Rutter
- Howard Hughes Medical Institute, Salt Lake City, UT, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.,Diabetes & Metabolism Research Center, University of Utah, Salt Lake City, UT, USA
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5
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Mast FD, Rachubinski RA, Aitchison JD. Peroxisome prognostications: Exploring the birth, life, and death of an organelle. J Cell Biol 2020; 219:133827. [PMID: 32211898 PMCID: PMC7054992 DOI: 10.1083/jcb.201912100] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 02/07/2023] Open
Abstract
Peroxisomes play a central role in human health and have biochemical properties that promote their use in many biotechnology settings. With a primary role in lipid metabolism, peroxisomes share a niche with lipid droplets within the endomembrane-secretory system. Notably, factors in the ER required for the biogenesis of peroxisomes also impact the formation of lipid droplets. The dynamic interface between peroxisomes and lipid droplets, and also between these organelles and the ER and mitochondria, controls their metabolic flux and their dynamics. Here, we review our understanding of peroxisome biogenesis to propose and reframe models for understanding how peroxisomes are formed in cells. To more fully understand the roles of peroxisomes and to take advantage of their many properties that may prove useful in novel therapeutics or biotechnology applications, we recast mechanisms controlling peroxisome biogenesis in a framework that integrates inference from these models with experimental data.
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Affiliation(s)
- Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA
| | | | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA.,Department of Pediatrics, University of Washington, Seattle, WA
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6
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Mahalingam SS, Shukla N, Farré JC, Zientara-Rytter K, Subramani S. Balancing the Opposing Principles That Govern Peroxisome Homeostasis. Trends Biochem Sci 2020; 46:200-212. [PMID: 33046344 DOI: 10.1016/j.tibs.2020.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/14/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022]
Abstract
Despite major advances in our understanding of players and mechanisms involved in peroxisome biogenesis and peroxisome degradation, very few studies have focused on unraveling the multi-layered connections between, and the coordination of, these two opposing processes that regulate peroxisome homeostasis. The intersection between these processes also provides exciting avenues for future research. This review highlights the links between peroxisome biogenesis and degradation, incorporating an integrative approach that is critical not only for a mechanistic understanding, but also for manipulating the balance between these processes in relevant disease models.
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Affiliation(s)
- Shanmuga S Mahalingam
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA
| | - Nandini Shukla
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA
| | - Jean-Claude Farré
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA
| | - Katarzyna Zientara-Rytter
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA
| | - Suresh Subramani
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA.
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7
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Choubey S, Das D, Majumdar S. Cell-to-cell variability in organelle abundance reveals mechanisms of organelle biogenesis. Phys Rev E 2020; 100:022405. [PMID: 31574672 DOI: 10.1103/physreve.100.022405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Indexed: 12/20/2022]
Abstract
How cells regulate the number of organelles is a fundamental question in cell biology. While decades of experimental work have uncovered four fundamental processes that regulate organelle biogenesis, namely, de novo synthesis, fission, fusion, and decay, a comprehensive understanding of how these processes together control organelle abundance remains elusive. Recent fluorescence microscopy experiments allow for the counting of organelles at the single-cell level. These measurements provide information about the cell-to-cell variability in organelle abundance in addition to the mean level. Motivated by such measurements, we build upon a recent study and analyze a general stochastic model of organelle biogenesis. We compute the exact analytical expressions for the probability distribution of organelle numbers, their mean, and variance across a population of single cells. It is shown that different mechanisms of organelle biogenesis lead to distinct signatures in the distribution of organelle numbers which allow us to discriminate between these various mechanisms. By comparing our theory against published data for peroxisome abundance measurements in yeast, we show that a widely believed model of peroxisome biogenesis that involves de novo synthesis, fission, and decay is inadequate in explaining the data. Also, our theory predicts bimodality in certain limits of the model. Overall, the framework developed here can be harnessed to gain mechanistic insights into the process of organelle biogenesis.
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Affiliation(s)
- Sandeep Choubey
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzerstraße 38, 01187 Dresden, Germany
| | - Dipjyoti Das
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Saptarshi Majumdar
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzerstraße 38, 01187 Dresden, Germany
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8
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Abstract
Due to their topology tail-anchored (TA) proteins must target to the membrane independently of the co-translational route defined by the signal sequence recognition particle (SRP), its receptor and the translocon Sec61. More than a decade of work has extensively characterized a highly conserved pathway, the yeast GET or mammalian TRC40 pathway, which is capable of countering the biogenetic challenge posed by the C-terminal TA anchor. In this review we briefly summarize current models of this targeting route and focus on emerging aspects such as the intricate interplay with the proteostatic network of cells and with other targeting pathways. Importantly, we consider the lessons provided by the in vivo analysis of the pathway in different model organisms and by the consideration of its full client spectrum in more recent studies. This analysis of the state of the field highlights directions in which the current models may be experimentally probed and conceptually extended.
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Affiliation(s)
- Nica Borgese
- Institute of Neuroscience and BIOMETRA Department, Consiglio Nazionale delle Ricerche and Università degli Studi di Milano, via Vanvitelli 32, 20129, Milan, Italy.
| | - Javier Coy-Vergara
- Department of Molecular Biology, University of Göttingen Medical Centre, Humboldtallee 23, 37073, Göttingen, Germany
| | - Sara Francesca Colombo
- Institute of Neuroscience and BIOMETRA Department, Consiglio Nazionale delle Ricerche and Università degli Studi di Milano, via Vanvitelli 32, 20129, Milan, Italy
| | - Blanche Schwappach
- Department of Molecular Biology, University of Göttingen Medical Centre, Humboldtallee 23, 37073, Göttingen, Germany.
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9
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Romano FB, Blok NB, Rapoport TA. Peroxisome protein import recapitulated in Xenopus egg extracts. J Cell Biol 2019; 218:2021-2034. [PMID: 30971414 PMCID: PMC6548129 DOI: 10.1083/jcb.201901152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/17/2019] [Accepted: 03/28/2019] [Indexed: 12/14/2022] Open
Abstract
Peroxisomes import proteins with a C-terminal SKL sequence by a poorly understood mechanism. Romano et al. use Xenopus egg extracts to study peroxisome import in vitro. The novel assay recapitulates import in vivo and provides mechanistic insights. Peroxisomes import their luminal proteins from the cytosol. Most substrates contain a C-terminal Ser-Lys-Leu (SKL) sequence that is recognized by the receptor Pex5. Pex5 binds to peroxisomes via a docking complex containing Pex14, and recycles back into the cytosol following its mono-ubiquitination at a conserved Cys residue. The mechanism of peroxisome protein import remains incompletely understood. Here, we developed an in vitro import system based on Xenopus egg extracts. Import is dependent on the SKL motif in the substrate and on the presence of Pex5 and Pex14, and is sustained by ATP hydrolysis. A protein lacking an SKL sequence can be coimported, providing strong evidence for import of a folded protein. The conserved cysteine in Pex5 is not essential for import or to clear import sites for subsequent rounds of translocation. This new in vitro assay will be useful for further dissecting the mechanism of peroxisome protein import.
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Affiliation(s)
- Fabian B Romano
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Neil B Blok
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA
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10
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Jansen RLM, Klei IJ. The peroxisome biogenesis factors Pex3 and Pex19: multitasking proteins with disputed functions. FEBS Lett 2019; 593:457-474. [DOI: 10.1002/1873-3468.13340] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/06/2019] [Accepted: 02/12/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Renate L. M. Jansen
- Molecular Cell Biology Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen The Netherlands
| | - Ida J. Klei
- Molecular Cell Biology Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen The Netherlands
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11
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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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12
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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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13
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Abstract
Peroxisomes are key metabolic organelles, which contribute to cellular lipid metabolism, e.g. the β-oxidation of fatty acids and the synthesis of myelin sheath lipids, as well as cellular redox balance. Peroxisomal dysfunction has been linked to severe metabolic disorders in man, but peroxisomes are now also recognized as protective organelles with a wider significance in human health and potential impact on a large number of globally important human diseases such as neurodegeneration, obesity, cancer, and age-related disorders. Therefore, the interest in peroxisomes and their physiological functions has significantly increased in recent years. In this review, we intend to highlight recent discoveries, advancements and trends in peroxisome research, and present an update as well as a continuation of two former review articles addressing the unsolved mysteries of this astonishing organelle. We summarize novel findings on the biological functions of peroxisomes, their biogenesis, formation, membrane dynamics and division, as well as on peroxisome-organelle contacts and cooperation. Furthermore, novel peroxisomal proteins and machineries at the peroxisomal membrane are discussed. Finally, we address recent findings on the role of peroxisomes in the brain, in neurological disorders, and in the development of cancer.
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Affiliation(s)
- Markus Islinger
- Institute of Neuroanatomy, Center for Biomedicine and Medical Technology Mannheim, Medical Faculty Manheim, University of Heidelberg, 68167, Mannheim, Germany
| | - Alfred Voelkl
- Institute for Anatomy and Cell Biology, University of Heidelberg, 69120, Heidelberg, Germany
| | - H Dariush Fahimi
- Institute for Anatomy and Cell Biology, University of Heidelberg, 69120, Heidelberg, Germany
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14
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Mix AK, Cenci U, Heimerl T, Marter P, Wirkner ML, Moog D. Identification and Localization of Peroxisomal Biogenesis Proteins Indicates the Presence of Peroxisomes in the Cryptophyte Guillardia theta and Other "Chromalveolates". Genome Biol Evol 2018; 10:2834-2852. [PMID: 30247558 PMCID: PMC6203080 DOI: 10.1093/gbe/evy214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2018] [Indexed: 12/11/2022] Open
Abstract
Peroxisomes are single-membrane-bound organelles with a huge metabolic versatility, including the degradation of fatty acids (β-oxidation) and the detoxification of reactive oxygen species as most conserved functions. Although peroxisomes seem to be present in the majority of investigated eukaryotes, where they are responsible for many eclectic and important spatially separated metabolic reactions, knowledge about their existence in the plethora of protists (eukaryotic microorganisms) is scarce. Here, we investigated genomic data of organisms containing complex plastids with red algal ancestry (so-called “chromalveolates”) for the presence of genes encoding peroxins—factors specific for the biogenesis, maintenance, and division of peroxisomes in eukaryotic cells. Our focus was on the cryptophyte Guillardia theta, a marine microalga, which possesses two phylogenetically different nuclei of host and endosymbiont origin, respectively, thus being of enormous evolutionary significance. Besides the identification of a complete set of peroxins in G. theta, we heterologously localized selected factors as GFP fusion proteins via confocal and electron microscopy in the model diatom Phaeodactylum tricornutum. Furthermore, we show that peroxins, and thus most likely peroxisomes, are present in haptophytes as well as eustigmatophytes, brown algae, and alveolates including dinoflagellates, chromerids, and noncoccidian apicomplexans. Our results indicate that diatoms are not the only “chromalveolate” group devoid of the PTS2 receptor Pex7, and thus a PTS2-dependent peroxisomal import pathway, which seems to be absent in haptophytes (Emiliania huxleyi) as well. Moreover, important aspects of peroxisomal biosynthesis and protein import in “chromalveolates”are highlighted.
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Affiliation(s)
- Ann-Kathrin Mix
- Laboratory for Cell Biology, Philipps University Marburg, Germany
| | - Ugo Cenci
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS-USTL, Université des Sciences et Technologies de Lille, Villeneuve d'Ascq Cedex, France
| | - Thomas Heimerl
- LOEWE Center for Synthetic Microbiology (Synmikro), Philipps University Marburg, Germany
| | - Pia Marter
- Laboratory for Cell Biology, Philipps University Marburg, Germany
| | | | - Daniel Moog
- Laboratory for Cell Biology, Philipps University Marburg, Germany
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15
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Wang S, Idrissi FZ, Hermansson M, Grippa A, Ejsing CS, Carvalho P. Seipin and the membrane-shaping protein Pex30 cooperate in organelle budding from the endoplasmic reticulum. Nat Commun 2018; 9:2939. [PMID: 30054465 PMCID: PMC6063905 DOI: 10.1038/s41467-018-05278-2] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 06/18/2018] [Indexed: 11/20/2022] Open
Abstract
Lipid droplets (LDs) and peroxisomes are ubiquitous organelles with central roles in eukaryotic cells. Although the mechanisms involved in biogenesis of these organelles remain elusive, both seem to require the endoplasmic reticulum (ER). Here we show that in yeast the ER budding of these structurally unrelated organelles has remarkably similar requirements and involves cooperation between Pex30 and the seipin complex. In the absence of these components, budding of both LDs and peroxisomes is inhibited, leading to the ER accumulation of their respective constituent molecules, such as triacylglycerols and peroxisomal membrane proteins, whereas COPII vesicle formation remains unaffected. This phenotype can be reversed by remodeling ER phospholipid composition highlighting a key function of these lipids in organelle biogenesis. We propose that seipin and Pex30 act in concert to organize membrane domains permissive for organelle budding, and that may have a lipid composition distinct from the bulk ER.
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Affiliation(s)
- Sihui Wang
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Fatima-Zahra Idrissi
- Cell and Developmental Biology Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Martin Hermansson
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Alexandra Grippa
- Cell and Developmental Biology Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Pedro Carvalho
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
- Cell and Developmental Biology Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Dr. Aiguader, 88, 08003, Barcelona, Spain.
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16
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Kuzmin E, VanderSluis B, Wang W, Tan G, Deshpande R, Chen Y, Usaj M, Balint A, Mattiazzi Usaj M, van Leeuwen J, Koch EN, Pons C, Dagilis AJ, Pryszlak M, Wang JZY, Hanchard J, Riggi M, Xu K, Heydari H, San Luis BJ, Shuteriqi E, Zhu H, Van Dyk N, Sharifpoor S, Costanzo M, Loewith R, Caudy A, Bolnick D, Brown GW, Andrews BJ, Boone C, Myers CL. Systematic analysis of complex genetic interactions. Science 2018; 360:eaao1729. [PMID: 29674565 PMCID: PMC6215713 DOI: 10.1126/science.aao1729] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 02/23/2018] [Indexed: 12/11/2022]
Abstract
To systematically explore complex genetic interactions, we constructed ~200,000 yeast triple mutants and scored negative trigenic interactions. We selected double-mutant query genes across a broad spectrum of biological processes, spanning a range of quantitative features of the global digenic interaction network and tested for a genetic interaction with a third mutation. Trigenic interactions often occurred among functionally related genes, and essential genes were hubs on the trigenic network. Despite their functional enrichment, trigenic interactions tended to link genes in distant bioprocesses and displayed a weaker magnitude than digenic interactions. We estimate that the global trigenic interaction network is ~100 times as large as the global digenic network, highlighting the potential for complex genetic interactions to affect the biology of inheritance, including the genotype-to-phenotype relationship.
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Affiliation(s)
- Elena Kuzmin
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Benjamin VanderSluis
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Wen Wang
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Guihong Tan
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Raamesh Deshpande
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Yiqun Chen
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Matej Usaj
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Attila Balint
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Department of Biochemistry, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Mojca Mattiazzi Usaj
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Jolanda van Leeuwen
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Elizabeth N Koch
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Carles Pons
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Andrius J Dagilis
- Department of Integrative Biology, 1 University Station C0990, University of Texas at Austin, Austin, TX 78712, USA
| | - Michael Pryszlak
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Jason Zi Yang Wang
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Julia Hanchard
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Margot Riggi
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
- iGE3 (Institute of Genetics and Genomics of Geneva), 1211 Geneva, Switzerland
- Swiss National Centre for Competence in Research Programme Chemical Biology, 1211 Geneva, Switzerland
| | - Kaicong Xu
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Hamed Heydari
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Bryan-Joseph San Luis
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Ermira Shuteriqi
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Hongwei Zhu
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Nydia Van Dyk
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Sara Sharifpoor
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Michael Costanzo
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Robbie Loewith
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
- iGE3 (Institute of Genetics and Genomics of Geneva), 1211 Geneva, Switzerland
- Swiss National Centre for Competence in Research Programme Chemical Biology, 1211 Geneva, Switzerland
| | - Amy Caudy
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Daniel Bolnick
- Department of Integrative Biology, 1 University Station C0990, University of Texas at Austin, Austin, TX 78712, USA
| | - Grant W Brown
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Department of Biochemistry, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Brenda J Andrews
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Charles Boone
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA.
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17
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Figueiredo Costa B, Cassella P, Colombo SF, Borgese N. Discrimination between the endoplasmic reticulum and mitochondria by spontaneously inserting tail‐anchored proteins. Traffic 2018; 19:182-197. [DOI: 10.1111/tra.12550] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/18/2018] [Accepted: 01/18/2018] [Indexed: 01/16/2023]
Affiliation(s)
- Bruna Figueiredo Costa
- CNR Institute of Neuroscience and BIOMETRA DepartmentUniversità degli Studi di Milano Milan Italy
| | - Patrizia Cassella
- CNR Institute of Neuroscience and BIOMETRA DepartmentUniversità degli Studi di Milano Milan Italy
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18
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Costello JL, Schrader M. Unloosing the Gordian knot of peroxisome formation. Curr Opin Cell Biol 2018; 50:50-56. [PMID: 29475136 PMCID: PMC6525147 DOI: 10.1016/j.ceb.2018.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/24/2018] [Accepted: 02/02/2018] [Indexed: 12/31/2022]
Abstract
Peroxisome biogenesis is governed by molecular machineries, which are either unique to peroxisomes or are partially shared with mitochondria. As peroxisomes have important protective functions in the cell, modulation of their number is important for human health and disease. Significant progress has been made towards our understanding of the mechanisms of peroxisome formation, revealing a remarkable plasticity of the peroxisome biogenesis pathway. Here we discuss most recent findings with particular focus on peroxisome formation in mammalian cells.
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Affiliation(s)
- Joseph L Costello
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Michael Schrader
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom.
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19
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Islinger M, Manner A, Völkl A. The Craft of Peroxisome Purification-A Technical Survey Through the Decades. Subcell Biochem 2018; 89:85-122. [PMID: 30378020 DOI: 10.1007/978-981-13-2233-4_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Purification technologies are one of the working horses in organelle proteomics studies as they guarantee the separation of organelle-specific proteins from the background contamination by other subcellular compartments. The development of methods for the separation of organelles was a major prerequisite for the initial detection and characterization of peroxisome as a discrete entity of the cell. Since then, isolated peroxisomes fractions have been used in numerous studies in order to characterize organelle-specific enzyme functions, to allocate the peroxisome-specific proteome or to unravel the organellar membrane composition. This review will give an overview of the fractionation methods used for the isolation of peroxisomes from animals, plants and fungi. In addition to "classic" centrifugation-based isolation methods, relying on the different densities of individual organelles, the review will also summarize work on alternative technologies like free-flow-electrophoresis or flow field fractionation which are based on distinct physicochemical parameters. A final chapter will further describe how different separation methods and quantitative mass spectrometry have been used in proteomics studies to assign the proteome of PO.
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Affiliation(s)
- Markus Islinger
- Institute for Neuroanatomy, Centre for Biomedicine and Medical Technology Mannheim, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany.
| | - Andreas Manner
- Institute for Neuroanatomy, Centre for Biomedicine and Medical Technology Mannheim, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Alfred Völkl
- Department of Medical Cell Biology, Institute of Anatomy, University of Heidelberg, Heidelberg, Germany
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20
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Wang W, Subramani S. Role of PEX5 ubiquitination in maintaining peroxisome dynamics and homeostasis. Cell Cycle 2017; 16:2037-2045. [PMID: 28933989 PMCID: PMC5731411 DOI: 10.1080/15384101.2017.1376149] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 08/24/2017] [Accepted: 09/01/2017] [Indexed: 12/15/2022] Open
Abstract
Peroxisomes are essential and dynamic organelles that allow cells to rapidly adapt and cope with changing environments and/or physiological conditions by modulation of both peroxisome biogenesis and turnover. Peroxisome biogenesis involves the assembly of peroxisome membranes and the import of peroxisomal matrix proteins. The latter depends on the receptor, PEX5, which recognizes peroxisomal matrix proteins in the cytosol directly or indirectly, and transports them to the peroxisomal lumen. In this review, we discuss the role of PEX5 ubiquitination in both peroxisome biogenesis and turnover, specifically in PEX5 receptor recycling, stability and abundance, as well as its role in pexophagy (autophagic degradation of peroxisomes).
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Affiliation(s)
- Wei Wang
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Suresh Subramani
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
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21
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Kovacs SB, Miao EA. Gasdermins: Effectors of Pyroptosis. Trends Cell Biol 2017; 27:673-684. [PMID: 28619472 PMCID: PMC5565696 DOI: 10.1016/j.tcb.2017.05.005] [Citation(s) in RCA: 789] [Impact Index Per Article: 112.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/18/2017] [Accepted: 05/19/2017] [Indexed: 12/20/2022]
Abstract
Pyroptosis is a form of lytic programmed cell death initiated by inflammasomes, which detect cytosolic contamination or perturbation. This drives activation of caspase-1 or caspase-11/4/5, which cleave gasdermin D, separating its N-terminal pore-forming domain (PFD) from the C-terminal repressor domain (RD). The PFD oligomerizes to form large pores in the membrane that drive swelling and membrane rupture. Gasdermin D is one of six (in humans) gasdermin family members; several other gasdermins have also been shown to form pores that cause pyroptosis after cleavage to activate their PFDs. One of these, gasdermin E, is activated by caspase-3 cleavage. We review our current understanding of pyroptosis as well as current knowledge of the gasdermin family.
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Affiliation(s)
- Stephen B Kovacs
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, and Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Edward A Miao
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, and Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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22
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Schrader M, Pellegrini L. The making of a mammalian peroxisome, version 2.0: mitochondria get into the mix. Cell Death Differ 2017; 24:1148-1152. [PMID: 28409773 PMCID: PMC5520164 DOI: 10.1038/cdd.2017.23] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 02/06/2017] [Indexed: 01/03/2023] Open
Abstract
A recent report from the Laboratory of Heidi McBride (McGill University) presents a role for mitochondria in the de novo biogenesis of peroxisomes in mammalian cells. Peroxisomes are essential organelles responsible for a wide variety of biochemical functions, from the generation of bile to plasmalogen synthesis, reduction of peroxides, and the oxidation of very-long-chain fatty acids. Like mitochondria, peroxisomes proliferate primarily through growth and division of pre-existing peroxisomes. However, unlike mitochondria, peroxisomes do not fuse; further, and perhaps most importantly, they can also be born de novo, a process thought to occur through the generation of pre-peroxisomal vesicles that originate from the endoplasmic reticulum. De novo peroxisome biogenesis has been extensively studied in yeast, with a major focus on the role of the ER in this process; however, in the mammalian system this field is much less explored. By exploiting patient cells lacking mature peroxisomes, the McBride laboratory now assigns a role to ER and mitochondria in de novo mammalian peroxisome biogenesis by showing that the formation of immature pre-peroxisomes occurs through the fusion of Pex3-/Pex14-containing mitochondria-derived vesicles with Pex16-containing ER-derived vesicles.
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Affiliation(s)
| | - Luca Pellegrini
- Faculty of Medicine, Department of Molecular Biology, Medical Biochemistry and Pathology, Universitè Laval, Quebec, QC, Canada
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23
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Costello JL, Castro IG, Schrader TA, Islinger M, Schrader M. Peroxisomal ACBD4 interacts with VAPB and promotes ER-peroxisome associations. Cell Cycle 2017; 16:1039-1045. [PMID: 28463579 PMCID: PMC5499832 DOI: 10.1080/15384101.2017.1314422] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 03/27/2017] [Indexed: 10/29/2022] Open
Abstract
Cooperation between cellular organelles such as mitochondria, peroxisomes and the ER is essential for a variety of important and diverse metabolic processes. Effective communication and metabolite exchange requires physical linkages between the organelles, predominantly in the form of organelle contact sites. At such contact sites organelle membranes are brought into close proximity by the action of molecular tethers, which often consist of specific protein pairs anchored in the membrane of the opposing organelles. Currently numerous tethering components have been identified which link the ER with multiple other organelles but knowledge of the factors linking the ER with peroxisomes is limited. Peroxisome-ER interplay is important because it is required for the biosynthesis of unsaturated fatty acids, ether-phospholipids and sterols with defects in these functions leading to severe diseases. Here, we characterize acyl-CoA binding domain protein 4 (ACBD4) as a tail-anchored peroxisomal membrane protein which interacts with the ER protein, vesicle-associated membrane protein-associated protein-B (VAPB) to promote peroxisome-ER associations.
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Affiliation(s)
| | - Inês G. Castro
- Department of Biosciences, University of Exeter, Exeter, UK
| | | | - Markus Islinger
- Institute of Neuroanatomy, Center for Biomedicine & Medical Technology Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
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24
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Nury T, Zarrouk A, Ragot K, Debbabi M, Riedinger JM, Vejux A, Aubourg P, Lizard G. 7-Ketocholesterol is increased in the plasma of X-ALD patients and induces peroxisomal modifications in microglial cells: Potential roles of 7-ketocholesterol in the pathophysiology of X-ALD. J Steroid Biochem Mol Biol 2017; 169:123-136. [PMID: 27041118 DOI: 10.1016/j.jsbmb.2016.03.037] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 12/09/2015] [Accepted: 03/31/2016] [Indexed: 01/08/2023]
Abstract
X-linked adrenoleukodystrophy (X-ALD) is a genetic disorder induced by a mutation in the ABCD1 gene, which causes the accumulation of very long-chain fatty acids in tissue and plasma. Oxidative stress may be a hallmark of X-ALD. In the plasma of X-ALD patients with different forms of the disease, characterized by high levels of C24:0 and C26:0, we observed the presence of oxidative stress revealed by decreased levels of GSH, α-tocopherol, and docosahexaenoic acid (DHA). We showed that oxidative stress caused the oxidation of cholesterol and linoleic acid, leading to the formation of cholesterol oxide derivatives oxidized at C7 (7-ketocholesterol (7KC), 7β-hydroxycholesterol (7β-OHC), and 7α-hydroxycholesrol (7α-OHC)) and of 9- and 13-hydroxyoctadecadienoic acids (9-HODE, 13-HODE), respectively. High levels of 7KC, 7β-OHC, 7α-OHC, 9-HODE and 13-HODE were found. As 7KC induces oxidative stress, inflammation and cell death, which could play key roles in the development of X-ALD, the impact of 7KC on the peroxisomal status was determined in microglial BV-2 cells. Indeed, environmental stress factors such as 7KC could exacerbate peroxisomal dysfunctions in microglial cells and thus determine the progression of the disease. 7KC induces oxiapoptophagy in BV-2 cells: overproduction of H2O2 and O2-, presence of cleaved caspase-3 and PARP, nuclear condensation and/or fragmentation; elevated [LC3-II/LC3-I] ratio, increased p62 levels. 7KC also induces several peroxisomal modifications: decreased Abcd1, Abcd2, Abcd3, Acox1 and/or Mfp2 mRNA and protein levels, increased catalase activity and decreased Acox1-activity. However, the Pex14 level was unchanged. It is suggested that high levels of 7KC in X-ALD patients could foster generalized peroxisomal dysfunction in microglial cells, which could in turn intensify brain damage.
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Affiliation(s)
- Thomas Nury
- Biochemistry of the Peroxisome, Inflammation and Lipid Metabolism' EA 7270/Univ. Bourgogne Franche Comté/INSERM, Dijon, France
| | - Amira Zarrouk
- Biochemistry of the Peroxisome, Inflammation and Lipid Metabolism' EA 7270/Univ. Bourgogne Franche Comté/INSERM, Dijon, France; Univ. Monastir, Faculty of Medicine, LR12ES05, Lab-NAFS Nutrition - Functional Food & Vascular Health, Monastir, Tunisia; Univ. Sousse, Faculty of Medicine, Sousse, Tunisia
| | - Kévin Ragot
- SYSMEX, Department of Cytometry, Roissy, France
| | - Meryam Debbabi
- Biochemistry of the Peroxisome, Inflammation and Lipid Metabolism' EA 7270/Univ. Bourgogne Franche Comté/INSERM, Dijon, France; Univ. Monastir, Faculty of Medicine, LR12ES05, Lab-NAFS Nutrition - Functional Food & Vascular Health, Monastir, Tunisia
| | | | - Anne Vejux
- Biochemistry of the Peroxisome, Inflammation and Lipid Metabolism' EA 7270/Univ. Bourgogne Franche Comté/INSERM, Dijon, France
| | - Patrick Aubourg
- INSERM UMR 1169, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Gérard Lizard
- Biochemistry of the Peroxisome, Inflammation and Lipid Metabolism' EA 7270/Univ. Bourgogne Franche Comté/INSERM, Dijon, France.
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25
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Cámara E, Landes N, Albiol J, Gasser B, Mattanovich D, Ferrer P. Increased dosage of AOX1 promoter-regulated expression cassettes leads to transcription attenuation of the methanol metabolism in Pichia pastoris. Sci Rep 2017; 7:44302. [PMID: 28295011 PMCID: PMC5353721 DOI: 10.1038/srep44302] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 02/07/2017] [Indexed: 12/11/2022] Open
Abstract
The methanol-regulated alcohol oxidase promoter (PAOX1) of Pichia pastoris is one of the strongest promoters for heterologous gene expression in this methylotrophic yeast. Although increasing gene dosage is one of the most common strategies to increase recombinant protein productivities, the increase of gene dosage of Rhizopus oryzae lipase (ROL) in P. pastoris has been previously shown to reduce cell growth, lipase production and substrate consumption in high-copy strains. To better assess that physiological response, transcriptomics analysis was performed of a subset of strains with 1 to 15 ROL copies. The macroscopic physiological parameters confirm that growth yield and carbon uptake rate are gene dosage dependent, and were supported by the transcriptomic data, showing the impact of increased dosage of AOX1 promoter-regulated expression cassettes on P. pastoris physiology under steady methanolic growth conditions. Remarkably, increased number of cassettes led to transcription attenuation of the methanol metabolism and peroxisome biogenesis in P. pastoris, concomitant with reduced secretion levels of the heterologous product. Moreover, our data also point to a block in ROL mRNA translation in the higher ROL-copies constructs, while the low productivities of multi-copy strains under steady growth conditions do not appear to be directly related to UPR and ERAD induction.
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Affiliation(s)
- Elena Cámara
- Department of Chemical, Biological, and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès) 08193, Catalonia, Spain
| | - Nils Landes
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190 Vienna, Austria
| | - Joan Albiol
- Department of Chemical, Biological, and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès) 08193, Catalonia, Spain
| | - Brigitte Gasser
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190 Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190 Vienna, Austria
| | - Pau Ferrer
- Department of Chemical, Biological, and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès) 08193, Catalonia, Spain
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26
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Abe S, Nagai T, Masukawa M, Okumoto K, Homma Y, Fujiki Y, Mizuno K. Localization of Protein Kinase NDR2 to Peroxisomes and Its Role in Ciliogenesis. J Biol Chem 2017; 292:4089-4098. [PMID: 28122914 DOI: 10.1074/jbc.m117.775916] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Indexed: 12/15/2022] Open
Abstract
Nuclear Dbf2-related (NDR) kinases, comprising NDR1 and NDR2, are serine/threonine kinases that play crucial roles in the control of cell proliferation, apoptosis, and morphogenesis. We recently showed that NDR2, but not NDR1, is involved in primary cilium formation; however, the mechanism underlying their functional difference in ciliogenesis is unknown. To address this issue, we examined their subcellular localization. Despite their close sequence similarity, NDR2 exhibited punctate localization in the cytoplasm, whereas NDR1 was diffusely distributed within the cell. Notably, NDR2 puncta mostly co-localized with the peroxisome marker proteins, catalase and CFP-SKL (cyan fluorescent protein carrying the C-terminal typical peroxisome-targeting signal type-1 (PTS1) sequence, Ser-Lys-Leu). NDR2 contains the PTS1-like sequence, Gly-Lys-Leu, at the C-terminal end, whereas the C-terminal end of NDR1 is Ala-Lys. An NDR2 mutant lacking the C-terminal Leu, NDR2(ΔL), exhibited almost diffuse distribution in cells. Additionally, NDR2, but neither NDR1 nor NDR2(ΔL), bound to the PTS1 receptor Pex5p. Together, these findings indicate that NDR2 localizes to the peroxisome by using the C-terminal GKL sequence. Intriguingly, topology analysis of NDR2 suggests that NDR2 is exposed to the cytosolic surface of the peroxisome. The expression of wild-type NDR2, but not NDR2(ΔL), recovered the suppressive effect of NDR2 knockdown on ciliogenesis. Furthermore, knockdown of peroxisome biogenesis factor genes (PEX1 or PEX3) partially suppressed ciliogenesis. These results suggest that the peroxisomal localization of NDR2 is implicated in its function to promote primary cilium formation.
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Affiliation(s)
- Shoko Abe
- From the Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578
| | - Tomoaki Nagai
- From the Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578
| | - Moe Masukawa
- From the Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578
| | - Kanji Okumoto
- the Graduate School of Systems Life Sciences, Kyushu University, Motooka, Fukuoka 819-0395, and
| | - Yuta Homma
- From the Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578
| | - Yukio Fujiki
- the Medical Institute of Bioregulation, Kyushu University, Maidashi, Fukuoka 812-8582, Japan
| | - Kensaku Mizuno
- From the Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578,
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27
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Hua R, Cheng D, Coyaud É, Freeman S, Di Pietro E, Wang Y, Vissa A, Yip CM, Fairn GD, Braverman N, Brumell JH, Trimble WS, Raught B, Kim PK. VAPs and ACBD5 tether peroxisomes to the ER for peroxisome maintenance and lipid homeostasis. J Cell Biol 2017; 216:367-377. [PMID: 28108526 PMCID: PMC5294787 DOI: 10.1083/jcb.201608128] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/14/2016] [Accepted: 01/04/2017] [Indexed: 12/15/2022] Open
Abstract
Peroxisomes and the ER exchange lipids for various metabolic and anabolic reactions. In this study, Hua et al. show that the interaction between the ER-resident VAPs with the peroxisomal protein ACBD5 tethers peroxisomes to the ER. This tether is required for the exchange of lipids, including cholesterol, between the two organelles. Lipid exchange between the endoplasmic reticulum (ER) and peroxisomes is necessary for the synthesis and catabolism of lipids, the trafficking of cholesterol, and peroxisome biogenesis in mammalian cells. However, how lipids are exchanged between these two organelles is not understood. In this study, we report that the ER-resident VAMP-associated proteins A and B (VAPA and VAPB) interact with the peroxisomal membrane protein acyl-CoA binding domain containing 5 (ACBD5) and that this interaction is required to tether the two organelles together, thereby facilitating the lipid exchange between them. Depletion of either ACBD5 or VAP expression results in increased peroxisome mobility, suggesting that VAP–ACBD5 complex acts as the primary ER–peroxisome tether. We also demonstrate that tethering of peroxisomes to the ER is necessary for peroxisome growth, the synthesis of plasmalogen phospholipids, and the maintenance of cellular cholesterol levels. Collectively, our data highlight the importance of VAP–ACBD5–mediated contact between the ER and peroxisomes for organelle maintenance and lipid homeostasis.
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Affiliation(s)
- Rong Hua
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada
| | - Derrick Cheng
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada
| | - Étienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G1L7, Canada
| | - Spencer Freeman
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada
| | - Erminia Di Pietro
- Department of Pediatrics and Human Genetics, Research Institute of the McGill University Health Center and McGill University, Montreal, Quebec H4A 3J1, Canada
| | - Yuqing Wang
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada
| | - Adriano Vissa
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S3E1, Canada
| | - Christopher M Yip
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada.,Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S3E1, Canada
| | - Gregory D Fairn
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada
| | - Nancy Braverman
- Department of Pediatrics and Human Genetics, Research Institute of the McGill University Health Center and McGill University, Montreal, Quebec H4A 3J1, Canada
| | - John H Brumell
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada.,SickKids Inflammatory Bowel Disease Centre, Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario M5S1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G1L7, Canada
| | - William S Trimble
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada
| | - Brian Raught
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G1L7, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G1L7, Canada
| | - Peter K Kim
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario M5G0A4, Canada .,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S1A8, Canada
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28
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Costello JL, Castro IG, Hacker C, Schrader TA, Metz J, Zeuschner D, Azadi AS, Godinho LF, Costina V, Findeisen P, Manner A, Islinger M, Schrader M. ACBD5 and VAPB mediate membrane associations between peroxisomes and the ER. J Cell Biol 2017; 216:331-342. [PMID: 28108524 PMCID: PMC5294785 DOI: 10.1083/jcb.201607055] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/31/2016] [Accepted: 12/22/2016] [Indexed: 01/20/2023] Open
Abstract
Costello et al. identify ACBD5 and VAPB as key components of a peroxisome–ER tether in mammalian cells. Disruption of this tethering complex leads to reduced peroxisomal membrane expansion and increased peroxisomal movement. Peroxisomes (POs) and the endoplasmic reticulum (ER) cooperate in cellular lipid metabolism and form tight structural associations, which were first observed in ultrastructural studies decades ago. PO–ER associations have been suggested to impact on a diverse number of physiological processes, including lipid metabolism, phospholipid exchange, metabolite transport, signaling, and PO biogenesis. Despite their fundamental importance to cell metabolism, the mechanisms by which regions of the ER become tethered to POs are unknown, in particular in mammalian cells. Here, we identify the PO membrane protein acyl-coenzyme A–binding domain protein 5 (ACBD5) as a binding partner for the resident ER protein vesicle-associated membrane protein-associated protein B (VAPB). We show that ACBD5–VAPB interaction regulates PO–ER associations. Moreover, we demonstrate that loss of PO–ER association perturbs PO membrane expansion and increases PO movement. Our findings reveal the first molecular mechanism for establishing PO–ER associations in mammalian cells and report a new function for ACBD5 in PO–ER tethering.
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Affiliation(s)
| | - Inês G Castro
- Biosciences, University of Exeter, Exeter EX4 4QD, England, UK
| | | | - Tina A Schrader
- Biosciences, University of Exeter, Exeter EX4 4QD, England, UK
| | - Jeremy Metz
- Biosciences, University of Exeter, Exeter EX4 4QD, England, UK
| | - Dagmar Zeuschner
- Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany
| | - Afsoon S Azadi
- Biosciences, University of Exeter, Exeter EX4 4QD, England, UK
| | - Luis F Godinho
- Biosciences, University of Exeter, Exeter EX4 4QD, England, UK
| | - Victor Costina
- Institute for Clinical Chemistry, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Peter Findeisen
- Institute for Clinical Chemistry, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Andreas Manner
- Institute of Neuroanatomy, Center for Biomedicine and Medical Technology Mannheim, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Markus Islinger
- Institute of Neuroanatomy, Center for Biomedicine and Medical Technology Mannheim, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
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29
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Global Fitness Profiling Identifies Arsenic and Cadmium Tolerance Mechanisms in Fission Yeast. G3-GENES GENOMES GENETICS 2016; 6:3317-3333. [PMID: 27558664 PMCID: PMC5068951 DOI: 10.1534/g3.116.033829] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Heavy metals and metalloids such as cadmium [Cd(II)] and arsenic [As(III)] are widespread environmental toxicants responsible for multiple adverse health effects in humans. However, the molecular mechanisms underlying metal-induced cytotoxicity and carcinogenesis, as well as the detoxification and tolerance pathways, are incompletely understood. Here, we use global fitness profiling by barcode sequencing to quantitatively survey the Schizosaccharomyces pombe haploid deletome for genes that confer tolerance of cadmium or arsenic. We identified 106 genes required for cadmium resistance and 110 genes required for arsenic resistance, with a highly significant overlap of 36 genes. A subset of these 36 genes account for almost all proteins required for incorporating sulfur into the cysteine-rich glutathione and phytochelatin peptides that chelate cadmium and arsenic. A requirement for Mms19 is explained by its role in directing iron–sulfur cluster assembly into sulfite reductase as opposed to promoting DNA repair, as DNA damage response genes were not enriched among those required for cadmium or arsenic tolerance. Ubiquinone, siroheme, and pyridoxal 5′-phosphate biosynthesis were also identified as critical for Cd/As tolerance. Arsenic-specific pathways included prefoldin-mediated assembly of unfolded proteins and protein targeting to the peroxisome, whereas cadmium-specific pathways included plasma membrane and vacuolar transporters, as well as Spt–Ada–Gcn5-acetyltransferase (SAGA) transcriptional coactivator that controls expression of key genes required for cadmium tolerance. Notable differences are apparent with corresponding screens in the budding yeast Saccharomyces cerevisiae, underscoring the utility of analyzing toxic metal defense mechanisms in both organisms.
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30
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Emmanouilidis L, Gopalswamy M, Passon DM, Wilmanns M, Sattler M. Structural biology of the import pathways of peroxisomal matrix proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:804-13. [DOI: 10.1016/j.bbamcr.2015.09.034] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 09/29/2015] [Accepted: 09/30/2015] [Indexed: 11/28/2022]
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31
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Reumann S, Chowdhary G, Lingner T. Characterization, prediction and evolution of plant peroxisomal targeting signals type 1 (PTS1s). BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1863:790-803. [PMID: 26772785 DOI: 10.1016/j.bbamcr.2016.01.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 01/01/2016] [Accepted: 01/04/2016] [Indexed: 12/22/2022]
Abstract
Our knowledge of the proteome of plant peroxisomes and their functional plasticity is far from being complete, primarily due to major technical challenges in experimental proteome research of the fragile cell organelle. Several unexpected novel plant peroxisome functions, for instance in biotin and phylloquinone biosynthesis, have been uncovered recently. Nevertheless, very few regulatory and membrane proteins of plant peroxisomes have been identified and functionally described up to now. To define the matrix proteome of plant peroxisomes, computational methods have emerged as important powerful tools. Novel prediction approaches of high sensitivity and specificity have been developed for peroxisome targeting signals type 1 (PTS1) and have been validated by in vivo subcellular targeting analyses and thermodynamic binding studies with the cytosolic receptor, PEX5. Accordingly, the algorithms allow the correct prediction of many novel peroxisome-targeted proteins from plant genome sequences and the discovery of additional organelle functions. In this review, we provide an overview of methodologies, capabilities and accuracies of available prediction algorithms for PTS1 carrying proteins. We also summarize and discuss recent quantitative, structural and mechanistic information of the interaction of PEX5 with PTS1 carrying proteins in relation to in vivo import efficiency. With this knowledge, we develop a model of how proteins likely evolved peroxisomal targeting signals in the past and still nowadays, in which order the two import pathways might have evolved in the ancient eukaryotic cell, and how the secondary loss of the PTS2 pathway probably happened in specific organismal groups.
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Affiliation(s)
- S Reumann
- Department of Plant Biochemistry and Infection Biology, Biocentre Klein Flottbek, University of Hamburg, D-22609 Hamburg, Germany; Centre for Organelle Research, University of Stavanger, N-4036 Stavanger, Norway.
| | - G Chowdhary
- Centre for Organelle Research, University of Stavanger, N-4036 Stavanger, Norway; KIIT School of Biotechnology, Campus XI, KIIT University, I-751024 Bhubaneswar, India.
| | - T Lingner
- Department of Bioinformatics, Institute for Microbiology and Genetics, D-37077 Goettingen, Germany.
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32
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Peroxisome homeostasis: Mechanisms of division and selective degradation of peroxisomes in mammals. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:984-91. [DOI: 10.1016/j.bbamcr.2015.09.032] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 09/25/2015] [Accepted: 09/28/2015] [Indexed: 12/25/2022]
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33
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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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34
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Mast FD, Jamakhandi A, Saleem RA, Dilworth DJ, Rogers RS, Rachubinski RA, Aitchison JD. Peroxins Pex30 and Pex29 Dynamically Associate with Reticulons to Regulate Peroxisome Biogenesis from the Endoplasmic Reticulum. J Biol Chem 2016; 291:15408-27. [PMID: 27129769 DOI: 10.1074/jbc.m116.728154] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 12/11/2022] Open
Abstract
Peroxisome proliferation occurs by at least two routes, division of existing peroxisomes and de novo biogenesis from the endoplasmic reticulum (ER). The proteins and molecular mechanisms governing peroxisome emergence from the ER are poorly characterized. In this study, we report that two integral membrane peroxins (proteins required for peroxisome biogenesis) in Saccharomyces cerevisiae, Pex29 and Pex30, reside in distinct regions of the ER and associate with Rtn1 and Yop1, reticulon family members that contribute to ER morphology, to govern peroxisome emergence from the ER. In vivo and in vitro analyses reveal that peroxisome proliferation is therefore not restricted to the peroxisome but begins at the level of the ER.
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Affiliation(s)
- Fred D Mast
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - Arvind Jamakhandi
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - Ramsey A Saleem
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - David J Dilworth
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - Richard S Rogers
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - Richard A Rachubinski
- the Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - John D Aitchison
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
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35
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Liu Y, Yagita Y, Fujiki Y. Assembly of Peroxisomal Membrane Proteins via the Direct Pex19p-Pex3p Pathway. Traffic 2016; 17:433-55. [PMID: 26777132 DOI: 10.1111/tra.12376] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 01/13/2016] [Accepted: 01/13/2016] [Indexed: 02/03/2023]
Abstract
Correct targeting of peroxisomal membrane proteins (PMPs) is essential for the formation and maintenance of functional peroxisomes. Activities of Pex19p to interact with PMPs on one hand and Pex3p on the other, including formation of ternary complexes between Pex19p, PMP and Pex3p, strongly support posttranslational translocation of PMPs via the Pex19p- and Pex3p-dependent direct pathway, termed the class I pathway. However, it remains elusive whether Pex19p-PMP complexes are indeed capable of being imported into peroxisomal membranes through the interaction between Pex19p and Pex3p. We resolve this issue by investigating the targeting process of several topologically distinct PMPs, including multimembrane spanning PMPs. We show here that Pex19p forms cytosolic complexes with PMPs and directly translocates them to peroxisomes. Using a semi-intact mammalian cell-based import assay system, we prove that PMPs in the cytosolic complexes are imported into peroxisomes via the interaction between cargo-loaded Pex19p and Pex3p. Furthermore, we demonstrate for the first time that peroxisomal targeting of ATAD1, an N-terminally signal-anchored protein that resides on both mitochondria and peroxisomes, is also achieved through the Pex19p- and Pex3p-dependent class I pathway. Together, our results suggest that translocation of PMPs via the class I pathway is a common event in mammalian cells.
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Affiliation(s)
- Yuqiong Liu
- Graduate School of Systems Life Sciences, Kyushu University Graduate School, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yuichi Yagita
- Department of Biology, Faculty of Sciences, Kyushu University, Nishi-ku, Fukuoka, 819-0395, Japan.,Present address: Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Yukio Fujiki
- Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan
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36
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Gabaldón T, Ginger ML, Michels PAM. Peroxisomes in parasitic protists. Mol Biochem Parasitol 2016; 209:35-45. [PMID: 26896770 DOI: 10.1016/j.molbiopara.2016.02.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/12/2016] [Accepted: 02/13/2016] [Indexed: 01/24/2023]
Abstract
Representatives of all major lineages of eukaryotes contain peroxisomes with similar morphology and mode of biogenesis, indicating a monophyletic origin of the organelles within the common ancestor of all eukaryotes. Peroxisomes originated from the endoplasmic reticulum, but despite a common origin and shared morphological features, peroxisomes from different organisms show a remarkable diversity of enzyme content and the metabolic processes present can vary dependent on nutritional or developmental conditions. A common characteristic and probable evolutionary driver for the origin of the organelle is an involvement in lipid metabolism, notably H2O2-dependent fatty-acid oxidation. Subsequent evolution of the organelle in different lineages involved multiple acquisitions of metabolic processes-often involving retargeting enzymes from other cell compartments-and losses. Information about peroxisomes in protists is still scarce, but available evidence, including new bioinformatics data reported here, indicate striking diversity amongst free-living and parasitic protists from different phylogenetic supergroups. Peroxisomes in only some protists show major involvement in H2O2-dependent metabolism, as in peroxisomes of mammalian, plant and fungal cells. Compartmentalization of glycolytic and gluconeogenic enzymes inside peroxisomes is characteristic of kinetoplastids and diplonemids, where the organelles are hence called glycosomes, whereas several other excavate parasites (Giardia, Trichomonas) have lost peroxisomes. Amongst alveolates and amoebozoans patterns of peroxisome loss are more complicated. Often, a link is apparent between the niches occupied by the parasitic protists, nutrient availability, and the absence of the organelles or their presence with a specific enzymatic content. In trypanosomatids, essentiality of peroxisomes may be considered for use in anti-parasite drug discovery.
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Affiliation(s)
- Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Michael L Ginger
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, UK; Department of Biological Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK.
| | - Paul A M Michels
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, UK; Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, UK; Laboratorio de Enzimología de Parásitos, Departamento de Biología, Universidad de Los Andes, Mérida, Venezuela.
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37
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Pomaznoy MY, Logacheva MD, Young ND, Penin AA, Ershov NI, Katokhin AV, Mordvinov VA. Whole transcriptome profiling of adult and infective stages of the trematode Opisthorchis felineus. Parasitol Int 2016; 65:12-19. [DOI: 10.1016/j.parint.2015.09.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/11/2015] [Accepted: 09/08/2015] [Indexed: 01/22/2023]
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38
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Oeljeklaus S, Schummer A, Mastalski T, Platta HW, Warscheid B. Regulation of peroxisome dynamics by phosphorylation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:1027-37. [PMID: 26775584 DOI: 10.1016/j.bbamcr.2015.12.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/22/2015] [Accepted: 12/24/2015] [Indexed: 12/31/2022]
Abstract
Peroxisomes are highly dynamic organelles that can rapidly change in size, abundance, and protein content in response to alterations in nutritional and other environmental conditions. These dynamic changes in peroxisome features, referred to as peroxisome dynamics, rely on the coordinated action of several processes of peroxisome biogenesis. Revealing the regulatory mechanisms of peroxisome dynamics is an emerging theme in cell biology. These mechanisms are inevitably linked to and synchronized with the biogenesis and degradation of peroxisomes. To date, the key players and basic principles of virtually all steps in the peroxisomal life cycle are known, but regulatory mechanisms remained largely elusive. A number of recent studies put the spotlight on reversible protein phosphorylation for the control of peroxisome dynamics and highlighted peroxisomes as hubs for cellular signal integration and regulation. Here, we will present and discuss the results of several studies performed using yeast and mammalian cells that convey a sense of the impact protein phosphorylation may have on the modulation of peroxisome dynamics by regulating peroxisomal matrix and membrane protein import, proliferation, inheritance, and degradation. We further put forward the idea to make use of current data on phosphorylation sites of peroxisomal and peroxisome-associated proteins reported in advanced large-scale phosphoproteomic studies.
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Affiliation(s)
- Silke Oeljeklaus
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, 79104 Freiburg, Germany
| | - Andreas Schummer
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Mastalski
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Harald W Platta
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Bettina Warscheid
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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Small GTPases in peroxisome dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:1006-13. [PMID: 26775587 DOI: 10.1016/j.bbamcr.2016.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 01/05/2016] [Accepted: 01/07/2016] [Indexed: 12/12/2022]
Abstract
In this review article, we summarize current knowledge on peroxisome biogenesis/functions and the role that small GTPases may play in these processes. Precise intracellular distribution of cell organelles requires their regulated association to microtubules and the actin cytoskeleton. In this respect, RhoGDP/RhoGTP favor binding of peroxisomes to microtubules and actin filaments. In its GTP-bound form, RhoA activates a regulatory cascade involving Rho kinaseII and non-muscle myosinIIA. Such interactions frequently depend on phosphoinositides (PIs) of which PI4P, PI(4,5)P2, and PI(3,5)P2 were found to be present in the peroxisomal membrane. PIs are pivotal determinants of intracellular signaling and known to regulate a wide range of cellular functions. In many of these functions, small GTPases are implicated. The small GTPase ADP-ribosylation factor 1 (Arf1), for example, is known to stimulate synthesis of PI4P and PI(4,5)P2 on the Golgi to regulate protein and lipid sorting. In vitro binding assays localized Arf1 and the COPI complex to peroxisomes. In light of the recent discussion of pre-peroxisomal vesicle generation at the ER, peroxisomal Arf1-COPI vesicles may serve retrograde transport of ER-resident components. A mass spectrometric screen localized various Rab proteins to peroxisomes. Overexpression of these proteins in combination with laser-scanning fluorescence microscopy co-localized Rab6, Rab8, Rab10, Rab14, and Rab18 with peroxisomal structures. By analogy to the role these proteins play in other organelle dynamics, we may envisage what the function of these proteins may be in relation to the peroxisomal compartment.
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Kamisugi Y, Mitsuya S, El‐Shami M, Knight CD, Cuming AC, Baker A. Giant peroxisomes in a moss (Physcomitrella patens) peroxisomal biogenesis factor 11 mutant. THE NEW PHYTOLOGIST 2016; 209:576-89. [PMID: 26542980 PMCID: PMC4738463 DOI: 10.1111/nph.13739] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/01/2015] [Indexed: 05/22/2023]
Abstract
Peroxisomal biogenesis factor 11 (PEX11) proteins are found in yeasts, mammals and plants, and play a role in peroxisome morphology and regulation of peroxisome division. The moss Physcomitrella patens has six PEX11 isoforms which fall into two subfamilies, similar to those found in monocots and dicots. We carried out targeted gene disruption of the Phypa_PEX11-1 gene and compared the morphological and cellular phenotypes of the wild-type and mutant strains. The mutant grew more slowly and the development of gametophores was retarded. Mutant chloronemal filaments contained large cellular structures which excluded all other cellular organelles. Expression of fluorescent reporter proteins revealed that the mutant strain had greatly enlarged peroxisomes up to 10 μm in diameter. Expression of a vacuolar membrane marker confirmed that the enlarged structures were not vacuoles, or peroxisomes sequestered within vacuoles as a result of pexophagy. Phypa_PEX11 targeted to peroxisome membranes could rescue the knock out phenotype and interacted with Fission1 on the peroxisome membrane. Moss PEX11 functions in peroxisome division similar to PEX11 in other organisms but the mutant phenotype is more extreme and environmentally determined, making P. patens a powerful system in which to address mechanisms of peroxisome proliferation and division.
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Affiliation(s)
- Yasuko Kamisugi
- Centre for Plant SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - Shiro Mitsuya
- Centre for Plant SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - Mahmoud El‐Shami
- Centre for Plant SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - Celia D. Knight
- Centre for Plant SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - Andrew C. Cuming
- Centre for Plant SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
| | - Alison Baker
- Centre for Plant SciencesFaculty of Biological SciencesUniversity of LeedsLeedsLS2 9JTUK
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Mayerhofer PU, Bañó-Polo M, Mingarro I, Johnson AE. Human Peroxin PEX3 Is Co-translationally Integrated into the ER and Exits the ER in Budding Vesicles. Traffic 2015; 17:117-30. [PMID: 26572236 PMCID: PMC5064655 DOI: 10.1111/tra.12350] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 11/13/2015] [Accepted: 11/13/2015] [Indexed: 01/19/2023]
Abstract
The long-standing paradigm that all peroxisomal proteins are imported post-translationally into pre-existing peroxisomes has been challenged by the detection of peroxisomal membrane proteins (PMPs) inside the endoplasmic reticulum (ER). In mammals, the mechanisms of ER entry and exit of PMPs are completely unknown. We show that the human PMP PEX3 inserts co-translationally into the mammalian ER via the Sec61 translocon. Photocrosslinking and fluorescence spectroscopy studies demonstrate that the N-terminal transmembrane segment (TMS) of ribosome-bound PEX3 is recognized by the signal recognition particle (SRP). Binding to SRP is a prerequisite for targeting of the PEX3-containing ribosome•nascent chain complex (RNC) to the translocon, where an ordered multistep pathway integrates the nascent chain into the membrane adjacent to translocon proteins Sec61α and TRAM. This insertion of PEX3 into the ER is physiologically relevant because PEX3 then exits the ER via budding vesicles in an ATP-dependent process. This study identifies early steps in human peroxisomal biogenesis by demonstrating sequential stages of PMP passage through the mammalian ER.
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Affiliation(s)
- Peter U Mayerhofer
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, 440 Reynolds Medical Building, College Station, TX, 77843, USA.,Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt, Germany.,Present address: School of Biosciences & Medicine, University of Surrey, Guildford, GU2 7XH, UK
| | - Manuel Bañó-Polo
- Departament de Bioquimica i Biologia Molecular, Universitat de Valencia, C/ Dr. Moliner, 50, E-46100, Burjassot, Spain
| | - Ismael Mingarro
- Departament de Bioquimica i Biologia Molecular, Universitat de Valencia, C/ Dr. Moliner, 50, E-46100, Burjassot, Spain
| | - Arthur E Johnson
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, 440 Reynolds Medical Building, College Station, TX, 77843, USA.,Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
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Fourcade S, Ferrer I, Pujol A. Oxidative stress, mitochondrial and proteostasis malfunction in adrenoleukodystrophy: A paradigm for axonal degeneration. Free Radic Biol Med 2015; 88:18-29. [PMID: 26073123 DOI: 10.1016/j.freeradbiomed.2015.05.041] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/07/2015] [Accepted: 05/26/2015] [Indexed: 12/15/2022]
Abstract
Peroxisomal and mitochondrial malfunction, which are highly intertwined through redox regulation, in combination with defective proteostasis, are hallmarks of the most prevalent multifactorial neurodegenerative diseases-including Alzheimer's (AD) and Parkinson's disease (PD)-and of the aging process, and are also found in inherited conditions. Here we review the interplay between oxidative stress and axonal degeneration, taking as groundwork recent findings on pathomechanisms of the peroxisomal neurometabolic disease adrenoleukodystrophy (X-ALD). We explore the impact of chronic redox imbalance caused by the excess of very long-chain fatty acids (VLCFA) on mitochondrial respiration and biogenesis, and discuss how this impairs protein quality control mechanisms essential for neural cell survival, such as the proteasome and autophagy systems. As consequence, prime molecular targets in the pathogenetic cascade emerge, such as the SIRT1/PGC-1α axis of mitochondrial biogenesis, and the inhibitor of autophagy mTOR. Thus, we propose that mitochondria-targeted antioxidants; mitochondrial biogenesis boosters such as the antidiabetic pioglitazone and the SIRT1 ligand resveratrol; and the autophagy activator temsirolimus, a derivative of the mTOR inhibitor rapamycin, hold promise as disease-modifying therapies for X-ALD.
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Affiliation(s)
- Stéphane Fourcade
- Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospitalet de Llobregat, 08908 Barcelona, Spain; Institut of Neuropathology, Pathologic Anatomy Service, Bellvitge Biomedical Research Institute, IDIBELL-Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, 08908 Barcelona, Spain; Center for Biomedical Research on Rare Diseases (CIBERER), U759, ISCIII, Spain.
| | - Isidre Ferrer
- Institut of Neuropathology, Pathologic Anatomy Service, Bellvitge Biomedical Research Institute, IDIBELL-Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, 08908 Barcelona, Spain; Center for Biomedical Research on Neurodegenerative Diseases (CIBERNED), Spain
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospitalet de Llobregat, 08908 Barcelona, Spain; Institut of Neuropathology, Pathologic Anatomy Service, Bellvitge Biomedical Research Institute, IDIBELL-Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, 08908 Barcelona, Spain; Center for Biomedical Research on Rare Diseases (CIBERER), U759, ISCIII, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona 08010, Catalonia, Spain.
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43
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Knoblach B, Rachubinski RA. Motors, anchors, and connectors: orchestrators of organelle inheritance. Annu Rev Cell Dev Biol 2015; 31:55-81. [PMID: 26443192 DOI: 10.1146/annurev-cellbio-100814-125553] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Organelle inheritance is a process whereby organelles are actively distributed between dividing cells at cytokinesis. Much valuable insight into the molecular mechanisms of organelle inheritance has come from the analysis of asymmetrically dividing cells, which transport a portion of their organelles to the bud while retaining another portion in the mother cell. Common principles apply to the inheritance of all organelles, although individual organelles use specific factors for their partitioning. Inheritance factors can be classified as motors, which are required for organelle transport; anchors, which immobilize organelles at distinct cell structures; or connectors, which mediate the attachment of organelles to motors and anchors. Here, we provide an overview of recent advances in the field of organelle inheritance and highlight how motor, anchor, and connector molecules choreograph the segregation of a multicopy organelle, the peroxisome. We also discuss the role of organelle population control in the generation of cellular diversity.
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Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada;
| | - Richard A Rachubinski
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada;
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Giannopoulou EA, Emmanouilidis L, Sattler M, Dodt G, Wilmanns M. Towards the molecular mechanism of the integration of peroxisomal membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:863-9. [PMID: 26434995 PMCID: PMC4819957 DOI: 10.1016/j.bbamcr.2015.09.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 09/22/2015] [Accepted: 09/28/2015] [Indexed: 11/30/2022]
Abstract
The correct topogenesis of peroxisomal membrane proteins is a crucial step for the formation of functioning peroxisomes. Although this process has been widely studied, the exact mechanism with which it occurs has not yet been fully characterized. Nevertheless, it is generally accepted that peroxisomes employ three proteins – Pex3, Pex19 and Pex16 in mammals – for the insertion of peroxisomal membrane proteins into the peroxisomal membrane. Structural biology approaches have been utilized for the elucidation of the mechanistic questions of peroxisome biogenesis, mainly by providing information on the architecture of the proteins significant for this process. This review aims to summarize, compare and put into perspective the structural knowledge that has been generated mainly for Pex3 and Pex19 and their interaction partners in recent years. This article is part of a Special Issue entitled: Peroxisomes edited by Ralf Erdmann. Structures of the PMP insertion factors Pex3 and Pex19 and their interactions with other protein ligands Structural insights provide a mechanistic understanding of the PMP functional network. Functional implications of structural order/disorder transitions
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Affiliation(s)
| | - Leonidas Emmanouilidis
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Center for Integrated Protein Science Munich (CIPSM) at Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Center for Integrated Protein Science Munich (CIPSM) at Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Gabriele Dodt
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Matthias Wilmanns
- EMBL Hamburg, c/o DESY, Building 25A, Notkestraße 85, 22603 Hamburg, Germany; University of Hamburg Clinical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany.
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45
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Schrader M, Costello JL, Godinho LF, Azadi AS, Islinger M. Proliferation and fission of peroxisomes - An update. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:971-83. [PMID: 26409486 DOI: 10.1016/j.bbamcr.2015.09.024] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/16/2015] [Accepted: 09/21/2015] [Indexed: 12/23/2022]
Abstract
In mammals, peroxisomes perform crucial functions in cellular metabolism, signalling and viral defense which are essential to the health and viability of the organism. In order to achieve this functional versatility peroxisomes dynamically respond to molecular cues triggered by changes in the cellular environment. Such changes elicit a corresponding response in peroxisomes, which manifests itself as a change in peroxisome number, altered enzyme levels and adaptations to the peroxisomal structure. In mammals the generation of new peroxisomes is a complex process which has clear analogies to mitochondria, with both sharing the same division machinery and undergoing a similar division process. How the regulation of this division process is integrated into the cell's response to different stimuli, the signalling pathways and factors involved, remains somewhat unclear. Here, we discuss the mechanism of peroxisomal fission, the contributions of the various division factors and examine the potential impact of post-translational modifications, such as phosphorylation, on the proliferation process. We also summarize the signalling process and highlight the most recent data linking signalling pathways with peroxisome proliferation.
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Affiliation(s)
- Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, EX4 4QJ, Exeter Devon, UK; Centre for Cell Biology, Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.
| | - Joseph L Costello
- College of Life and Environmental Sciences, Biosciences, University of Exeter, EX4 4QJ, Exeter Devon, UK
| | - Luis F Godinho
- Centre for Cell Biology, Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Afsoon S Azadi
- College of Life and Environmental Sciences, Biosciences, University of Exeter, EX4 4QJ, Exeter Devon, UK
| | - Markus Islinger
- Neuroanatomy, Center for Biomedicine and Medical Technology Mannheim, University of Heidelberg, 68167 Mannheim, Germany
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46
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Targeting and insertion of peroxisomal membrane proteins: ER trafficking versus direct delivery to peroxisomes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:870-80. [PMID: 26392202 DOI: 10.1016/j.bbamcr.2015.09.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/11/2015] [Accepted: 09/16/2015] [Indexed: 12/11/2022]
Abstract
The importance of peroxisomes is highlighted by severe inherited human disorders linked to impaired peroxisomal biogenesis. Besides the simple architecture of these ubiquitous and dynamic organelles, their biogenesis is surprisingly complex and involves specialized proteins, termed peroxins, which mediate targeting and insertion of peroxisomal membrane proteins (PMPs) into the peroxisomal bilayer, and the import of soluble proteins into the protein-dense matrix of the organelle. The long-standing paradigm that all peroxisomal proteins are imported directly into preexisting peroxisomes has been challenged by the detection of PMPs inside the endoplasmic reticulum (ER). New models propose that the ER originates peroxisomal biogenesis by mediating PMP trafficking to the peroxisomes via budding vesicles. However, the relative contribution of this ER-derived pathway to the total peroxisome population in vivo, and the detailed mechanisms of ER entry and exit of PMPs are controversially discussed. This review aims to summarize present knowledge about how PMPs are targeted to the ER, instead of being inserted directly into preexisting peroxisomes. Moreover, molecular mechanisms that facilitate bilayer insertion of PMPs among different species are discussed.
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47
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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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49
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Haimovich G, Cohen-Zontag O, Gerst JE. A role for mRNA trafficking and localized translation in peroxisome biogenesis and function? BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:911-21. [PMID: 26367800 DOI: 10.1016/j.bbamcr.2015.09.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/08/2015] [Accepted: 09/09/2015] [Indexed: 02/03/2023]
Abstract
Peroxisomes are distinct membrane-enclosed organelles involved in the β-oxidation of fatty acids and synthesis of ether phospholipids (e.g. plasmalogens), as well as cholesterol and its derivatives (e.g. bile acids). Peroxisomes comprise a distinct and highly segregated subset of cellular proteins, including those of the peroxisome membrane and the interior matrix, and while the mechanisms of protein import into peroxisomes have been extensively studied, they are not fully understood. Here we will examine the potential role of RNA trafficking and localized translation on protein import into peroxisomes and its role in peroxisome biogenesis and function. Given that RNAs encoding peroxisome biogenesis (PEX) and matrix proteins have been found in association with the endoplasmic reticulum and peroxisomes, it suggests that localized translation may play a significant role in the import pathways of these different peroxisomal constituents.
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Affiliation(s)
- Gal Haimovich
- Dept. of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Osnat Cohen-Zontag
- Dept. of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jeffrey E Gerst
- Dept. of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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50
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Mast FD, Rachubinski RA, Aitchison JD. Signaling dynamics and peroxisomes. Curr Opin Cell Biol 2015; 35:131-6. [PMID: 26042681 DOI: 10.1016/j.ceb.2015.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 05/09/2015] [Indexed: 02/08/2023]
Abstract
Peroxisomes are remarkably responsive organelles. Their composition, abundance and even their mechanism of biogenesis are influenced strongly by cell type and the environment. This plasticity underlies peroxisomal functions in metabolism and the detoxification of dangerous reactive oxygen species. However, peroxisomes are integrated into the cellular system as a whole such that they communicate intimately with other organelles, control signaling dynamics as in the case of innate immune responses to infectious disease, and contribute to processes as fundamental as longevity. The increasing evidence for peroxisomes having roles in various cellular and organismal functions, combined with their malleability, suggests complex mechanisms operate to control cellular dynamics and the specificity of cellular responses and functions extending well beyond the peroxisome itself. A deeper understanding of the functions of peroxisomes and the mechanisms that control their plasticity could offer opportunities for exploiting changes in peroxisome abundance to control cellular function.
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Affiliation(s)
- Fred D Mast
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, USA; Institute for Systems Biology, Seattle, USA
| | | | - John D Aitchison
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, USA; Institute for Systems Biology, Seattle, USA.
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