1
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Boutry M, DiGiovanni LF, Demers N, Fountain A, Mamand S, Botelho RJ, Kim PK. Arf1-PI4KIIIβ positive vesicles regulate PI(3)P signaling to facilitate lysosomal tubule fission. J Cell Biol 2023; 222:e202205128. [PMID: 37289133 PMCID: PMC10250553 DOI: 10.1083/jcb.202205128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 04/03/2023] [Accepted: 05/22/2023] [Indexed: 06/09/2023] Open
Abstract
Formation and fission of tubules from autolysosomes, endolysosomes, or phagolysosomes are required for lysosome reformation. However, the mechanisms governing these processes in these different lysosomal organelles are poorly understood. Thus, the role of phosphatidylinositol-4-phosphate (PI(4)P) is unclear as it was shown to promote the formation of tubules from phagolysosomes but was proposed to inhibit tubule formation on autolysosomes because the loss of PI4KIIIβ causes extensive lysosomal tubulation. Using super-resolution live-cell imaging, we show that Arf1-PI4KIIIβ positive vesicles are recruited to tubule fission sites from autolysosomes, endolysosomes, and phagolysosomes. Moreover, we show that PI(4)P is required to form autolysosomal tubules and that increased lysosomal tubulation caused by loss of PI4KIIIβ represents impaired tubule fission. At the site of fission, we propose that Arf1-PI4KIIIβ positive vesicles mediate a PI(3)P signal on lysosomes in a process requiring the lipid transfer protein SEC14L2. Our findings indicate that Arf1-PI4KIIIβ positive vesicles and their regulation of PI(3)P are critical components of the lysosomal tubule fission machinery.
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Affiliation(s)
- Maxime Boutry
- Cell Biology Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Laura F. DiGiovanni
- Cell Biology Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas Demers
- Cell Biology Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Aaron Fountain
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Ontario, Canada
- Graduate Program in Molecular Science, Toronto Metropolitan University, Toronto, Ontario, Canada
| | - Sami Mamand
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Ontario, Canada
- Graduate Program in Molecular Science, Toronto Metropolitan University, Toronto, Ontario, Canada
- Polytechnic Research Center, Erbil Polytechnic University, Erbil, Kurdistan, Iraq
| | - Roberto J. Botelho
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Ontario, Canada
- Graduate Program in Molecular Science, Toronto Metropolitan University, Toronto, Ontario, Canada
| | - Peter K. Kim
- Cell Biology Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, South Korea
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2
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Abstract
Peroxisomes are involved in a multitude of metabolic and catabolic pathways, as well as the innate immune system. Their dysfunction is linked to severe peroxisome-specific diseases, as well as cancer and neurodegenerative diseases. To ensure the ability of peroxisomes to fulfill their many roles in the organism, more than 100 different proteins are post-translationally imported into the peroxisomal membrane and matrix, and their functionality must be closely monitored. In this Review, we briefly discuss the import of peroxisomal membrane proteins, and we emphasize an updated view of both classical and alternative peroxisomal matrix protein import pathways. We highlight different quality control pathways that ensure the degradation of dysfunctional peroxisomal proteins. Finally, we compare peroxisomal matrix protein import with other systems that transport folded proteins across membranes, in particular the twin-arginine translocation (Tat) system and the nuclear pore.
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Affiliation(s)
- Markus Rudowitz
- Systems Biochemistry , Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Ralf Erdmann
- Systems Biochemistry , Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum, Germany
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3
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Bittner E, Stehlik T, Freitag J. Sharing the wealth: The versatility of proteins targeted to peroxisomes and other organelles. Front Cell Dev Biol 2022; 10:934331. [PMID: 36225313 PMCID: PMC9549241 DOI: 10.3389/fcell.2022.934331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Peroxisomes are eukaryotic organelles with critical functions in cellular energy and lipid metabolism. Depending on the organism, cell type, and developmental stage, they are involved in numerous other metabolic and regulatory pathways. Many peroxisomal functions require factors also relevant to other cellular compartments. Here, we review proteins shared by peroxisomes and at least one different site within the cell. We discuss the mechanisms to achieve dual targeting, their regulation, and functional consequences. Characterization of dual targeting is fundamental to understand how peroxisomes are integrated into the metabolic and regulatory circuits of eukaryotic cells.
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Affiliation(s)
| | | | - Johannes Freitag
- Department of Biology, Philipps-University Marburg, Marburg, Germany
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4
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Ueda K, Anderson-Baron MN, Haskins J, Hughes SC, Simmonds AJ. Recruitment of Peroxin14 to lipid droplets affects lipid storage in Drosophila. J Cell Sci 2022; 135:275042. [PMID: 35274690 DOI: 10.1242/jcs.259092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 02/20/2022] [Indexed: 10/18/2022] Open
Abstract
Both peroxisomes and lipid droplets regulate cellular lipid homeostasis. Direct inter-organellar contacts as well as novel roles for proteins associated with peroxisome or lipid droplets occur when cells are induced to liberate fatty acids from lipid droplets. We have shown a non-canonical role for as subset of peroxisome-assembly (Peroxin) proteins in this process. Transmembrane proteins Peroxin3, Peroxin13 and Peroxin14 surround newly formed lipid droplets. Trafficking of Peroxin14 to lipid droplets was enhanced by loss of Peroxin19, which directs insertion of transmembrane proteins like Peroxin14 into the peroxisome bilayer membrane. Accumulation of Peroxin14 around lipid droplets did not induce changes to peroxisome size or number, nor was co-recruitment of the remaining Peroxins needed to assemble peroxisomes observed. Increasing the relative level of Peroxin14 surrounding lipid droplets affected recruitment of Hsl lipase. Fat-body specific reduction of these lipid droplet-associated Peroxins causes a unique effect on larval fat body development and affected their survival on lipid-enriched or minimal diets.
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Affiliation(s)
- Kazuki Ueda
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta. Edmonton, AB T6G 2H7, Canada
| | - Matthew N Anderson-Baron
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta. Edmonton, AB T6G 2H7, Canada.,Future Fields, 11130 105 Ave NW, Edmonton, AB T5H 0L5, Canada
| | - Julie Haskins
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta. Edmonton, AB T6G 2H7, Canada
| | - Sarah C Hughes
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta. Edmonton, AB T6G 2H7, Canada.,Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta. Edmonton, AB T6G 2H7, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta. Edmonton, AB T6G 2H7, Canada
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5
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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: 24] [Impact Index Per Article: 8.0] [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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6
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Hao Z, Li Z, Huo J, Li J, Liu F, Yin P. Effects of Chinese wolfberry and Astragalus extract on the antioxidant capacity of Tibetan pig liver. PLoS One 2021; 16:e0245749. [PMID: 33503027 PMCID: PMC7840052 DOI: 10.1371/journal.pone.0245749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/07/2021] [Indexed: 11/19/2022] Open
Abstract
The objective of this study is to determine the effect of Chinese wolfberry (Lycium barbarum) and Astragalus (Astragalus membranaceus) extract (WAE) on the antioxidant capacity of Tibetan pig liver, and discussed the regulatory effect of WAE on the liver antioxidant mechanism. Twelve healthy 120-day-old Tibetan black pigs (35±2 kg) were divided randomly into two groups. The WAE group was fed a basal diet supplemented with 1% WAE for 90 days. The control group was fed the same diet, but without the WAE. We found that liver superoxide dismutase 1 (SOD1) activity (P<0.05), total antioxidative capacity (T-AOC) (P<0.05), and catalase (CAT) activity (P<0.01) significantly increased in the WAE group compared with the control group; malondialdehyde (MDA) content decreased, but this was not significant (P >0.05). Transcriptome sequencing analysis detected 106 differentially expressed genes (DEGs) related to oxidative stress. GO enrichment analysis showed these DEGs were involved in the positive regulation of reactive oxygen metabolism and biosynthesis, process regulation, and regulation of the oxidative stress response. KEGG Pathway enrichment analysis showed they were enriched in the PI3K-Akt, AMPK, Rap1, and peroxisome signaling pathways. The expression levels of key peroxisome biosynthesis genes (e.g., PEX3 and PEX11B) and key antioxidant genes (e.g., CAT and SOD1) were significantly higher in the WAE group than in the control group. The PRDX1 and PRDX5 content also was significantly higher in the WAE group. This study showed that the WAE regulated the antioxidant and anti-stress ability of Tibetan pig liver through a "peroxisome antioxidant-oxidant stress" signaling pathway.
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Affiliation(s)
- Zhuang Hao
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Zhen Li
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Jinjin Huo
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Jiandong Li
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Fenghua Liu
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Peng Yin
- Institute of Microbiology Chinese Academy of Sciences, Beijing, China
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7
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Jiang H. Quality control pathways of tail-anchored proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118922. [PMID: 33285177 DOI: 10.1016/j.bbamcr.2020.118922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/14/2020] [Accepted: 12/01/2020] [Indexed: 12/20/2022]
Abstract
Tail-anchored (TA) proteins have an N-terminal domain in the cytosol and a C-terminal transmembrane domain anchored to a variety of organelle membranes. TA proteins are recognized by targeting factors at the transmembrane domain and C-terminal sequence and are guided to distinct membranes. The promiscuity of targeting sequences and the dysfunction of targeting pathways cause mistargeting of TA proteins. TA proteins are under surveillance by quality control pathways. For resident TA proteins at mitochondrial and ER membranes, intrinsic instability or stimuli induced degrons of the cytosolic and transmembrane domains are sensed by quality control factors to initiate degradation of TA proteins. These pathways are summarized as TA protein degradation-Cytosol (TAD-C) and TAD-Membrane (TAD-M) pathways. For mistargeted and a subset of solitary TA proteins at mitochondrial and peroxisomal membranes, a unique pathway has been revealed in recent years. Msp1/ATAD1 is an AAA-ATPase dually-localized to mitochondrial and peroxisomal membranes. It directly recognizes mistargeted and solitary TA proteins and dislocates them out of membrane. Dislocated substrates are subsequently ubiquitinated by the ER-resident Doa10 ubiquitin E3 ligase complex for degradation. We summarize and discuss the substrate recognition, dislocation and degradation mechanisms of the Msp1 pathway.
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Affiliation(s)
- Hui Jiang
- National Institute of Biological Sciences, Beijing 102206, China; Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100871, China.
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8
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Shen S, Faouzi S, Souquere S, Roy S, Routier E, Libenciuc C, André F, Pierron G, Scoazec JY, Robert C. Melanoma Persister Cells Are Tolerant to BRAF/MEK Inhibitors via ACOX1-Mediated Fatty Acid Oxidation. Cell Rep 2020; 33:108421. [DOI: 10.1016/j.celrep.2020.108421] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 07/10/2020] [Accepted: 11/01/2020] [Indexed: 12/21/2022] Open
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9
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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: 17] [Impact Index Per Article: 4.3] [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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10
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Baune MC, Lansing H, Fischer K, Meyer T, Charton L, Linka N, von Schaewen A. The Arabidopsis Plastidial Glucose-6-Phosphate Transporter GPT1 is Dually Targeted to Peroxisomes via the Endoplasmic Reticulum. THE PLANT CELL 2020; 32:1703-1726. [PMID: 32111666 PMCID: PMC7203913 DOI: 10.1105/tpc.19.00959] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/28/2020] [Accepted: 02/28/2020] [Indexed: 05/22/2023]
Abstract
Studies on Glucose-6-phosphate (G6P)/phosphate translocator isoforms GPT1 and GPT2 reported the viability of Arabidopsis (Arabidopsis thaliana) gpt2 mutants, whereas heterozygous gpt1 mutants exhibited a variety of defects during fertilization/seed set, indicating that GPT1 is essential for this process. Among other functions, GPT1 was shown to be important for pollen and embryo-sac development. Because our previous work on the irreversible part of the oxidative pentose phosphate pathway (OPPP) revealed comparable effects, we investigated whether GPT1 may dually localize to plastids and peroxisomes. In reporter fusions, GPT2 localized to plastids, but GPT1 also localized to the endoplasmic reticulum (ER) and around peroxisomes. GPT1 contacted two oxidoreductases and also peroxins that mediate import of peroxisomal membrane proteins from the ER, hinting at dual localization. Reconstitution in yeast (Saccharomyces cerevisiae) proteoliposomes revealed that GPT1 preferentially exchanges G6P for ribulose-5-phosphate (Ru5P). Complementation analyses of heterozygous +/gpt1 plants demonstrated that GPT2 is unable to compensate for GPT1 in plastids, whereas GPT1 without the transit peptide (enforcing ER/peroxisomal localization) increased gpt1 transmission significantly. Because OPPP activity in peroxisomes is essential for fertilization, and immunoblot analyses hinted at the presence of unprocessed GPT1-specific bands, our findings suggest that GPT1 is indispensable in both plastids and peroxisomes. Together with its G6P-Ru5P exchange preference, GPT1 appears to play a role distinct from that of GPT2 due to dual targeting.
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Affiliation(s)
- Marie-Christin Baune
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Hannes Lansing
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Kerstin Fischer
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Tanja Meyer
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Lennart Charton
- Biochemie der Pflanzen, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Nicole Linka
- Biochemie der Pflanzen, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Antje von Schaewen
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
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11
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A Global Analysis of Enzyme Compartmentalization to Glycosomes. Pathogens 2020; 9:pathogens9040281. [PMID: 32290588 PMCID: PMC7237986 DOI: 10.3390/pathogens9040281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 12/28/2022] Open
Abstract
In kinetoplastids, the first seven steps of glycolysis are compartmentalized into a glycosome along with parts of other metabolic pathways. This organelle shares a common ancestor with the better-understood eukaryotic peroxisome. Much of our understanding of the emergence, evolution, and maintenance of glycosomes is limited to explorations of the dixenous parasites, including the enzymatic contents of the organelle. Our objective was to determine the extent that we could leverage existing studies in model kinetoplastids to determine the composition of glycosomes in species lacking evidence of experimental localization. These include diverse monoxenous species and dixenous species with very different hosts. For many of these, genome or transcriptome sequences are available. Our approach initiated with a meta-analysis of existing studies to generate a subset of enzymes with highest evidence of glycosome localization. From this dataset we extracted the best possible glycosome signal peptide identification scheme for in silico identification of glycosomal proteins from any kinetoplastid species. Validation suggested that a high glycosome localization score from our algorithm would be indicative of a glycosomal protein. We found that while metabolic pathways were consistently represented across kinetoplastids, individual proteins within those pathways may not universally exhibit evidence of glycosome localization.
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12
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Burkhart SE, Llinas RJ, Bartel B. PEX16 contributions to peroxisome import and metabolism revealed by viable Arabidopsis pex16 mutants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:853-870. [PMID: 30761735 PMCID: PMC6613983 DOI: 10.1111/jipb.12789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/10/2019] [Indexed: 06/09/2023]
Abstract
Peroxisomes rely on peroxins (PEX proteins) for biogenesis, importing membrane and matrix proteins, and fission. PEX16, which is implicated in peroxisomal membrane protein targeting and forming nascent peroxisomes from the endoplasmic reticulum (ER), is unusual among peroxins because it is inserted co-translationally into the ER and localizes to both ER and peroxisomal membranes. PEX16 mutations in humans, yeast, and plants confer some common peroxisomal defects; however, apparent functional differences have impeded the development of a unified model for PEX16 action. The only reported pex16 mutant in plants, the Arabidopsis shrunken seed1 mutant, is inviable, complicating analysis of PEX16 function after embryogenesis. Here, we characterized two viable Arabidopsis pex16 alleles that accumulate negligible PEX16 protein levels. Both mutants displayed impaired peroxisome function - slowed consumption of stored oil bodies, decreased import of matrix proteins, and increased peroxisome size. Moreover, one pex16 allele exhibited reduced growth that could be alleviated by an external fixed carbon source, decreased responsiveness to peroxisomally processed hormone precursors, and worsened or improved peroxisome function in combination with other pex mutants. Because the mutations impact different regions of the PEX16 gene, these viable pex16 alleles allow assessment of the importance of Arabidopsis PEX16 and its functional domains.
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13
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Abstract
Peroxisomes are considered to form either by growth and division of existing peroxisomes or de novo from the endoplasmic reticulum. A recent study now demonstrates that mitochondria-derived vesicles are also required for de novo peroxisome biogenesis.
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Affiliation(s)
- Peter Kim
- Cell Biology Program, The Hospital for Sick Children, Department of Biochemistry, University of Toronto, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Rm. 19.9708, Toronto, ON M5G 0A4, Canada.
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14
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Schrul B, Schliebs W. Intracellular communication between lipid droplets and peroxisomes: the Janus face of PEX19. Biol Chem 2019; 399:741-749. [PMID: 29500918 DOI: 10.1515/hsz-2018-0125] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 02/23/2018] [Indexed: 02/06/2023]
Abstract
In order to adapt to environmental changes, such as nutrient availability, cells have to orchestrate multiple metabolic pathways, which are catalyzed in distinct specialized organelles. Lipid droplets (LDs) and peroxisomes are both endoplasmic reticulum (ER)-derived organelles that fulfill complementary functions in lipid metabolism: Upon nutrient supply, LDs store metabolic energy in the form of neutral lipids and, when energy is needed, supply fatty acids for oxidation in peroxisomes and mitochondria. How these organelles communicate with each other for a concerted metabolic output remains a central question. Here, we summarize recent insights into the biogenesis and function of LDs and peroxisomes with emphasis on the role of PEX19 in these processes.
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Affiliation(s)
- Bianca Schrul
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Faculty of Medicine, Saarland University, Kirrberger Str. 100, D-66421 Homburg/Saar, Germany
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr University Bochum, D-44780 Bochum, Germany
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15
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Park H, He A, Tan M, Johnson JM, Dean JM, Pietka TA, Chen Y, Zhang X, Hsu FF, Razani B, Funai K, Lodhi IJ. Peroxisome-derived lipids regulate adipose thermogenesis by mediating cold-induced mitochondrial fission. J Clin Invest 2019; 129:694-711. [PMID: 30511960 PMCID: PMC6355224 DOI: 10.1172/jci120606] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 11/20/2018] [Indexed: 12/27/2022] Open
Abstract
Peroxisomes perform essential functions in lipid metabolism, including fatty acid oxidation and plasmalogen synthesis. Here, we describe a role for peroxisomal lipid metabolism in mitochondrial dynamics in brown and beige adipocytes. Adipose tissue peroxisomal biogenesis was induced in response to cold exposure through activation of the thermogenic coregulator PRDM16. Adipose-specific knockout of the peroxisomal biogenesis factor Pex16 (Pex16-AKO) in mice impaired cold tolerance, decreased energy expenditure, and increased diet-induced obesity. Pex16 deficiency blocked cold-induced mitochondrial fission, decreased mitochondrial copy number, and caused mitochondrial dysfunction. Adipose-specific knockout of the peroxisomal β-oxidation enzyme acyl-CoA oxidase 1 (Acox1-AKO) was not sufficient to affect adiposity, thermogenesis, or mitochondrial copy number, but knockdown of the plasmalogen synthetic enzyme glyceronephosphate O-acyltransferase (GNPAT) recapitulated the effects of Pex16 inactivation on mitochondrial morphology and function. Plasmalogens are present in mitochondria and decreased with Pex16 inactivation. Dietary supplementation with plasmalogens increased mitochondrial copy number, improved mitochondrial function, and rescued thermogenesis in Pex16-AKO mice. These findings support a surprising interaction between peroxisomes and mitochondria regulating mitochondrial dynamics and thermogenesis.
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Affiliation(s)
- Hongsuk Park
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Anyuan He
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Min Tan
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Jordan M. Johnson
- Diabetes & Metabolism Research Center, University of Utah, Salt Lake City, Utah, USA
| | - John M. Dean
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | | | - Yali Chen
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Xiangyu Zhang
- Cardiology Division, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Fong-Fu Hsu
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Babak Razani
- Cardiology Division, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Veterans Affairs St. Louis Healthcare System, John Cochran Division, St. Louis, Missouri, USA
| | - Katsuhiko Funai
- Diabetes & Metabolism Research Center, University of Utah, Salt Lake City, Utah, USA
| | - Irfan J. Lodhi
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
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16
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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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17
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Farré JC, Mahalingam SS, Proietto M, Subramani S. Peroxisome biogenesis, membrane contact sites, and quality control. EMBO Rep 2018; 20:embr.201846864. [PMID: 30530632 DOI: 10.15252/embr.201846864] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 10/08/2018] [Accepted: 11/16/2018] [Indexed: 12/19/2022] Open
Abstract
Peroxisomes are conserved organelles of eukaryotic cells with important roles in cellular metabolism, human health, redox homeostasis, as well as intracellular metabolite transfer and signaling. We review here the current status of the different co-existing modes of biogenesis of peroxisomal membrane proteins demonstrating the fascinating adaptability in their targeting and sorting pathways. While earlier studies focused on peroxisomes as autonomous organelles, the necessity of the ER and potentially even mitochondria as sources of peroxisomal membrane proteins and lipids has come to light in recent years. Additionally, the intimate physical juxtaposition of peroxisomes with other organelles has transitioned from being viewed as random encounters to a growing appreciation of the expanding roles of such inter-organellar membrane contact sites in metabolic and regulatory functions. Peroxisomal quality control mechanisms have also come of age with a variety of mechanisms operating both during biogenesis and in the cellular response to environmental cues.
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Affiliation(s)
- Jean-Claude Farré
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, CA, USA
| | - Shanmuga S Mahalingam
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, CA, USA
| | - Marco Proietto
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, CA, USA
| | - Suresh Subramani
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, CA, USA
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18
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Peroxisomes and cancer: The role of a metabolic specialist in a disease of aberrant metabolism. Biochim Biophys Acta Rev Cancer 2018; 1870:103-121. [PMID: 30012421 DOI: 10.1016/j.bbcan.2018.07.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/30/2018] [Accepted: 07/10/2018] [Indexed: 01/02/2023]
Abstract
Cancer is irrevocably linked to aberrant metabolic processes. While once considered a vestigial organelle, we now know that peroxisomes play a central role in the metabolism of reactive oxygen species, bile acids, ether phospholipids (e.g. plasmalogens), very-long chain, and branched-chain fatty acids. Immune system evasion is a hallmark of cancer, and peroxisomes have an emerging role in the regulation of cellular immune responses. Investigations of individual peroxisome proteins and metabolites support their pro-tumorigenic functions. However, a significant knowledge gap remains regarding how individual functions of proteins and metabolites of the peroxisome orchestrate its potential role as a pro-tumorigenic organelle. This review highlights new advances in our understanding of biogenesis, enzymatic functions, and autophagic degradation of peroxisomes (pexophagy), and provides evidence linking these activities to tumorigenesis. Finally, we propose avenues that may be exploited to target peroxisome-related processes as a mode of combatting cancer.
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19
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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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20
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Kunze M. Predicting Peroxisomal Targeting Signals to Elucidate the Peroxisomal Proteome of Mammals. Subcell Biochem 2018; 89:157-199. [PMID: 30378023 DOI: 10.1007/978-981-13-2233-4_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peroxisomes harbor a plethora of proteins, but the peroxisomal proteome as the entirety of all peroxisomal proteins is still unknown for mammalian species. Computational algorithms can be used to predict the subcellular localization of proteins based on their amino acid sequence and this method has been amply used to forecast the intracellular fate of individual proteins. However, when applying such algorithms systematically to all proteins of an organism the prediction of its peroxisomal proteome in silico should be possible. Therefore, a reliable detection of peroxisomal targeting signals (PTS ) acting as postal codes for the intracellular distribution of the encoding protein is crucial. Peroxisomal proteins can utilize different routes to reach their destination depending on the type of PTS. Accordingly, independent prediction algorithms have been developed for each type of PTS, but only those for type-1 motifs (PTS1) have so far reached a satisfying predictive performance. This is partially due to the low number of peroxisomal proteins limiting the power of statistical analyses and partially due to specific properties of peroxisomal protein import, which render functional PTS motifs inactive in specific contexts. Moreover, the prediction of the peroxisomal proteome is limited by the high number of proteins encoded in mammalian genomes, which causes numerous false positive predictions even when using reliable algorithms and buries the few yet unidentified peroxisomal proteins. Thus, the application of prediction algorithms to identify all peroxisomal proteins is currently ineffective as stand-alone method, but can display its full potential when combined with other methods.
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Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
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21
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Abstract
Plant peroxisomes are required for a number of fundamental physiological processes, such as primary and secondary metabolism, development and stress response. Indexing the dynamic peroxisome proteome is prerequisite to fully understanding the importance of these organelles. Mass Spectrometry (MS)-based proteome analysis has allowed the identification of novel peroxisomal proteins and pathways in a relatively high-throughput fashion and significantly expanded the list of proteins and biochemical reactions in plant peroxisomes. In this chapter, we summarize the experimental proteomic studies performed in plants, compile a list of ~200 confirmed Arabidopsis peroxisomal proteins, and discuss the diverse plant peroxisome functions with an emphasis on the role of Arabidopsis MS-based proteomics in discovering new peroxisome functions. Many plant peroxisome proteins and biochemical pathways are specific to plants, substantiating the complexity, plasticity and uniqueness of plant peroxisomes. Mapping the full plant peroxisome proteome will provide a knowledge base for the improvement of crop production, quality and stress tolerance.
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Affiliation(s)
- Ronghui Pan
- MSU-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Jianping Hu
- MSU-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA.
- Plant Biology Department, Michigan State University, East Lansing, MI, 48824, USA.
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22
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Using Pull Down Strategies to Analyze the Interactome of Peroxisomal Membrane Proteins in Human Cells. Subcell Biochem 2018; 89:261-285. [PMID: 30378027 DOI: 10.1007/978-981-13-2233-4_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Different pull-down strategies were successfully applied to gain novel insight into the interactome of human membrane-associated proteins. Here, we compare the outcome, efficiency and potential of pull-down strategies applied to human peroxisomal membrane proteins. Stable membrane-bound protein complexes can be affinity-purified from genetically engineered human cells or subfractions thereof after detergent solubilization, followed by size exclusion chromatography and analysis by mass spectrometry (MS). As exemplified for Protein A-tagged human PEX14, one of the central constituents of the peroxisomal matrix protein import machinery, MS analyses of the affinity-purified complexes revealed an unexpected association of PEX14 with other protein assemblies like the microtubular network or the insertion apparatus for peroxisomal membrane proteins comprising PEX3, PEX16 and PEX19. The latter association was recently supported by using a different pull-down strategy following in vivo proximity labeling with biotin, named BioID, which enabled the identification of various membrane proteins in close proximity of PEX16 in living cells.
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23
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Stefan CJ, Trimble WS, Grinstein S, Drin G, Reinisch K, De Camilli P, Cohen S, Valm AM, Lippincott-Schwartz J, Levine TP, Iaea DB, Maxfield FR, Futter CE, Eden ER, Judith D, van Vliet AR, Agostinis P, Tooze SA, Sugiura A, McBride HM. Membrane dynamics and organelle biogenesis-lipid pipelines and vesicular carriers. BMC Biol 2017; 15:102. [PMID: 29089042 PMCID: PMC5663033 DOI: 10.1186/s12915-017-0432-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Discoveries spanning several decades have pointed to vital membrane lipid trafficking pathways involving both vesicular and non-vesicular carriers. But the relative contributions for distinct membrane delivery pathways in cell growth and organelle biogenesis continue to be a puzzle. This is because lipids flow from many sources and across many paths via transport vesicles, non-vesicular transfer proteins, and dynamic interactions between organelles at membrane contact sites. This forum presents our latest understanding, appreciation, and queries regarding the lipid transport mechanisms necessary to drive membrane expansion during organelle biogenesis and cell growth.
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Affiliation(s)
- Christopher J. Stefan
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London, WC1E 6BT UK
| | - William S. Trimble
- Cell Biology Program, The Hospital for Sick Children and Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Sergio Grinstein
- Cell Biology Program, The Hospital for Sick Children and Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Guillaume Drin
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Karin Reinisch
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520 USA
| | - Pietro De Camilli
- Department of Neuroscience and Cell Biology, Howard Hughes Medical Institute, Kavli Institute for Neuroscience and Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT 06510 USA
| | | | | | | | - Tim P. Levine
- UCL Institute of Ophthalmology, 11-43 Bath Street, London, EC1V 9EL UK
| | - David B. Iaea
- Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Frederick R. Maxfield
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Ave, New York, NY 10065 USA
| | - Clare E. Futter
- UCL Institute of Ophthalmology, 11-43 Bath Street, London, EC1V 9EL UK
| | - Emily R. Eden
- UCL Institute of Ophthalmology, 11-43 Bath Street, London, EC1V 9EL UK
| | - Delphine Judith
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London, UK
| | - Alexander R. van Vliet
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London, UK
- Laboratory of Cell Death Research and Therapy, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Patrizia Agostinis
- Laboratory of Cell Death Research and Therapy, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Sharon A. Tooze
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London, UK
| | - Ayumu Sugiura
- Kobe University Graduate School of Medicine, 1-5-6 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047 Japan
| | - Heidi M. McBride
- Montreal Neurological Institute, McGill University, 3801 University Avenue, Montreal, Quebec H3A 2B4 Canada
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24
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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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25
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Newly born peroxisomes are a hybrid of mitochondrial and ER-derived pre-peroxisomes. Nature 2017; 542:251-254. [PMID: 28146471 DOI: 10.1038/nature21375] [Citation(s) in RCA: 271] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 01/10/2017] [Indexed: 01/24/2023]
Abstract
Peroxisomes function together with mitochondria in a number of essential biochemical pathways, from bile acid synthesis to fatty acid oxidation. Peroxisomes grow and divide from pre-existing organelles, but can also emerge de novo in the cell. The physiological regulation of de novo peroxisome biogenesis remains unclear, and it is thought that peroxisomes emerge from the endoplasmic reticulum in both mammalian and yeast cells. However, in contrast to the yeast system, a number of integral peroxisomal membrane proteins are imported into mitochondria in mammalian cells in the absence of peroxisomes, including Pex3, Pex12, Pex13, Pex14, Pex26, PMP34 and ALDP. Overall, the mitochondrial localization of peroxisomal membrane proteins in mammalian cells has largely been considered a mis-targeting artefact in which de novo biogenesis occurs exclusively from endoplasmic reticulum-targeted peroxins. Here, in following the generation of new peroxisomes within human patient fibroblasts lacking peroxisomes, we show that the essential import receptors Pex3 and Pex14 target mitochondria, where they are selectively released into vesicular pre-peroxisomal structures. Maturation of pre-peroxisomes containing Pex3 and Pex14 requires fusion with endoplasmic reticulum-derived vesicles carrying Pex16, thereby providing full import competence. These findings demonstrate the hybrid nature of newly born peroxisomes, expanding their functional links to mitochondria.
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26
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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: 187] [Impact Index Per Article: 26.7] [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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27
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Buentzel J, Thoms S. The Use of Glycosylation Tags as Reporters for Protein Entry into the Endoplasmic Reticulum in Yeast and Mammalian Cells. Methods Mol Biol 2017; 1595:221-232. [PMID: 28409466 DOI: 10.1007/978-1-4939-6937-1_21] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
N-glycosylation is a process occurring in the Endoplasmic Reticulum (ER) in nearly every organism. Proteins containing a glycosylation site are quickly glycosylated by oligosaccharyltransferases once the glycosylation site is exposed to the ER lumen. The oligosaccharide tree is then modified and proteins are targeted to specific organelles or subcompartments. For a long time peroxisomal membrane proteins (PMP) were thought to be targeted directly to the peroxisome. However, in the course of recent years, several PMPs were found to be targeted via the ER. Glycosylation increases the molecular weight of a protein, which is easily detected by Western blotting. Glycosylation tags like the opsin tag are therefore useful tools in the study of ER entry of peroxisomal proteins.
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Affiliation(s)
- Judith Buentzel
- Department of Pediatrics and Adolescent Health, University Medical Center, University of Goettingen, Robert-Koch-Str. 40, 37075, Goettingen, Germany
| | - Sven Thoms
- Department of Pediatrics and Adolescent Health, University Medical Center, University of Goettingen, Robert-Koch-Str. 40, 37075, Goettingen, Germany.
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28
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Yonemura Y, Li X, Müller K, Krämer A, Atigbire P, Mentrup T, Feuerhake T, Kroll T, Shomron O, Nohl R, Arndt HD, Hoischen C, Hemmerich P, Hirschberg K, Kaether C. Inhibition of cargo export at ER exit sites and the trans-Golgi network by the secretion inhibitor FLI-06. J Cell Sci 2016; 129:3868-3877. [PMID: 27587840 DOI: 10.1242/jcs.186163] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 08/25/2016] [Indexed: 12/21/2022] Open
Abstract
Export out of the endoplasmic reticulum (ER) involves the Sar1 and COPII machinery acting at ER exit sites (ERES). Whether and how cargo proteins are recruited upstream of Sar1 and COPII is unclear. Two models are conceivable, a recruitment model where cargo is actively transported through a transport factor and handed over to the Sar1 and COPII machinery in ERES, and a capture model, where cargo freely diffuses into ERES where it is captured by the Sar1 and COPII machinery. Using the novel secretion inhibitor FLI-06, we show that recruitment of the cargo VSVG to ERES is an active process upstream of Sar1 and COPII. Applying FLI-06 before concentration of VSVG in ERES completely abolishes its recruitment. In contrast, applying FLI-06 after VSVG concentration in ERES does not lead to dispersal of the concentrated VSVG, arguing that it inhibits recruitment to ERES as opposed to capture in ERES. FLI-06 also inhibits export out of the trans-Golgi network (TGN), suggesting that similar mechanisms might orchestrate cargo selection and concentration at the ER and TGN. FLI-06 does not inhibit autophagosome biogenesis and the ER-peroxisomal transport route, suggesting that these rely on different mechanisms.
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Affiliation(s)
- Yoji Yonemura
- Leibniz Institut für Alternsforschung-Fritz Lipmann Institut, Jena 07745, Germany
| | - Xiaolin Li
- Leibniz Institut für Alternsforschung-Fritz Lipmann Institut, Jena 07745, Germany
| | - Katja Müller
- Leibniz Institut für Alternsforschung-Fritz Lipmann Institut, Jena 07745, Germany
| | - Andreas Krämer
- Leibniz Institut für Alternsforschung-Fritz Lipmann Institut, Jena 07745, Germany
| | - Paul Atigbire
- Leibniz Institut für Alternsforschung-Fritz Lipmann Institut, Jena 07745, Germany
| | - Torben Mentrup
- Leibniz Institut für Alternsforschung-Fritz Lipmann Institut, Jena 07745, Germany
| | - Talitha Feuerhake
- Leibniz Institut für Alternsforschung-Fritz Lipmann Institut, Jena 07745, Germany
| | - Torsten Kroll
- Leibniz Institut für Alternsforschung-Fritz Lipmann Institut, Jena 07745, Germany
| | - Olga Shomron
- Pathology Department, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Richard Nohl
- Lehrstuhl für organische Chemie I, Friedrich-Schiller Universität, Jena 07743, Germany
| | - Hans-Dieter Arndt
- Lehrstuhl für organische Chemie I, Friedrich-Schiller Universität, Jena 07743, Germany
| | - Christian Hoischen
- Leibniz Institut für Alternsforschung-Fritz Lipmann Institut, Jena 07745, Germany
| | - Peter Hemmerich
- Leibniz Institut für Alternsforschung-Fritz Lipmann Institut, Jena 07745, Germany
| | - Koret Hirschberg
- Pathology Department, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Christoph Kaether
- Leibniz Institut für Alternsforschung-Fritz Lipmann Institut, Jena 07745, Germany
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Peroxin-dependent targeting of a lipid-droplet-destined membrane protein to ER subdomains. Nat Cell Biol 2016; 18:740-51. [PMID: 27295553 PMCID: PMC4925261 DOI: 10.1038/ncb3373] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 05/11/2016] [Indexed: 12/23/2022]
Abstract
Lipid droplets (LDs) are endoplasmic reticulum (ER)-derived lipid storage organelles uniquely encapsulated by phospholipid monolayers. LD membrane proteins are embedded into the monolayer in a monotopic hairpin-topology and therefore likely have requirements for their biogenesis distinct from those inserting as bitopic and polytopic proteins into phospholipid bilayers. UBXD8 belongs to a subfamily of hairpin-proteins that localize to both the ER and LDs, and are initially inserted into the cytoplasmic leaflet of the ER bilayer before partitioning to the LD monolayer. The molecular machinery responsible for inserting hairpin-proteins into membranes, however, is unknown. Here, we report that newly synthesized UBXD8 is posttranslationally inserted into discrete ER-subdomains by a mechanism requiring cytosolic PEX19 and membrane-integrated PEX3, proteins hitherto exclusively implicated in peroxisome biogenesis. Farnesylation of PEX19 uncouples ER/LD- and peroxisome targeting, expanding the function of this peroxin to an ER targeting pathway and suggesting a coordinated biogenesis of LDs and peroxisomes.
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30
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Hua R, Kim PK. Multiple paths to peroxisomes: Mechanism of peroxisome maintenance in mammals. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:881-91. [DOI: 10.1016/j.bbamcr.2015.09.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 09/18/2015] [Accepted: 09/21/2015] [Indexed: 12/19/2022]
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31
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Agrawal G, Subramani S. De novo peroxisome biogenesis: Evolving concepts and conundrums. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1863:892-901. [PMID: 26381541 PMCID: PMC4791208 DOI: 10.1016/j.bbamcr.2015.09.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 09/10/2015] [Accepted: 09/11/2015] [Indexed: 10/23/2022]
Abstract
Peroxisomes proliferate by growth and division of pre-existing peroxisomes or could arise de novo. Though the de novo pathway of peroxisome biogenesis is a more recent discovery, several studies have highlighted key mechanistic details of the pathway. The endoplasmic reticulum (ER) is the primary source of lipids and proteins for the newly-formed peroxisomes. More recently, an intricate sorting process functioning at the ER has been proposed, that segregates specific PMPs first to peroxisome-specific ER domains (pER) and then assembles PMPs selectively into distinct pre-peroxisomal vesicles (ppVs) that later fuse to form import-competent peroxisomes. In addition, plausible roles of the three key peroxins Pex3, Pex16 and Pex19, which are also central to the growth and division pathway, have been suggested in the de novo process. In this review, we discuss key developments and highlight the unexplored avenues in de novo peroxisome biogenesis.
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Affiliation(s)
- Gaurav Agrawal
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, UC San Diego, La Jolla, CA 92093-0322, USA
| | - Suresh Subramani
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, UC San Diego, La Jolla, CA 92093-0322, USA.
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32
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How peroxisomes partition between cells. A story of yeast, mammals and filamentous fungi. Curr Opin Cell Biol 2016; 41:73-80. [PMID: 27128775 DOI: 10.1016/j.ceb.2016.04.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/07/2016] [Accepted: 04/11/2016] [Indexed: 11/21/2022]
Abstract
Eukaryotic cells are subcompartmentalized into discrete, membrane-enclosed organelles. These organelles must be preserved in cells over many generations to maintain the selective advantages afforded by compartmentalization. Cells use complex molecular mechanisms of organelle inheritance to achieve high accuracy in the sharing of organelles between daughter cells. Here we focus on how a multi-copy organelle, the peroxisome, is partitioned in yeast, mammalian cells, and filamentous fungi, which differ in their mode of cell division. Cells achieve equidistribution of their peroxisomes through organelle transport and retention processes that act coordinately, although the strategies employed vary considerably by organism. Nevertheless, we propose that mechanisms common across species apply to the partitioning of all membrane-enclosed organelles.
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33
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Sibirny AA. Yeast peroxisomes: structure, functions and biotechnological opportunities. FEMS Yeast Res 2016; 16:fow038. [DOI: 10.1093/femsyr/fow038] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2016] [Indexed: 01/02/2023] Open
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34
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Motley AM, Galvin PC, Ekal L, Nuttall JM, Hettema EH. Reevaluation of the role of Pex1 and dynamin-related proteins in peroxisome membrane biogenesis. J Cell Biol 2016; 211:1041-56. [PMID: 26644516 PMCID: PMC4674274 DOI: 10.1083/jcb.201412066] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Analysis of Pex1 and dynamin-related protein function indicates peroxisomes multiply mainly by growth and division in Saccharomyces cerevisiae, whereas no evidence was found for the previously proposed role for Pex1 in peroxisome formation by fusion of ER-derived preperoxisomal vesicles. A recent model for peroxisome biogenesis postulates that peroxisomes form de novo continuously in wild-type cells by heterotypic fusion of endoplasmic reticulum–derived vesicles containing distinct sets of peroxisomal membrane proteins. This model proposes a role in vesicle fusion for the Pex1/Pex6 complex, which has an established role in matrix protein import. The growth and division model proposes that peroxisomes derive from existing peroxisomes. We tested these models by reexamining the role of Pex1/Pex6 and dynamin-related proteins in peroxisome biogenesis. We found that induced depletion of Pex1 blocks the import of matrix proteins but does not affect membrane protein delivery to peroxisomes; markers for the previously reported distinct vesicles colocalize in pex1 and pex6 cells; peroxisomes undergo continued growth if fission is blocked. Our data are compatible with the established primary role of the Pex1/Pex6 complex in matrix protein import and show that peroxisomes in Saccharomyces cerevisiae multiply mainly by growth and division.
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Affiliation(s)
- Alison M Motley
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, England, UK
| | - Paul C Galvin
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, England, UK
| | - Lakhan Ekal
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, England, UK
| | - James M Nuttall
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, England, UK
| | - Ewald H Hettema
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, England, UK
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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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FUJIKI Y. Peroxisome biogenesis and human peroxisome-deficiency disorders. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2016; 92:463-477. [PMID: 27941306 PMCID: PMC5328784 DOI: 10.2183/pjab.92.463] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Peroxisome is a single-membrane-bounded ubiquitous organelle containing a hundred different enzymes that catalyze various metabolic pathways such as β-oxidation of very long-chain fatty acids and synthesis of plasmalogens. To investigate peroxisome biogenesis and human peroxisome biogenesis disorders (PBDs) including Zellweger syndrome, more than a dozen different complementation groups of Chinese hamster ovary (CHO) cell mutants impaired in peroxisome biogenesis are isolated as a model experimental system. By taking advantage of rapid functional complementation assay of the CHO cell mutants, successful cloning of PEX genes encoding peroxins required for peroxisome assembly invaluably contributed to the accomplishment of cloning of pathogenic genes responsible for PBDs. Peroxins are divided into three groups: 1) peroxins including Pex3p, Pex16p and Pex19p, are responsible for peroxisome membrane biogenesis via Pex19p- and Pex3p-dependent class I and Pex19p- and Pex16p-dependent class II pathways; 2) peroxins that function in matrix protein import; 3) those such as Pex11pβ are involved in peroxisome division where DLP1, Mff, and Fis1 coordinately function.
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Affiliation(s)
- Yukio FUJIKI
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Correspondence should be addressed: Y. Fujiki, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan (e-mail: )
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37
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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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38
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Conserved targeting information in mammalian and fungal peroxisomal tail-anchored proteins. Sci Rep 2015; 5:17420. [PMID: 26627908 PMCID: PMC4667187 DOI: 10.1038/srep17420] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 10/22/2015] [Indexed: 11/22/2022] Open
Abstract
The targeting signals and mechanisms of soluble peroxisomal proteins are well understood, whereas less is known about the signals and targeting routes of peroxisomal membrane proteins (PMP). Pex15 and PEX26, tail-anchored proteins in yeast and mammals, respectively, exert a similar cellular function in the recruitment of AAA peroxins at the peroxisomal membrane. But despite their common role, Pex15 and PEX26 are neither homologs nor they are known to follow similar targeting principles. Here we show that Pex15 targets to peroxisomes in mammalian cells, and PEX26 reaches peroxisomes when expressed in yeast cells. In both proteins C-terminal targeting information is sufficient for correct sorting to the peroxisomal membrane. In yeast, PEX26 follows the pathway that also ensures correct targeting of Pex15: PEX26 enters the endoplasmic reticulum (ER) in a GET-dependent and Pex19-independent manner. Like in yeast, PEX26 enters the ER in mammalian cells, however, independently of GET/TRC40. These data show that conserved targeting information is employed in yeast and higher eukaryotes during the biogenesis of peroxisomal tail-anchored proteins.
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39
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Knoblach B, Rachubinski RA. Sharing with your children: Mechanisms of peroxisome inheritance. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:1014-8. [PMID: 26620799 DOI: 10.1016/j.bbamcr.2015.11.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 10/22/2022]
Abstract
Organelle inheritance is the process by which eukaryotic cells actively replicate and equitably partition their organelles between mother cell and daughter cell at cytokinesis to maintain the benefits of subcellular compartmentalization. The budding yeast Saccharomyces cerevisiae has proven invaluable in helping to define the factors involved in the inheritance of different organelles and in understanding how these factors act and interact to maintain balance in the organelle populations of actively dividing cells. Inheritance factors can be classified as motors that transport organelles, tethers that retain organelles, and connectors (receptors) that mediate the attachment of organelles to motors and anchors. This article will review how peroxisomes are inherited by cells, with a focus on budding yeast, and will discuss common themes and mechanisms of action that underlie the inheritance of all membrane-enclosed organelles.
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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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40
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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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41
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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: 42] [Impact Index Per Article: 4.7] [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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42
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Hua R, Gidda SK, Aranovich A, Mullen RT, Kim PK. Multiple Domains in PEX16 Mediate Its Trafficking and Recruitment of Peroxisomal Proteins to the ER. Traffic 2015; 16:832-52. [PMID: 25903784 DOI: 10.1111/tra.12292] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/09/2015] [Accepted: 04/09/2015] [Indexed: 12/27/2022]
Abstract
Peroxisomes rely on a diverse array of mechanisms to ensure the specific targeting of their protein constituents. Peroxisomal membrane proteins (PMPs), for instance, are targeted by at least two distinct pathways: directly to peroxisomes from their sites of synthesis in the cytosol or indirectly via the endoplasmic reticulum (ER). However, the extent to which each PMP targeting pathway is involved in the maintenance of pre-existing peroxisomes is unclear. Recently, we showed that human PEX16 plays a critical role in the ER-dependent targeting of PMPs by mediating the recruitment of two other PMPs, PEX3 and PMP34, to the ER. Here, we extend these results by carrying out a comprehensive mutational analysis of PEX16 aimed at gaining insights into the molecular targeting signals responsible for its ER-to-peroxisome trafficking and the domain(s) involved in PMP recruitment function at the ER. We also show that the recruitment of PMPs to the ER by PEX16 is conserved in plants. The implications of these results in terms of the function of PEX16 and the role of the ER in peroxisome maintenance in general are discussed.
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Affiliation(s)
- Rong Hua
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON, Canada M5G 0A4.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5G 1A8
| | - Satinder K Gidda
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Alexander Aranovich
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON, Canada M5G 0A4
| | - Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Peter K Kim
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON, Canada M5G 0A4.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5G 1A8
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43
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Kim PK, Hettema EH. Multiple pathways for protein transport to peroxisomes. J Mol Biol 2015; 427:1176-90. [PMID: 25681696 PMCID: PMC4726662 DOI: 10.1016/j.jmb.2015.02.005] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 02/05/2015] [Accepted: 02/06/2015] [Indexed: 12/15/2022]
Abstract
Peroxisomes are unique among the organelles of the endomembrane system. Unlike other organelles that derive most if not all of their proteins from the ER (endoplasmic reticulum), peroxisomes contain dedicated machineries for import of matrix proteins and insertion of membrane proteins. However, peroxisomes are also able to import a subset of their membrane proteins from the ER. One aspect of peroxisome biology that has remained ill defined is the role the various import pathways play in peroxisome maintenance. In this review, we discuss the available data on matrix and membrane protein import into peroxisomes. Peroxisomal membrane and matrix proteins require distinct factors for their transport. Matrix proteins fold in the cytosol prior to their import. Loaded targeting receptors form part of the matrix protein translocation pore. Many membrane proteins are directly inserted into the peroxisomal membrane. Some peroxisomal membrane proteins are transported via the ER to peroxisomes.
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Affiliation(s)
- P K Kim
- Program in Cell Biology, Hospital for Sick Children, Toronto, ON, Canada M5G 1X8; Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - E H Hettema
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, South Yorkshire S10 2TN, United Kingdom.
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