1
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Bajdzienko J, Bremm A. Mammalian pexophagy at a glance. J Cell Sci 2024; 137:jcs259775. [PMID: 38752931 DOI: 10.1242/jcs.259775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2024] Open
Abstract
Peroxisomes are highly plastic organelles that are involved in several metabolic processes, including fatty acid oxidation, ether lipid synthesis and redox homeostasis. Their abundance and activity are dynamically regulated in response to nutrient availability and cellular stress. Damaged or superfluous peroxisomes are removed mainly by pexophagy, the selective autophagy of peroxisomes induced by ubiquitylation of peroxisomal membrane proteins or ubiquitin-independent processes. Dysregulated pexophagy impairs peroxisome homeostasis and has been linked to the development of various human diseases. Despite many recent insights into mammalian pexophagy, our understanding of this process is still limited compared to our understanding of pexophagy in yeast. In this Cell Science at a Glance article and the accompanying poster, we summarize current knowledge on the control of mammalian pexophagy and highlight which aspects require further attention. We also discuss the role of ubiquitylation in pexophagy and describe the ubiquitin machinery involved in regulating signals for the recruitment of phagophores to peroxisomes.
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Affiliation(s)
- Justyna Bajdzienko
- Goethe University Frankfurt, Medical Faculty , Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Anja Bremm
- Goethe University Frankfurt, Medical Faculty , Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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2
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Oh J, Kim DK, Ahn SH, Kim HM, Cho H. A dual role of the conserved PEX19 helix in safeguarding peroxisomal membrane proteins. iScience 2024; 27:109537. [PMID: 38585659 PMCID: PMC10995880 DOI: 10.1016/j.isci.2024.109537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/13/2024] [Accepted: 03/18/2024] [Indexed: 04/09/2024] Open
Abstract
Accurate localization of membrane proteins is essential for proper cellular functioning and the integrity of cellular membranes. Post-translational targeting of peroxisomal membrane proteins (PMPs) is mediated by the cytosolic chaperone PEX19 and its membrane receptor PEX3. However, the molecular mechanisms underlying PMP targeting are poorly understood. Here, using biochemical and mass spectrometry analysis, we find that a conserved PEX19 helix, αd, is critical to prevent improper exposure of the PEX26 transmembrane domain (TMD) to cytosolic chaperones. Furthermore, the αd helix of PEX19 interacts with the cytosolic domain of the PEX3 receptor, thereby triggering PEX26 release at the correct destination membrane. The peroxisome-deficient PEX3-G138E mutant completely abolishes this secondary interaction, leading to lack of PEX3-induced PEX26 release from PEX19. These findings elucidate a dual molecular mechanism that is essential to membrane protein protection and destination-specific release by a molecular chaperone.
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Affiliation(s)
- Jeonghyun Oh
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Do Kyung Kim
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Seung Hae Ahn
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Ho Min Kim
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hyunju Cho
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
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3
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Qin X, Wang B, Lu X, Song Y, Wang W. Identification and Validation of a PEX5-Dependent Signature for Prognostic Prediction in Glioma. Biomolecules 2024; 14:314. [PMID: 38540734 PMCID: PMC10967733 DOI: 10.3390/biom14030314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 02/22/2024] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Gliomas, the most prevalent and lethal form of brain cancer, are known to exhibit metabolic alterations that facilitate tumor growth, invasion, and resistance to therapies. Peroxisomes, essential organelles responsible for fatty acid oxidation and reactive oxygen species (ROS) homeostasis, rely on the receptor PEX5 for the import of metabolic enzymes into their matrix. However, the prognostic significance of peroxisomal enzymes for glioma patients remains unclear. In this study, we elucidate that PEX5 is indispensable for the cell growth, migration, and invasion of glioma cells. We establish a robust prognosis model based on the expression of peroxisomal enzymes, whose localization relies on PEX5. This PEX5-dependent signature not only serves as a robust prognosis model capable of accurately predicting outcomes for glioma patients, but also effectively distinguishes several clinicopathological features, including the grade, isocitrate dehydrogenase (IDH) mutation, and 1p19q codeletion status. Furthermore, we developed a nomogram that integrates the prognostic model with other clinicopathological factors, demonstrating highly accurate performance in estimating patient survival. Patients classified into the high-risk group based on our prognostic model exhibited an immunosuppressive microenvironment. Finally, our validation reveals that the elevated expression of GSTK1, an antioxidant enzyme within the signature, promotes the cell growth and migration of glioma cells, with this effect dependent on the peroxisomal targeting signal recognized by PEX5. These findings identify the PEX5-dependent signature as a promising prognostic tool for gliomas.
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Affiliation(s)
| | | | | | | | - Wei Wang
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430070, China
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4
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Germain K, So RWL, DiGiovanni LF, Watts JC, Bandsma RHJ, Kim PK. Upregulated pexophagy limits the capacity of selective autophagy. Nat Commun 2024; 15:375. [PMID: 38195640 PMCID: PMC10776696 DOI: 10.1038/s41467-023-44005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/27/2023] [Indexed: 01/11/2024] Open
Abstract
Selective autophagy is an essential process to maintain cellular homeostasis through the constant recycling of damaged or superfluous components. Over a dozen selective autophagy pathways mediate the degradation of diverse cellular substrates, but whether these pathways can influence one another remains unknown. We address this question using pexophagy, the autophagic degradation of peroxisomes, as a model. We show in cells that upregulated pexophagy impairs the selective autophagy of both mitochondria and protein aggregates by exhausting the autophagy initiation factor, ULK1. We confirm this finding in cell models of the pexophagy-mediated form of Zellweger Spectrum Disorder, a disease characterized by peroxisome dysfunction. Further, we extend the generalizability of limited selective autophagy by determining that increased protein aggregate degradation reciprocally reduces pexophagy using cell models of Parkinson's Disease and Huntington's Disease. Our findings suggest that the degradative capacity of selective autophagy can become limited by an increase in one substrate.
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Affiliation(s)
- Kyla Germain
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Raphaella W L So
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, Toronto, ON, M5T 0S8, Canada
| | - Laura F DiGiovanni
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Joel C Watts
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, Toronto, ON, M5T 0S8, Canada
| | - Robert H J Bandsma
- Translational Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1A8, Canada.
| | - Peter K Kim
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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5
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Hu D, Tan M, Lu D, Kleiboeker B, Liu X, Park H, Kravitz AV, Shoghi KI, Tseng YH, Razani B, Ikeda A, Lodhi IJ. TMEM135 links peroxisomes to the regulation of brown fat mitochondrial fission and energy homeostasis. Nat Commun 2023; 14:6099. [PMID: 37773161 PMCID: PMC10541902 DOI: 10.1038/s41467-023-41849-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 09/20/2023] [Indexed: 10/01/2023] Open
Abstract
Mitochondrial morphology, which is controlled by mitochondrial fission and fusion, is an important regulator of the thermogenic capacity of brown adipocytes. Adipose-specific peroxisome deficiency impairs thermogenesis by inhibiting cold-induced mitochondrial fission due to decreased mitochondrial membrane content of the peroxisome-derived lipids called plasmalogens. Here, we identify TMEM135 as a critical mediator of the peroxisomal regulation of mitochondrial fission and thermogenesis. Adipose-specific TMEM135 knockout in mice blocks mitochondrial fission, impairs thermogenesis, and increases diet-induced obesity and insulin resistance. Conversely, TMEM135 overexpression promotes mitochondrial division, counteracts obesity and insulin resistance, and rescues thermogenesis in peroxisome-deficient mice. Mechanistically, thermogenic stimuli promote association between peroxisomes and mitochondria and plasmalogen-dependent localization of TMEM135 in mitochondria, where it mediates PKA-dependent phosphorylation and mitochondrial retention of the fission factor Drp1. Together, these results reveal a previously unrecognized inter-organelle communication regulating mitochondrial fission and energy homeostasis and identify TMEM135 as a potential target for therapeutic activation of BAT.
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Affiliation(s)
- Donghua Hu
- Division of Endocrinology, Metabolism & Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Min Tan
- Division of Endocrinology, Metabolism & Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Dongliang Lu
- Division of Endocrinology, Metabolism & Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Brian Kleiboeker
- Division of Endocrinology, Metabolism & Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Xuejing Liu
- Division of Endocrinology, Metabolism & Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Hongsuk Park
- Division of Endocrinology, Metabolism & Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Alexxai V Kravitz
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Kooresh I Shoghi
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yu-Hua Tseng
- Section on Integrative Physiology and Metabolism, Research Division, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Babak Razani
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- University of Pittsburgh School of Medicine and UPMC, Pittsburgh, PA, USA
| | - Akihiro Ikeda
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Irfan J Lodhi
- Division of Endocrinology, Metabolism & Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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6
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Krishna CK, Schmidt N, Tippler BG, Schliebs W, Jung M, Winklhofer KF, Erdmann R, Kalel VC. Molecular basis of the glycosomal targeting of PEX11 and its mislocalization to mitochondrion in trypanosomes. Front Cell Dev Biol 2023; 11:1213761. [PMID: 37664461 PMCID: PMC10469627 DOI: 10.3389/fcell.2023.1213761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/03/2023] [Indexed: 09/05/2023] Open
Abstract
PEX19 binding sites are essential parts of the targeting signals of peroxisomal membrane proteins (mPTS). In this study, we characterized PEX19 binding sites of PEX11, the most abundant peroxisomal and glycosomal membrane protein from Trypanosoma brucei and Saccharomyces cerevisiae. TbPEX11 contains two PEX19 binding sites, one close to the N-terminus (BS1) and a second in proximity to the first transmembrane domain (BS2). The N-terminal BS1 is highly conserved across different organisms and is required for maintenance of the steady-state concentration and efficient targeting to peroxisomes and glycosomes in both baker's yeast and Trypanosoma brucei. The second PEX19 binding site in TbPEX11 is essential for its glycosomal localization. Deletion or mutations of the PEX19 binding sites in TbPEX11 or ScPEX11 results in mislocalization of the proteins to mitochondria. Bioinformatic analysis indicates that the N-terminal region of TbPEX11 contains an amphiphilic helix and several putative TOM20 recognition motifs. We show that the extreme N-terminal region of TbPEX11 contains a cryptic N-terminal signal that directs PEX11 to the mitochondrion if its glycosomal transport is blocked.
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Affiliation(s)
- Chethan K. Krishna
- Department of Systems Biochemistry, Institute for Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Nadine Schmidt
- Department of Systems Biochemistry, Institute for Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Bettina G. Tippler
- Department of Systems Biochemistry, Institute for Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Wolfgang Schliebs
- Department of Systems Biochemistry, Institute for Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Martin Jung
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Konstanze F. Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Ralf Erdmann
- Department of Systems Biochemistry, Institute for Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Vishal C. Kalel
- Department of Systems Biochemistry, Institute for Biochemistry and Pathobiochemistry, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
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7
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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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8
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Wanders RJA, Baes M, Ribeiro D, Ferdinandusse S, Waterham HR. The physiological functions of human peroxisomes. Physiol Rev 2023; 103:957-1024. [PMID: 35951481 DOI: 10.1152/physrev.00051.2021] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Peroxisomes are subcellular organelles that play a central role in human physiology by catalyzing a range of unique metabolic functions. The importance of peroxisomes for human health is exemplified by the existence of a group of usually severe diseases caused by an impairment in one or more peroxisomal functions. Among others these include the Zellweger spectrum disorders, X-linked adrenoleukodystrophy, and Refsum disease. To fulfill their role in metabolism, peroxisomes require continued interaction with other subcellular organelles including lipid droplets, lysosomes, the endoplasmic reticulum, and mitochondria. In recent years it has become clear that the metabolic alliance between peroxisomes and other organelles requires the active participation of tethering proteins to bring the organelles physically closer together, thereby achieving efficient transfer of metabolites. This review intends to describe the current state of knowledge about the metabolic role of peroxisomes in humans, with particular emphasis on the metabolic partnership between peroxisomes and other organelles and the consequences of genetic defects in these processes. We also describe the biogenesis of peroxisomes and the consequences of the multiple genetic defects therein. In addition, we discuss the functional role of peroxisomes in different organs and tissues and include relevant information derived from model systems, notably peroxisomal mouse models. Finally, we pay particular attention to a hitherto underrated role of peroxisomes in viral infections.
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Affiliation(s)
- Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, Amsterdam, The Netherlands
| | - Myriam Baes
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Daniela Ribeiro
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, Amsterdam, The Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, Amsterdam, The Netherlands
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9
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Deori NM, Nagotu S. Peroxisome biogenesis and inter-organelle communication: an indispensable role for Pex11 and Pex30 family proteins in yeast. Curr Genet 2022; 68:537-550. [PMID: 36242632 DOI: 10.1007/s00294-022-01254-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/26/2022]
Abstract
Peroxisomes are highly dynamic organelles present in most eukaryotic cells. They also play an important role in human health and the optimum functioning of cells. An extensive repertoire of proteins is associated with the biogenesis and function of these organelles. Two protein families that are involved in regulating peroxisome number in a cell directly or indirectly are Pex11 and Pex30. Interestingly, these proteins are also reported to regulate the contact sites between peroxisomes and other cell organelles such as mitochondria, endoplasmic reticulum and lipid droplets. In this manuscript, we review our current knowledge of the role of these proteins in peroxisome biogenesis in various yeast species. Further, we also discuss in detail the role of these protein families in the regulation of inter-organelle contacts in yeast.
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Affiliation(s)
- Nayan Moni Deori
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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10
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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] [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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11
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Insights into the Structure and Function of the Pex1/Pex6 AAA-ATPase in Peroxisome Homeostasis. Cells 2022; 11:cells11132067. [PMID: 35805150 PMCID: PMC9265785 DOI: 10.3390/cells11132067] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/25/2022] [Accepted: 06/26/2022] [Indexed: 02/01/2023] Open
Abstract
The AAA-ATPases Pex1 and Pex6 are required for the formation and maintenance of peroxisomes, membrane-bound organelles that harbor enzymes for specialized metabolism. Together, Pex1 and Pex6 form a heterohexameric AAA-ATPase capable of unfolding substrate proteins via processive threading through a central pore. Here, we review the proposed roles for Pex1/Pex6 in peroxisome biogenesis and degradation, discussing how the unfolding of potential substrates contributes to peroxisome homeostasis. We also consider how advances in cryo-EM, computational structure prediction, and mechanisms of related ATPases are improving our understanding of how Pex1/Pex6 converts ATP hydrolysis into mechanical force. Since mutations in PEX1 and PEX6 cause the majority of known cases of peroxisome biogenesis disorders such as Zellweger syndrome, insights into Pex1/Pex6 structure and function are important for understanding peroxisomes in human health and disease.
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12
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The MFN1 and MFN2 mitofusins promote clustering between mitochondria and peroxisomes. Commun Biol 2022; 5:423. [PMID: 35523862 PMCID: PMC9076876 DOI: 10.1038/s42003-022-03377-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 04/18/2022] [Indexed: 11/08/2022] Open
Abstract
Mitochondria and peroxisomes are two types of functionally close-related organelles, and both play essential roles in lipid and ROS metabolism. However, how they physically interact with each other is not well understood. In this study, we apply the proximity labeling method with peroxisomal proteins and report that mitochondrial protein mitofusins (MFNs) are in proximity to peroxisomes. Overexpression of MFNs induces not only the mitochondria clustering but also the co-clustering of peroxisomes. We also report the enrichment of MFNs at the mitochondria-peroxisome interface. Induced mitofusin expression gives rise to more mitochondria-peroxisome contacting sites. Furthermore, the tethering of peroxisomes to mitochondria can be inhibited by the expression of a truncated MFN2, which lacks the transmembrane region. Collectively, our study suggests MFNs as regulators for mitochondria-peroxisome contacts. Our findings are essential for future studies of inter-organelle metabolism regulation and signaling, and may help understand the pathogenesis of mitofusin dysfunction-related disease.
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13
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Cheung A, Argyriou C, Yergeau C, D’Souza Y, Riou É, Lévesque S, Raymond G, Daba M, Rtskhiladze I, Tkemaladze T, Adang L, La Piana R, Bernard G, Braverman N. Clinical, neuroradiological, and molecular characterization of patients with atypical Zellweger spectrum disorder caused by PEX16 mutations: a case series. Neurogenetics 2022; 23:115-127. [DOI: 10.1007/s10048-022-00684-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/12/2022] [Indexed: 10/19/2022]
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14
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Carmichael RE, Schrader M. Determinants of Peroxisome Membrane Dynamics. Front Physiol 2022; 13:834411. [PMID: 35185625 PMCID: PMC8853631 DOI: 10.3389/fphys.2022.834411] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
Organelles within the cell are highly dynamic entities, requiring dramatic morphological changes to support their function and maintenance. As a result, organelle membranes are also highly dynamic, adapting to a range of topologies as the organelle changes shape. In particular, peroxisomes—small, ubiquitous organelles involved in lipid metabolism and reactive oxygen species homeostasis—display a striking plasticity, for example, during the growth and division process by which they proliferate. During this process, the membrane of an existing peroxisome elongates to form a tubule, which then constricts and ultimately undergoes scission to generate new peroxisomes. Dysfunction of this plasticity leads to diseases with developmental and neurological phenotypes, highlighting the importance of peroxisome dynamics for healthy cell function. What controls the dynamics of peroxisomal membranes, and how this influences the dynamics of the peroxisomes themselves, is just beginning to be understood. In this review, we consider how the composition, biophysical properties, and protein-lipid interactions of peroxisomal membranes impacts on their dynamics, and in turn on the biogenesis and function of peroxisomes. In particular, we focus on the effect of the peroxin PEX11 on the peroxisome membrane, and its function as a major regulator of growth and division. Understanding the roles and regulation of peroxisomal membrane dynamics necessitates a multidisciplinary approach, encompassing knowledge across a range of model species and a number of fields including lipid biochemistry, biophysics and computational biology. Here, we present an integrated overview of our current understanding of the determinants of peroxisome membrane dynamics, and reflect on the outstanding questions still remaining to be solved.
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Affiliation(s)
- Ruth E Carmichael
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
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15
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Farelo MA, Korrou-Karava D, Brooks KF, Russell TA, Maringer K, Mayerhofer PU. Dengue and Zika Virus Capsid Proteins Contain a Common PEX19-Binding Motif. Viruses 2022; 14:v14020253. [PMID: 35215846 PMCID: PMC8874546 DOI: 10.3390/v14020253] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
Flaviviruses such as dengue virus (DENV) and Zika virus (ZIKV) have evolved sophisticated mechanisms to suppress the host immune system. For instance, flavivirus infections were found to sabotage peroxisomes, organelles with an important role in innate immunity. The current model suggests that the capsid (C) proteins of DENV and ZIKV downregulate peroxisomes, ultimately resulting in reduced production of interferons by interacting with the host protein PEX19, a crucial chaperone in peroxisomal biogenesis. Here, we aimed to explore the importance of peroxisomes and the role of C interaction with PEX19 in the flavivirus life cycle. By infecting cells lacking peroxisomes we show that this organelle is required for optimal DENV replication. Moreover, we demonstrate that DENV and ZIKV C bind PEX19 through a conserved PEX19-binding motif, which is also commonly found in cellular peroxisomal membrane proteins (PMPs). However, in contrast to PMPs, this interaction does not result in the targeting of C to peroxisomes. Furthermore, we show that the presence of C results in peroxisome loss due to impaired peroxisomal biogenesis, which appears to occur by a PEX19-independent mechanism. Hence, these findings challenge the current model of how flavivirus C might downregulate peroxisomal abundance and suggest a yet unknown role of peroxisomes in flavivirus biology.
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Affiliation(s)
- Mafalda A. Farelo
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
| | - Despoina Korrou-Karava
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
| | - Katrina F. Brooks
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
| | - Tiffany A. Russell
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
| | - Kevin Maringer
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
- The Pirbright Institute, Pirbright GU24 0NF, UK
- Correspondence: (K.M.); (P.U.M.)
| | - Peter U. Mayerhofer
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
- Correspondence: (K.M.); (P.U.M.)
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16
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Li M, Gaussmann S, Tippler B, Ott J, Popowicz GM, Schliebs W, Sattler M, Erdmann R, Kalel VC. Novel Trypanocidal Inhibitors that Block Glycosome Biogenesis by Targeting PEX3-PEX19 Interaction. Front Cell Dev Biol 2022; 9:737159. [PMID: 34988071 PMCID: PMC8721105 DOI: 10.3389/fcell.2021.737159] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 11/15/2021] [Indexed: 12/02/2022] Open
Abstract
Human pathogenic trypanosomatid parasites harbor a unique form of peroxisomes termed glycosomes that are essential for parasite viability. We and others previously identified and characterized the essential Trypanosoma brucei ortholog TbPEX3, which is the membrane-docking factor for the cytosolic receptor PEX19 bound to the glycosomal membrane proteins. Knockdown of TbPEX3 expression leads to mislocalization of glycosomal membrane and matrix proteins, and subsequent cell death. As an early step in glycosome biogenesis, the PEX3–PEX19 interaction is an attractive drug target. We established a high-throughput assay for TbPEX3–TbPEX19 interaction and screened a compound library for small-molecule inhibitors. Hits from the screen were further validated using an in vitro ELISA assay. We identified three compounds, which exhibit significant trypanocidal activity but show no apparent toxicity to human cells. Furthermore, we show that these compounds lead to mislocalization of glycosomal proteins, which is toxic to the trypanosomes. Moreover, NMR-based experiments indicate that the inhibitors bind to PEX3. The inhibitors interfering with glycosomal biogenesis by targeting the TbPEX3–TbPEX19 interaction serve as starting points for further optimization and anti-trypanosomal drug development.
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Affiliation(s)
- Mengqiao Li
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Stefan Gaussmann
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Garching, Germany
| | - Bettina Tippler
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Julia Ott
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Garching, Germany
| | - Wolfgang Schliebs
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Garching, Germany
| | - Ralf Erdmann
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Vishal C Kalel
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
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17
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Zientara-Rytter KM, Mahalingam SS, Farré JC, Carolino K, Subramani S. Recognition and Chaperoning by Pex19, Followed by Trafficking and Membrane Insertion of the Peroxisome Proliferation Protein, Pex11. Cells 2022; 11:cells11010157. [PMID: 35011719 PMCID: PMC8750153 DOI: 10.3390/cells11010157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/24/2021] [Accepted: 12/28/2021] [Indexed: 01/27/2023] Open
Abstract
Pex11, an abundant peroxisomal membrane protein (PMP), is required for division of peroxisomes and is robustly imported to peroxisomal membranes. We present a comprehensive analysis of how the Pichia pastoris Pex11 is recognized and chaperoned by Pex19, targeted to peroxisome membranes and inserted therein. We demonstrate that Pex11 contains one Pex19-binding site (Pex19-BS) that is required for Pex11 insertion into peroxisomal membranes by Pex19, but is non-essential for peroxisomal trafficking. We provide extensive mutational analyses regarding the recognition of Pex19-BS in Pex11 by Pex19. Pex11 also has a second, Pex19-independent membrane peroxisome-targeting signal (mPTS) that is preserved among Pex11-family proteins and anchors the human HsPex11γ to the outer leaflet of the peroxisomal membrane. Thus, unlike most PMPs, Pex11 can use two mechanisms of transport to peroxisomes, where only one of them depends on its direct interaction with Pex19, but the other does not. However, Pex19 is necessary for membrane insertion of Pex11. We show that Pex11 can self-interact, using both homo- and/or heterotypic interactions involving its N-terminal helical domains. We demonstrate that Pex19 acts as a chaperone by interacting with the Pex19-BS in Pex11, thereby protecting Pex11 from spontaneous oligomerization that would otherwise cause its aggregation and subsequent degradation.
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18
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Stocks B, Gonzalez-Franquesa A, Borg ML, Björnholm M, Niu L, Zierath JR, Deshmukh AS. Integrated liver and plasma proteomics in obese mice reveals complex metabolic regulation. Mol Cell Proteomics 2022; 21:100207. [PMID: 35093608 PMCID: PMC8928073 DOI: 10.1016/j.mcpro.2022.100207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/23/2022] [Indexed: 11/28/2022] Open
Abstract
Obesity leads to the development of nonalcoholic fatty liver disease (NAFLD) and associated alterations to the plasma proteome. To elucidate the underlying changes associated with obesity, we performed liquid chromatography–tandem mass spectrometry in the liver and plasma of obese leptin-deficient ob/ob mice and integrated these data with publicly available transcriptomic and proteomic datasets of obesity and metabolic diseases in preclinical and clinical cohorts. We quantified 7173 and 555 proteins in the liver and plasma proteomes, respectively. The abundance of proteins related to fatty acid metabolism were increased, alongside peroxisomal proliferation in ob/ob liver. Putatively secreted proteins and the secretory machinery were also dysregulated in the liver, which was mirrored by a substantial alteration of the plasma proteome. Greater than 50% of the plasma proteins were differentially regulated, including NAFLD biomarkers, lipoproteins, the 20S proteasome, and the complement and coagulation cascades of the immune system. Integration of the liver and plasma proteomes identified proteins that were concomitantly regulated in the liver and plasma in obesity, suggesting that the systemic abundance of these plasma proteins is regulated by secretion from the liver. Many of these proteins are systemically regulated during type 2 diabetes and/or NAFLD in humans, indicating the clinical importance of liver–plasma cross talk and the relevance of our investigations in ob/ob mice. Together, these analyses yield a comprehensive insight into obesity and provide an extensive resource for obesity research in a prevailing model organism. Proteomics reveals liver-derived proteins systemically dysregulated in obesity. Obesity increases hepatic lipid metabolism via peroxisomal biogenesis. Obesity dysregulates secretory machinery and secreted proteins within the liver. Metabolic and immune proteins dysregulated in plasma of obese mice. Comparative proteomics of high-fat diet and monogenic (ob/ob) models of obesity.
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19
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Ferreira AR, Marques M, Ramos B, Kagan JC, Ribeiro D. Emerging roles of peroxisomes in viral infections. Trends Cell Biol 2021; 32:124-139. [PMID: 34696946 DOI: 10.1016/j.tcb.2021.09.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 01/01/2023]
Abstract
Peroxisomes, essential subcellular organelles that fulfill important functions in lipid and reactive oxygen species metabolism, have recently emerged as key players during viral infections. Their importance for the establishment of the cellular antiviral response has been highlighted by numerous reports of specific evasion of peroxisome-dependent signaling by different viruses. Recent data demonstrate that peroxisomes also assume important proviral functions. Here, we review and discuss the recent advances in the study of the diverse roles of peroxisomes during viral infections, from animal to plant viruses, and from basic to translational perspectives. We further discuss the future development of this emerging area and propose that peroxisome-related mechanisms represent a promising target for the development of novel antiviral strategies.
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Affiliation(s)
- Ana Rita Ferreira
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Mariana Marques
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Bruno Ramos
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Jonathan C Kagan
- Division of Gastroenterology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Daniela Ribeiro
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.
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20
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Hypothyroidism Intensifies Both Canonic and the De Novo Pathway of Peroxisomal Biogenesis in Rat Brown Adipocytes in a Time-Dependent Manner. Cells 2021; 10:cells10092248. [PMID: 34571897 PMCID: PMC8472630 DOI: 10.3390/cells10092248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 02/08/2023] Open
Abstract
Despite peroxisomes being important partners of mitochondria by carrying out fatty acid oxidation in brown adipocytes, no clear evidence concerning peroxisome origin and way(s) of biogenesis exists. Herein we used methimazole-induced hypothyroidism for 7, 15, and 21 days to study peroxisomal remodeling and origin in rat brown adipocytes. We found that peroxisomes originated via both canonic, and de novo pathways. Each pathway operates in euthyroid control and over the course of hypothyroidism, in a time-dependent manner. Hypothyroidism increased the peroxisomal number by 1.8-, 3.6- and 5.8-fold on days 7, 15, and 21. Peroxisomal presence, their distribution, and their degree of maturation were heterogeneous in brown adipocytes in a Harlequin-like manner, reflecting differences in their origin. The canonic pathway, through numerous dumbbell-like and “pearls on strings” structures, supported by high levels of Pex11β and Drp1, prevailed on day 7. The de novo pathway of peroxisomal biogenesis started on day 15 and became dominant by day 21. The transition of peroxisomal biogenesis from canonic to the de novo pathway was driven by increased levels of Pex19, PMP70, Pex5S, and Pex26 and characterized by numerous tubular structures. Furthermore, specific peroxisomal origin from mitochondria, regardless of thyroid status, indicates their mutual regulation in rat brown adipocytes.
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21
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Nuebel E, Morgan JT, Fogarty S, Winter JM, Lettlova S, Berg JA, Chen YC, Kidwell CU, Maschek JA, Clowers KJ, Argyriou C, Chen L, Wittig I, Cox JE, Roh-Johnson M, Braverman N, Bonkowsky J, Gygi SP, Rutter J. The biochemical basis of mitochondrial dysfunction in Zellweger Spectrum Disorder. EMBO Rep 2021; 22:e51991. [PMID: 34351705 DOI: 10.15252/embr.202051991] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 06/21/2021] [Accepted: 07/12/2021] [Indexed: 01/09/2023] Open
Abstract
Peroxisomal biogenesis disorders (PBDs) are genetic disorders of peroxisome biogenesis and metabolism that are characterized by profound developmental and neurological phenotypes. The most severe class of PBDs-Zellweger spectrum disorder (ZSD)-is caused by mutations in peroxin genes that result in both non-functional peroxisomes and mitochondrial dysfunction. It is unclear, however, how defective peroxisomes contribute to mitochondrial impairment. In order to understand the molecular basis of this inter-organellar relationship, we investigated the fate of peroxisomal mRNAs and proteins in ZSD model systems. We found that peroxins were still expressed and a subset of them accumulated on the mitochondrial membrane, which resulted in gross mitochondrial abnormalities and impaired mitochondrial metabolic function. We showed that overexpression of ATAD1, a mitochondrial quality control factor, was sufficient to rescue several aspects of mitochondrial function in human ZSD fibroblasts. Together, these data suggest that aberrant peroxisomal protein localization is necessary and sufficient for the devastating mitochondrial morphological and metabolic phenotypes in ZSDs.
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Affiliation(s)
- Esther Nuebel
- Howard Hughes Medical Institute, Salt Lake City, UT, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.,Department of Biomedical Sciences, Noorda College of Osteopathic Medicine, Provo, USA
| | - Jeffrey T Morgan
- Howard Hughes Medical Institute, Salt Lake City, UT, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Sarah Fogarty
- Howard Hughes Medical Institute, Salt Lake City, UT, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Jacob M Winter
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Sandra Lettlova
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Jordan A Berg
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Yu-Chan Chen
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Chelsea U Kidwell
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - J Alan Maschek
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.,Diabetes & Metabolism Research Center, University of Utah, Salt Lake City, UT, USA.,Metabolomics, Proteomics and Mass Spectrometry Core Research Facilities, University of Utah, Salt Lake City, UT, USA
| | - Katie J Clowers
- Department of Cell Biology, Harvard University School of Medicine, Boston, MA, USA
| | | | - Lingxiao Chen
- Department of Pathology, McGill University, Montreal, ON, Canada
| | - Ilka Wittig
- Functional Proteomics, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - James E Cox
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.,Diabetes & Metabolism Research Center, University of Utah, Salt Lake City, UT, USA.,Metabolomics, Proteomics and Mass Spectrometry Core Research Facilities, University of Utah, Salt Lake City, UT, USA
| | - Minna Roh-Johnson
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Nancy Braverman
- Department of Human Genetics, McGill University, Montreal, ON, Canada.,Department of Pediatrics, Research Institute of the McGill University Health Centre, Montreal, ON, Canada
| | - Joshua Bonkowsky
- Primary Children's Hospital, University of Utah, Salt Lake City, UT, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard University School of Medicine, Boston, MA, USA
| | - Jared Rutter
- Howard Hughes Medical Institute, Salt Lake City, UT, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.,Diabetes & Metabolism Research Center, University of Utah, Salt Lake City, UT, USA
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22
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He A, Dean JM, Lodhi IJ. Peroxisomes as cellular adaptors to metabolic and environmental stress. Trends Cell Biol 2021; 31:656-670. [PMID: 33674166 PMCID: PMC8566112 DOI: 10.1016/j.tcb.2021.02.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 02/06/2023]
Abstract
Peroxisomes are involved in multiple metabolic processes, including fatty acid oxidation, ether lipid synthesis, and reactive oxygen species (ROS) metabolism. Recent studies suggest that peroxisomes are critical mediators of cellular responses to various forms of stress, including oxidative stress, hypoxia, starvation, cold exposure, and noise. As dynamic organelles, peroxisomes can modulate their proliferation, morphology, and movement within cells, and engage in crosstalk with other organelles in response to external cues. Although peroxisome-derived hydrogen peroxide has a key role in cellular signaling related to stress, emerging studies suggest that other products of peroxisomal metabolism, such as acetyl-CoA and ether lipids, are also important for metabolic adaptation to stress. Here, we review molecular mechanisms through which peroxisomes regulate metabolic and environmental stress.
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Affiliation(s)
- Anyuan He
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA.
| | - John M Dean
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Irfan J Lodhi
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA.
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23
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Wei X, Maharjan Y, Dorotea D, Dutta RK, Kim D, Kim H, Mu Y, Park C, Park R. Knockdown of PEX16 Induces Autophagic Degradation of Peroxisomes. Int J Mol Sci 2021; 22:ijms22157989. [PMID: 34360754 PMCID: PMC8348608 DOI: 10.3390/ijms22157989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/16/2021] [Accepted: 07/23/2021] [Indexed: 01/16/2023] Open
Abstract
Peroxisome abundance is regulated by homeostasis between the peroxisomal biogenesis and degradation processes. Peroxin 16 (PEX16) is a peroxisomal protein involved in trafficking membrane proteins for de novo peroxisome biogenesis. The present study demonstrates that PEX16 also modulates peroxisome abundance through pexophagic degradation. PEX16 knockdown in human retinal pigment epithelial-1 cells decreased peroxisome abundance and function, represented by reductions in the expression of peroxisome membrane protein ABCD3 and the levels of cholesterol and plasmalogens, respectively. The activation of pexophagy under PEX16 knockdown was shown by (i) abrogated peroxisome loss under PEX16 knockdown in autophagy-deficient ATG5 knockout cell lines, and (ii) increased autophagy flux and co-localization of p62-an autophagy adaptor protein-with ABCD3 in the presence of the autophagy inhibitor chloroquine. However, the levels of cholesterol and plasmalogens did not recover despite the restoration of peroxisome abundance following chloroquine treatment. Thus, PEX16 is indispensable for maintaining peroxisome homeostasis by regulating not only the commonly known biogenesis pathway but also the autophagic degradation of peroxisomes.
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24
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Khantisitthiporn O, Shue B, Eyre NS, Nash CW, Turnbull L, Whitchurch CB, Van der Hoek KH, Helbig KJ, Beard MR. Viperin interacts with PEX19 to mediate peroxisomal augmentation of the innate antiviral response. Life Sci Alliance 2021; 4:e202000915. [PMID: 34108265 PMCID: PMC8200297 DOI: 10.26508/lsa.202000915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022] Open
Abstract
Peroxisomes are recognized as significant platforms for the activation of antiviral innate immunity where stimulation of the key adapter molecule mitochondrial antiviral signaling protein (MAVS) within the RIG-I like receptor (RLR) pathway culminates in the up-regulation of hundreds of ISGs, some of which drive augmentation of multiple innate sensing pathways. However, whether ISGs can augment peroxisome-driven RLR signaling is currently unknown. Using a proteomics-based screening approach, we identified Pex19 as a binding partner of the ISG viperin. Viperin colocalized with numerous peroxisomal proteins and its interaction with Pex19 was in close association with lipid droplets, another emerging innate signaling platform. Augmentation of the RLR pathway by viperin was lost when Pex19 expression was reduced. Expression of organelle-specific MAVS demonstrated that viperin requires both mitochondria and peroxisome MAVS for optimal induction of IFN-β. These results suggest that viperin is required to enhance the antiviral cellular response with a possible role to position the peroxisome at the mitochondrial/MAM MAVS signaling synapse, furthering our understanding of the importance of multiple organelles driving the innate immune response against viral infection.
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Affiliation(s)
- Onruedee Khantisitthiporn
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Byron Shue
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Nicholas S Eyre
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Colt W Nash
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Lynne Turnbull
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Australia
| | - Cynthia B Whitchurch
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Australia
| | - Kylie H Van der Hoek
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | - Karla J Helbig
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Australia
| | - Michael R Beard
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, Australia
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25
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Guillén-Samander A, Leonzino M, Hanna MG, Tang N, Shen H, De Camilli P. VPS13D bridges the ER to mitochondria and peroxisomes via Miro. J Cell Biol 2021; 220:e202010004. [PMID: 33891013 PMCID: PMC8077184 DOI: 10.1083/jcb.202010004] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/08/2021] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
Mitochondria, which are excluded from the secretory pathway, depend on lipid transport proteins for their lipid supply from the ER, where most lipids are synthesized. In yeast, the outer mitochondrial membrane GTPase Gem1 is an accessory factor of ERMES, an ER-mitochondria tethering complex that contains lipid transport domains and that functions, partially redundantly with Vps13, in lipid transfer between the two organelles. In metazoa, where VPS13, but not ERMES, is present, the Gem1 orthologue Miro was linked to mitochondrial dynamics but not to lipid transport. Here we show that Miro, including its peroxisome-enriched splice variant, recruits the lipid transport protein VPS13D, which in turn binds the ER in a VAP-dependent way and thus could provide a lipid conduit between the ER and mitochondria. These findings reveal a so far missing link between function(s) of Gem1/Miro in yeast and higher eukaryotes, where Miro is a Parkin substrate, with potential implications for Parkinson's disease pathogenesis.
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Affiliation(s)
- Andrés Guillén-Samander
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Marianna Leonzino
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Michael G. Hanna
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
| | - Ni Tang
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Hongying Shen
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT
- Systems Biology Institute, Yale West Campus, West Haven, CT
| | - Pietro De Camilli
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD
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26
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Phithakrotchanakoon C, Puseenam A, Kruasuwan W, Likhitrattanapisal S, Phaonakrop N, Roytrakul S, Ingsriswang S, Tanapongpipat S, Roongsawang N. Identification of proteins responsive to heterologous protein production in thermotolerant methylotrophic yeast Ogataea thermomethanolica TBRC656. Yeast 2021; 38:316-325. [PMID: 33445217 DOI: 10.1002/yea.3548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 11/09/2022] Open
Abstract
The thermotolerant methylotrophic yeast Ogataea thermomethanolica TBRC656 is a potential host for heterologous protein production. However, overproduction of heterologous protein can induce cellular stress and limit the level of its secretion. To improve the secretion of heterologous protein, we identified the candidate proteins with altered production during production of heterologous protein in O. thermomethanolica by using a label-free comparative proteomic approach. Four hundred sixty-four proteins with various biological functions showed differential abundance between O. thermomethanolica expressing fungal xylanase (OT + Xyl) and a control strain. The induction of proteins in transport and proteasomal proteolysis was prominently observed. Eight candidate proteins involved in cell wall biosynthesis (Chs3, Gas4), chaperone (Sgt2, Pex19), glycan metabolism (Csf1), protein transport (Ypt35), and vacuole and protein sorting (Cof1, Npr2) were mutated by a CRISPR/Cas9 approach. An Sgt2 mutant showed higher phytase and xylanase activity compared with the control strain (13%-20%), whereas mutants of other genes including Cof1, Pex19, Gas4, and Ypt35 showed lower xylanase activity compared with the control strain (15%-25%). In addition, an Npr2 mutant showed defective growth, while overproduction of Npr2 enhanced xylanase activity. These results reveal genes that can be mutated to modulate heterologous protein production and growth of O. thermomethanolica TBRC656.
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Affiliation(s)
- Chitwadee Phithakrotchanakoon
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Aekkachai Puseenam
- Microbial Cell Factory Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Worarat Kruasuwan
- Microbial Cell Factory Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Somsak Likhitrattanapisal
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Narumon Phaonakrop
- Functional Proteomics Technology, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Supawadee Ingsriswang
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sutipa Tanapongpipat
- Microbial Cell Factory Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Niran Roongsawang
- Microbial Cell Factory Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
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27
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Qu W, Suazo KF, Liu W, Cheng S, Jeong A, Hottman D, Yuan LL, Distefano MD, Li L. Neuronal Protein Farnesylation Regulates Hippocampal Synaptic Plasticity and Cognitive Function. Mol Neurobiol 2020; 58:1128-1144. [PMID: 33098528 DOI: 10.1007/s12035-020-02169-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/12/2020] [Indexed: 12/30/2022]
Abstract
Protein prenylation is a post-translational lipid modification that governs a variety of important cellular signaling pathways, including those regulating synaptic functions and cognition in the nervous system. Two enzymes, farnesyltransferase (FT) and geranylgeranyltransferase type I (GGT), are essential for the prenylation process. Genetic reduction of FT or GGT ameliorates neuropathology but only FT haplodeficiency rescues cognitive function in transgenic mice of Alzheimer's disease. A follow-up study showed that systemic or forebrain neuron-specific deficiency of GGT leads to synaptic and cognitive deficits under physiological conditions. Whether FT plays different roles in shaping neuronal functions and cognition remains elusive. This study shows that in contrast to the detrimental effects of GGT reduction, systemic haplodeficiency of FT has little to no impact on hippocampal synaptic plasticity and cognition. However, forebrain neuron-specific FT deletion also leads to reduced synaptic plasticity, memory retention, and hippocampal dendritic spine density. Furthermore, a novel prenylomic analysis identifies distinct pools of prenylated proteins that are affected in the brain of forebrain neuron-specific FT and GGT knockout mice, respectively. Taken together, this study uncovers that physiological levels of FT and GGT in neurons are essential for normal synaptic/cognitive functions and that the prenylation status of specific signaling molecules regulates neuronal functions.
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Affiliation(s)
- Wenhui Qu
- Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Kiall F Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Wenfeng Liu
- Department of Experimental and Clinical Pharmacology, University of Minnesota, McGuire Translational Research Facility (MTRF) 4-208, 2001 6th Street SE, Minneapolis, MN, 55455, USA
| | - Shaowu Cheng
- Department of Experimental and Clinical Pharmacology, University of Minnesota, McGuire Translational Research Facility (MTRF) 4-208, 2001 6th Street SE, Minneapolis, MN, 55455, USA
| | - Angela Jeong
- Department of Experimental and Clinical Pharmacology, University of Minnesota, McGuire Translational Research Facility (MTRF) 4-208, 2001 6th Street SE, Minneapolis, MN, 55455, USA
| | - David Hottman
- Department of Experimental and Clinical Pharmacology, University of Minnesota, McGuire Translational Research Facility (MTRF) 4-208, 2001 6th Street SE, Minneapolis, MN, 55455, USA
| | - Li-Lian Yuan
- Department of Physiology and Pharmacology, Des Moines University, Des Moines, IA, 50312, USA
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ling Li
- Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, 55455, USA. .,Department of Experimental and Clinical Pharmacology, University of Minnesota, McGuire Translational Research Facility (MTRF) 4-208, 2001 6th Street SE, Minneapolis, MN, 55455, USA. .,Graduate Program in Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA.
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28
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Mast FD, Rachubinski RA, Aitchison JD. Peroxisome prognostications: Exploring the birth, life, and death of an organelle. J Cell Biol 2020; 219:133827. [PMID: 32211898 PMCID: PMC7054992 DOI: 10.1083/jcb.201912100] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 02/07/2023] Open
Abstract
Peroxisomes play a central role in human health and have biochemical properties that promote their use in many biotechnology settings. With a primary role in lipid metabolism, peroxisomes share a niche with lipid droplets within the endomembrane-secretory system. Notably, factors in the ER required for the biogenesis of peroxisomes also impact the formation of lipid droplets. The dynamic interface between peroxisomes and lipid droplets, and also between these organelles and the ER and mitochondria, controls their metabolic flux and their dynamics. Here, we review our understanding of peroxisome biogenesis to propose and reframe models for understanding how peroxisomes are formed in cells. To more fully understand the roles of peroxisomes and to take advantage of their many properties that may prove useful in novel therapeutics or biotechnology applications, we recast mechanisms controlling peroxisome biogenesis in a framework that integrates inference from these models with experimental data.
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Affiliation(s)
- Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA
| | | | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA.,Department of Pediatrics, University of Washington, Seattle, WA
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29
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Jo DS, Park NY, Cho DH. Peroxisome quality control and dysregulated lipid metabolism in neurodegenerative diseases. Exp Mol Med 2020; 52:1486-1495. [PMID: 32917959 PMCID: PMC8080768 DOI: 10.1038/s12276-020-00503-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/11/2020] [Accepted: 07/14/2020] [Indexed: 12/15/2022] Open
Abstract
In recent decades, the role of the peroxisome in physiology and disease conditions has become increasingly important. Together with the mitochondria and other cellular organelles, peroxisomes support key metabolic platforms for the oxidation of various fatty acids and regulate redox conditions. In addition, peroxisomes contribute to the biosynthesis of essential lipid molecules, such as bile acid, cholesterol, docosahexaenoic acid, and plasmalogen. Therefore, the quality control mechanisms that regulate peroxisome biogenesis and degradation are important for cellular homeostasis. Current evidence indicates that peroxisomal function is often reduced or dysregulated in various human disease conditions, such as neurodegenerative diseases. Here, we review the recent progress that has been made toward understanding the quality control systems that regulate peroxisomes and their pathological implications. Systematic studies of cellular organelles called peroxisomes are needed to determine their influence on the progression of neurodegenerative diseases. Peroxisomes play vital roles in biological processes including the metabolism of lipids and reactive oxygen species, and the synthesis of key molecules, including bile acid and cholesterol. Disruption to peroxisome activity has been linked to metabolic disorders, cancers and neurodegenerative conditions. Dong-Hyung Cho at Kyungpook National University in Daegu, South Korea, and coworkers reviewed current understanding of peroxisome regulation, with a particular focus on brain disorders. The quantity and activity of peroxisomes alter according to environmental and stress cues. The brain is lipid-rich, and even small changes in fatty acid composition may influence neuronal function. Changes in fatty acid metabolism are found in early stage Alzheimer’s and Parkinson’s diseases, but whether peroxisome disruption is responsible requires clarification.
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Affiliation(s)
- Doo Sin Jo
- Brain Science and Engineering Institute, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Na Yeon Park
- School of Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Dong-Hyung Cho
- Brain Science and Engineering Institute, Kyungpook National University, Daegu, 41566, Republic of Korea. .,School of Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
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30
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Honsho M, Tanaka M, Zoeller RA, Fujiki Y. Distinct Functions of Acyl/Alkyl Dihydroxyacetonephosphate Reductase in Peroxisomes and Endoplasmic Reticulum. Front Cell Dev Biol 2020; 8:855. [PMID: 33042986 PMCID: PMC7517302 DOI: 10.3389/fcell.2020.00855] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/10/2020] [Indexed: 01/03/2023] Open
Abstract
Plasmalogens are a subclass of ether glycerophospholipids characterized by a vinyl-ether bond at the sn-1 position of the glycerol backbone. Plasmalogen biosynthesis is initiated in peroxisomes. At the third step of plasmalogen synthesis, alkyl-dihydroxyacetonephosphate (DHAP) is enzymatically reduced to 1-alkyl-sn-glycero-3-phospate by acyl/alkyl DHAP reductase (ADHAPR), whose activity is found in both peroxisomes and microsomes. We herein show that knockdown of ADHAPR in HeLa cells reduced the synthesis of ethanolamine plasmalogen (PlsEtn), similar to the Chinese hamster ovary cell mutant FAA.K1B deficient in ADHAPR activity. Endogenous ADHAPR and ectopically expressed FLAG-tagged ADHAPR were localized to peroxisomes and endoplasmic reticulum (ER) as a type I integral membrane protein in HeLa cells. ADHAPR targets to peroxisomes via a Pex19p-dependent class I pathway. In addition, it is also inserted into the ER via the SRP-dependent mechanism. The ADHAPR mutant lacking the N-terminal domain preferentially targets to the ER, restoring the reduced level of PlsEtn synthesis in FAA.K1B cell. In contrast, the expression of full-length ADHAPR in the mutant cells elevates the synthesis of phosphatidylethanolamine, but not PlsEtn. Taken together, these results suggest that the third step of plasmalogen synthesis is mediated by ER-localized ADHAPR.
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Affiliation(s)
- Masanori Honsho
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Megumi Tanaka
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Raphael A Zoeller
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA, United States
| | - Yukio Fujiki
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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31
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Germain K, Kim PK. Pexophagy: A Model for Selective Autophagy. Int J Mol Sci 2020; 21:ijms21020578. [PMID: 31963200 PMCID: PMC7013971 DOI: 10.3390/ijms21020578] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/09/2020] [Accepted: 01/13/2020] [Indexed: 01/03/2023] Open
Abstract
The removal of damaged or superfluous organelles from the cytosol by selective autophagy is required to maintain organelle function, quality control and overall cellular homeostasis. Precisely how substrate selectivity is achieved, and how individual substrates are degraded during selective autophagy in response to both extracellular and intracellular cues is not well understood. The aim of this review is to highlight pexophagy, the autophagic degradation of peroxisomes, as a model for selective autophagy. Peroxisomes are dynamic organelles whose abundance is rapidly modulated in response to metabolic demands. Peroxisomes are routinely turned over by pexophagy for organelle quality control yet can also be degraded by pexophagy in response to external stimuli such as amino acid starvation or hypoxia. This review discusses the molecular machinery and regulatory mechanisms governing substrate selectivity during both quality-control pexophagy and pexophagy in response to external stimuli, in yeast and mammalian systems. We draw lessons from pexophagy to infer how the cell may coordinate the degradation of individual substrates by selective autophagy across different cellular cues.
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Affiliation(s)
- Kyla Germain
- Cell Biology Program, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada;
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Peter K. Kim
- Cell Biology Program, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada;
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Correspondence: ; Tel.: +1-416-813-5983
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32
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Covill-Cooke C, Toncheva VS, Drew J, Birsa N, López-Doménech G, Kittler JT. Peroxisomal fission is modulated by the mitochondrial Rho-GTPases, Miro1 and Miro2. EMBO Rep 2020; 21:e49865. [PMID: 31894645 PMCID: PMC7001505 DOI: 10.15252/embr.201949865] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 11/08/2019] [Accepted: 11/13/2019] [Indexed: 11/09/2022] Open
Abstract
Peroxisomes are essential for a number of cellular functions, including reactive oxygen species metabolism, fatty acid β‐oxidation and lipid synthesis. To ensure optimal functionality, peroxisomal size, shape and number must be dynamically maintained; however, many aspects of how this is regulated remain poorly characterised. Here, we show that the localisation of Miro1 and Miro2—outer mitochondrial membrane proteins essential for mitochondrial trafficking—to peroxisomes is not required for basal peroxisomal distribution and long‐range trafficking, but rather for the maintenance of peroxisomal size and morphology through peroxisomal fission. Mechanistically, this is achieved by Miro negatively regulating Drp1‐dependent fission, a function that is shared with the mitochondria. We further find that the peroxisomal localisation of Miro is regulated by its first GTPase domain and is mediated by an interaction through its transmembrane domain with the peroxisomal‐membrane protein chaperone, Pex19. Our work highlights a shared regulatory role of Miro in maintaining the morphology of both peroxisomes and mitochondria, supporting a crosstalk between peroxisomal and mitochondrial biology.
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Affiliation(s)
- Christian Covill-Cooke
- Neuroscience, Physiology and Pharmacology Department, University College London, London, UK
| | - Viktoriya S Toncheva
- Neuroscience, Physiology and Pharmacology Department, University College London, London, UK
| | - James Drew
- Neuroscience, Physiology and Pharmacology Department, University College London, London, UK
| | - Nicol Birsa
- Neuroscience, Physiology and Pharmacology Department, University College London, London, UK
| | | | - Josef T Kittler
- Neuroscience, Physiology and Pharmacology Department, University College London, London, UK
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33
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Okumoto K, Tamura S, Honsho M, Fujiki Y. Peroxisome: Metabolic Functions and Biogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1299:3-17. [PMID: 33417203 DOI: 10.1007/978-3-030-60204-8_1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Peroxisome is an organelle conserved in almost all eukaryotic cells with a variety of functions in cellular metabolism, including fatty acid β-oxidation, synthesis of ether glycerolipid plasmalogens, and redox homeostasis. Such metabolic functions and the exclusive importance of peroxisomes have been highlighted in fatal human genetic disease called peroxisomal biogenesis disorders (PBDs). Recent advances in this field have identified over 30 PEX genes encoding peroxins as essential factors for peroxisome biogenesis in various species from yeast to humans. Functional delineation of the peroxins has revealed that peroxisome biogenesis comprises the processes, involving peroxisomal membrane assembly, matrix protein import, division, and proliferation. Catalase, the most abundant peroxisomal enzyme, catalyzes decomposition of hydrogen peroxide. Peroxisome plays pivotal roles in the cellular redox homeostasis and the response to oxidative stresses, depending on intracellular localization of catalase.
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Affiliation(s)
- Kanji Okumoto
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | | | | | - Yukio Fujiki
- Institute of Rheological Functions of Food, Fukuoka, Japan. .,Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
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34
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Huang TY, Zheng D, Hickner RC, Brault JJ, Cortright RN. Peroxisomal gene and protein expression increase in response to a high-lipid challenge in human skeletal muscle. Metabolism 2019; 98:53-61. [PMID: 31226353 PMCID: PMC7031862 DOI: 10.1016/j.metabol.2019.06.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 05/22/2019] [Accepted: 06/14/2019] [Indexed: 12/13/2022]
Abstract
Peroxisomes are essential for lipid metabolism and disruption of liver peroxisomal function results in neonatal death. Little is known about how peroxisomal content and activity respond to changes in the lipid environment in human skeletal muscle (HSkM). AIMS We hypothesized and tested that increased peroxisomal gene/protein expression and functionality occur in HSkM as an adaptive response to lipid oversupply. MATERIALS AND METHODS HSkM biopsies, derived from a total of sixty-two subjects, were collected for 1) examining correlations between peroxisomal proteins and intramyocellular lipid content (IMLC) as well as between peroxisomal functionality and IMLC, 2) assessing peroxisomal gene expression in response to acute- or 7-day high fat meal (HFM), and in human tissue derived primary myotubes for 3) treating with high fatty acids to induce peroxisomal adaptions. IMLC were measured by both biochemical analyses and fluorescent staining. Peroxisomal membrane protein PMP70 and biogenesis gene (PEX) expression were assessed using western blotting and realtime qRT-PCR respectively. 1-14C radiolabeled lignocerate and palmitate oxidation assays were performed for peroxisomal and mitochondrial functionality respectively. RESULTS 1) Under fasting conditions, HSkM tissue demonstrated a significant correlation (P ≪ 0.05) between IMCL and the peroxisomal biogenesis factor 19 (PEX19) protein as well as between lipid content and palmitate and lignocerate complete oxidation. 2) Similarly, post-HFM, additional PEX genes (Pex19, PEX11A, and PEX5) were significantly (P ≪ 0.05) upregulated. 3) Increments in PMP70, carnitine octanoyl transferase (CrOT), PGC-1α, and ERRα mRNA were observed post-fatty acid incubation in HSkM cells. PMP70 protein was significantly (P ≪ 0.05) elevated 48-h post lipid treatment. CONCLUSIONS These results are the first to associate IMLC with peroxisomal gene/protein expression and function in HSkM suggesting an adaptive role for peroxisomes in lipid metabolism in this tissue.
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Affiliation(s)
- Tai-Yu Huang
- Department of Kinesiology, East Carolina University, Greenville, NC, United States of America
| | - Donghai Zheng
- Department of Kinesiology, East Carolina University, Greenville, NC, United States of America; Diabetes and Obesity Institute, East Carolina University, Greenville, NC, United States of America
| | - Robert C Hickner
- Department of Kinesiology, East Carolina University, Greenville, NC, United States of America; Department of Physiology, East Carolina University, Greenville, NC, United States of America; Diabetes and Obesity Institute, East Carolina University, Greenville, NC, United States of America; College of Human Sciences, Florida State University, Tallahassee, FL, United States of America; School of Health Sciences, University of KwaZulu-Natal, Westville, South Africa
| | - Jeffrey J Brault
- Department of Kinesiology, East Carolina University, Greenville, NC, United States of America; Department of Physiology, East Carolina University, Greenville, NC, United States of America; Diabetes and Obesity Institute, East Carolina University, Greenville, NC, United States of America
| | - Ronald N Cortright
- Department of Kinesiology, East Carolina University, Greenville, NC, United States of America; Department of Physiology, East Carolina University, Greenville, NC, United States of America; Department of Surgery, East Carolina University, Greenville, NC, United States of America; Diabetes and Obesity Institute, East Carolina University, Greenville, NC, United States of America.
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35
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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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36
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Exner T, Romero-Brey I, Yifrach E, Rivera-Monroy J, Schrul B, Zouboulis CC, Stremmel W, Honsho M, Bartenschlager R, Zalckvar E, Poppelreuther M, Füllekrug J. An alternative membrane topology permits lipid droplet localization of peroxisomal fatty acyl-CoA reductase 1. J Cell Sci 2019; 132:jcs.223016. [PMID: 30745342 DOI: 10.1242/jcs.223016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 02/01/2019] [Indexed: 01/02/2023] Open
Abstract
Fatty acyl-CoA reductase 1 (Far1) is a ubiquitously expressed peroxisomal membrane protein that generates the fatty alcohols required for the biosynthesis of ether lipids. Lipid droplet localization of exogenously expressed and endogenous human Far1 was observed by fluorescence microscopy under conditions of increased triglyceride synthesis in tissue culture cells. This unexpected finding was supported further by correlative light electron microscopy and subcellular fractionation. Selective permeabilization, protease sensitivity and N-glycosylation tagging suggested that Far1 is able to assume two different membrane topologies, differing in the orientation of the short hydrophilic C-terminus towards the lumen or the cytosol, respectively. Two closely spaced hydrophobic domains are contained within the C-terminal region. When analyzed separately, the second domain was sufficient for the localization of a fluorescent reporter to lipid droplets. Targeting of Far1 to lipid droplets was not impaired in either Pex19 or ASNA1 (also known as TRC40) CRISPR/Cas9 knockout cells. In conclusion, our data suggest that Far1 is a novel member of the rather exclusive group of dual topology membrane proteins. At the same time, Far1 shows lipid metabolism-dependent differential subcellular localizations to peroxisomes and lipid droplets.
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Affiliation(s)
- Tarik Exner
- Molecular Cell Biology Laboratory Internal Medicine IV, University of Heidelberg, 69120 Heidelberg, Germany
| | - Inés Romero-Brey
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Eden Yifrach
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Jhon Rivera-Monroy
- Department of Molecular Biology, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Bianca Schrul
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Saarland University, 66421 Homburg/Saar, Germany
| | - Christos C Zouboulis
- Departments of Dermatology, Venereology, Allergology and Immunology, Dessau Medical Center, Brandenburg Medical School Theodor Fontane, 06847 Dessau, Germany
| | - Wolfgang Stremmel
- Molecular Cell Biology Laboratory Internal Medicine IV, University of Heidelberg, 69120 Heidelberg, Germany
| | - Masanori Honsho
- Medical Institute of Bioregulation, Kyushu University, 812-8582 Fukuoka, Japan
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Margarete Poppelreuther
- Molecular Cell Biology Laboratory Internal Medicine IV, University of Heidelberg, 69120 Heidelberg, Germany
| | - Joachim Füllekrug
- Molecular Cell Biology Laboratory Internal Medicine IV, University of Heidelberg, 69120 Heidelberg, Germany
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37
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Li L, Zheng J, Wu X, Jiang H. Mitochondrial AAA-ATPase Msp1 detects mislocalized tail-anchored proteins through a dual-recognition mechanism. EMBO Rep 2019; 20:embr.201846989. [PMID: 30858337 DOI: 10.15252/embr.201846989] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 01/28/2019] [Accepted: 02/11/2019] [Indexed: 01/09/2023] Open
Abstract
The conserved AAA-ATPase Msp1 is embedded in the outer mitochondrial membrane and removes mislocalized tail-anchored (TA) proteins upon dysfunction of the guided entry of tail-anchored (GET) pathway. It remains unclear how Msp1 recognizes its substrates. Here, we extensively characterize Msp1 and its substrates, including the mitochondrially targeted Pex15Δ30, and full-length Pex15, which mislocalizes to mitochondria upon dysfunction of Pex19 but not the GET pathway. Moreover, we identify two new substrates, Frt1 and Ysy6. Our results suggest that mislocalized TA proteins expose hydrophobic surfaces in the cytoplasm and are recognized by Msp1 through conserved hydrophobic residues. Introducing a hydrophobic patch into mitochondrial TA proteins transforms them into Msp1 substrates. In addition, Pex15Δ30 and Frt1 contain basic inter-membrane space (IMS) residues critical for their mitochondrial mistargeting. Remarkably, Msp1 recognizes this feature through the acidic D12 residue in its IMS domain. This dual-recognition mechanism involving interactions at the cytoplasmic and IMS domains of Msp1 and substrates greatly facilitates substrate recognition and is required by Msp1 to safeguard mitochondrial functions.
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Affiliation(s)
- Lanlan Li
- College of Life Sciences, Beijing Normal University, Beijing, China.,National Institute of Biological Sciences, Beijing, China.,Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing, China
| | - Jing Zheng
- National Institute of Biological Sciences, Beijing, China.,Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Xi Wu
- National Institute of Biological Sciences, Beijing, China
| | - Hui Jiang
- National Institute of Biological Sciences, Beijing, China .,Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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38
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Jansen RLM, Klei IJ. The peroxisome biogenesis factors Pex3 and Pex19: multitasking proteins with disputed functions. FEBS Lett 2019; 593:457-474. [DOI: 10.1002/1873-3468.13340] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/06/2019] [Accepted: 02/12/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Renate L. M. Jansen
- Molecular Cell Biology Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen The Netherlands
| | - Ida J. Klei
- Molecular Cell Biology Groningen Biomolecular Sciences and Biotechnology Institute University of Groningen The Netherlands
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39
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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: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [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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40
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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: 82] [Impact Index Per Article: 13.7] [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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41
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Lu B, Li C, Chen Q, Song J. ProBAPred: Inferring protein–protein binding affinity by incorporating protein sequence and structural features. J Bioinform Comput Biol 2018; 16:1850011. [PMID: 29954286 DOI: 10.1142/s0219720018500117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein-protein binding interaction is the most prevalent biological activity that mediates a great variety of biological processes. The increasing availability of experimental data of protein–protein interaction allows a systematic construction of protein–protein interaction networks, significantly contributing to a better understanding of protein functions and their roles in cellular pathways and human diseases. Compared to well-established classification for protein–protein interactions (PPIs), limited work has been conducted for estimating protein–protein binding free energy, which can provide informative real-value regression models for characterizing the protein–protein binding affinity. In this study, we propose a novel ensemble computational framework, termed ProBAPred (Protein–protein Binding Affinity Predictor), for quantitative estimation of protein–protein binding affinity. A large number of sequence and structural features, including physical–chemical properties, binding energy and conformation annotations, were collected and calculated from currently available protein binding complex datasets and the literature. Feature selection based on the WEKA package was performed to identify and characterize the most informative and contributing feature subsets. Experiments on the independent test showed that our ensemble method achieved the lowest Mean Absolute Error (MAE; 1.657[Formula: see text]kcal/mol) and the second highest correlation coefficient ([Formula: see text]), compared with the existing methods. The datasets and source codes of ProBAPred, and the supplementary materials in this study can be downloaded at http://lightning.med.monash.edu/probapred/ for academic use. We anticipate that the developed ProBAPred regression models can facilitate computational characterization and experimental studies of protein–protein binding affinity.
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Affiliation(s)
- Bangli Lu
- School of Computer, Electronic and Information, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, 100 Daxue Road, 530004 Nanning, P. R. China
| | - Chen Li
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
| | - Qingfeng Chen
- School of Computer, Electronic and Information, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, 100 Daxue Road, 530004 Nanning, P. R. China
| | - Jiangning Song
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, VIC 3800, Australia
- ARC Centre of Excellence for Advanced Molecular Imaging, Monash University, VIC 3800, Australia
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42
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Akşit A, van der Klei IJ. Yeast peroxisomes: How are they formed and how do they grow? Int J Biochem Cell Biol 2018; 105:24-34. [PMID: 30268746 DOI: 10.1016/j.biocel.2018.09.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 01/01/2023]
Abstract
Peroxisomes are single membrane enclosed cell organelles, which are present in almost all eukaryotic cells. In addition to the common peroxisomal pathways such as β-oxidation of fatty acids and decomposition of H2O2, these organelles fulfil a range of metabolic and non-metabolic functions. Peroxisomes are very important since various human disorders exist that are caused by a defect in peroxisome function. Here we describe our current knowledge on the molecular mechanisms of peroxisome biogenesis in yeast, including peroxisomal protein sorting, organelle dynamics and peroxisomal membrane contact sites.
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Affiliation(s)
- Arman Akşit
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands
| | - Ida J van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands.
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43
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Cichocki BA, Krumpe K, Vitali DG, Rapaport D. Pex19 is involved in importing dually targeted tail-anchored proteins to both mitochondria and peroxisomes. Traffic 2018; 19:770-785. [DOI: 10.1111/tra.12604] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 07/17/2018] [Accepted: 07/19/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Bogdan A. Cichocki
- Interfaculty Institute of Biochemistry; University of Tübingen; Tübingen Germany
| | - Katrin Krumpe
- Interfaculty Institute of Biochemistry; University of Tübingen; Tübingen Germany
| | - Daniela G. Vitali
- Interfaculty Institute of Biochemistry; University of Tübingen; Tübingen Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry; University of Tübingen; Tübingen Germany
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44
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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: 45] [Impact Index Per Article: 7.5] [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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45
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Hac1 function revealed by the protein expression profile of a OtHAC1 mutant of thermotolerant methylotrophic yeast Ogataea thermomethanolica. Mol Biol Rep 2018; 45:1311-1319. [DOI: 10.1007/s11033-018-4287-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 07/26/2018] [Indexed: 12/13/2022]
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46
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Choi YB, Choi Y, Harhaj EW. Peroxisomes support human herpesvirus 8 latency by stabilizing the viral oncogenic protein vFLIP via the MAVS-TRAF complex. PLoS Pathog 2018; 14:e1007058. [PMID: 29746593 PMCID: PMC5963799 DOI: 10.1371/journal.ppat.1007058] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 05/22/2018] [Accepted: 04/25/2018] [Indexed: 12/22/2022] Open
Abstract
Human herpesvirus 8 (HHV-8) is causally related to human malignancies. HHV-8 latent viral FLICE-inhibitory protein (vFLIP) is a viral oncoprotein that is linked to pathogenesis, but how its expression is regulated is largely unknown. In an attempt to understand the role of the mitochondrial antiviral signaling (MAVS) adaptor in HHV-8 infection, we discovered that vFLIP expression was post-translationally up-regulated by the MAVS signaling complex on peroxisomes. Furthermore, we demonstrated that vFLIP could be targeted to the peroxisomes, where it was oncogenically active, in a PEX19-dependent manner. Targeted disruption of vFLIP and MAVS interaction resulted in a decrease in vFLIP expression and selectively promoted death of latently HHV-8-infected cells, providing therapeutic potential for treating HHV-8 diseases. Collectively, our experimental results suggest novel involvement of peroxisomes and MAVS in the stabilization of vFLIP and thereby in the establishment or maintenance of HHV-8 latency and associated pathogenesis.
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Affiliation(s)
- Young Bong Choi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
| | - Yeeun Choi
- Centennial High School, Ellicott City, Maryland, United States of America
| | - Edward William Harhaj
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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47
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Law KB, Bronte-Tinkew D, Di Pietro E, Snowden A, Jones RO, Moser A, Brumell JH, Braverman N, Kim PK. The peroxisomal AAA ATPase complex prevents pexophagy and development of peroxisome biogenesis disorders. Autophagy 2018; 13:868-884. [PMID: 28521612 PMCID: PMC5446072 DOI: 10.1080/15548627.2017.1291470] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Peroxisome biogenesis disorders (PBDs) are metabolic disorders caused by the loss of peroxisomes. The majority of PBDs result from mutation in one of 3 genes that encode for the peroxisomal AAA ATPase complex (AAA-complex) required for cycling PEX5 for peroxisomal matrix protein import. Mutations in these genes are thought to result in a defect in peroxisome assembly by preventing the import of matrix proteins. However, we show here that loss of the AAA-complex does not prevent matrix protein import, but instead causes an upregulation of peroxisome degradation by macroautophagy, or pexophagy. The loss of AAA-complex function in cells results in the accumulation of ubiquitinated PEX5 on the peroxisomal membrane that signals pexophagy. Inhibiting autophagy by genetic or pharmacological approaches rescues peroxisome number, protein import and function. Our findings suggest that the peroxisomal AAA-complex is required for peroxisome quality control, whereas its absence results in the selective degradation of the peroxisome. Thus the loss of peroxisomes in PBD patients with mutations in their peroxisomal AAA-complex is a result of increased pexophagy. Our study also provides a framework for the development of novel therapeutic treatments for PBDs.
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Affiliation(s)
- Kelsey B Law
- a Cell Biology Program , Hospital for Sick Children, Peter Gilgan Centre for Research and Learning , Toronto , ON , Canada.,b Department of Biochemistry , University of Toronto , Toronto , ON , Canada
| | - Dana Bronte-Tinkew
- a Cell Biology Program , Hospital for Sick Children, Peter Gilgan Centre for Research and Learning , Toronto , ON , Canada
| | - Erminia Di Pietro
- c Research Institute of the MUHC and McGill University , Montreal , QC , Canada
| | - Ann Snowden
- d Kennedy Krieger Institute , Baltimore , MD , USA
| | | | - Ann Moser
- d Kennedy Krieger Institute , Baltimore , MD , USA
| | - John H Brumell
- a Cell Biology Program , Hospital for Sick Children, Peter Gilgan Centre for Research and Learning , Toronto , ON , Canada.,e Department of Molecular Genetics , University of Toronto , Toronto , ON , Canada.,f Institute of Medical Science, University of Toronto , Toronto , ON , Canada.,g SickKids IBD Centre , Hospital for Sick Children , Toronto , ON , Canada
| | - Nancy Braverman
- c Research Institute of the MUHC and McGill University , Montreal , QC , Canada
| | - Peter K Kim
- a Cell Biology Program , Hospital for Sick Children, Peter Gilgan Centre for Research and Learning , Toronto , ON , Canada.,b Department of Biochemistry , University of Toronto , Toronto , ON , Canada
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48
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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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49
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Kalel VC, Erdmann R. Unraveling of the Structure and Function of Peroxisomal Protein Import Machineries. Subcell Biochem 2018; 89:299-321. [PMID: 30378029 DOI: 10.1007/978-981-13-2233-4_13] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peroxisomes are dynamic organelles of eukaryotic cells performing a wide range of functions including fatty acid oxidation, peroxide detoxification and ether-lipid synthesis in mammals. Peroxisomes lack their own DNA and therefore have to import proteins post-translationally. Peroxisomes can import folded, co-factor bound and even oligomeric proteins. The involvement of cycling receptors is a special feature of peroxisomal protein import. Complex machineries of peroxin (PEX) proteins mediate peroxisomal matrix and membrane protein import. Identification of PEX genes was dominated by forward genetic techniques in the early 90s. However, recent developments in proteomic techniques has revolutionized the detailed characterization of peroxisomal protein import. Here, we summarize the current knowledge on peroxisomal protein import with emphasis on the contribution of proteomic approaches to our understanding of the composition and function of the peroxisomal protein import machineries.
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Affiliation(s)
- Vishal C Kalel
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany.
| | - Ralf Erdmann
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany
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50
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Okumoto K, Ono T, Toyama R, Shimomura A, Nagata A, Fujiki Y. New splicing variants of mitochondrial Rho GTPase-1 (Miro1) transport peroxisomes. J Cell Biol 2017; 217:619-633. [PMID: 29222186 PMCID: PMC5800816 DOI: 10.1083/jcb.201708122] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/27/2017] [Accepted: 11/06/2017] [Indexed: 01/31/2023] Open
Abstract
The mechanisms underlying microtubule-dependent long-distance movement of peroxisomes in mammalian cells are unclear. Okumoto et al. identify splicing variants of human mitochondrial Rho GTPase-1 (Miro1) that localize to peroxisomes and that link these organelles to microtubule-dependent transport complexes including TRAK2. Microtubule-dependent long-distance movement of peroxisomes occurs in mammalian cells. However, its molecular mechanisms remain undefined. In this study, we identified three distinct splicing variants of human mitochondrial Rho GTPase-1 (Miro1), each containing amino acid sequence insertions 1 (named Miro1-var2), 2 (Miro1-var3), and both 1 and 2 (Miro1-var4), respectively, at upstream of the transmembrane domain. Miro1-var4 and Miro1-var2 are localized to peroxisomes in a manner dependent on the insertion 1 that is recognized by the cytosolic receptor Pex19p. Exogenous expression of Miro1-var4 induces accumulation of peroxisomes at the cell periphery and augments long-range movement of peroxisomes along microtubules. Depletion of all Miro1 variants by knocking down MIRO1 suppresses the long-distance movement of peroxisomes. Such abrogated movement is restored by reexpression of peroxisomal Miro1 variants. Collectively, our findings identify for the first time peroxisome-localized Miro1 variants as adapter proteins that link peroxisomes to the microtubule-dependent transport complexes including TRAK2 in the intracellular translocation of peroxisomes in mammalian cells.
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Affiliation(s)
- Kanji Okumoto
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan.,Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Tatsuaki Ono
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Ryusuke Toyama
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Ayako Shimomura
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Aiko Nagata
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Yukio Fujiki
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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