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Lu Y, George J. Interaction between fatty acid oxidation and ethanol metabolism in liver. Am J Physiol Gastrointest Liver Physiol 2024; 326:G483-G494. [PMID: 38573193 DOI: 10.1152/ajpgi.00281.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 04/05/2024]
Abstract
Fatty acid oxidation (FAO) releases the energy stored in fat to maintain basic biological processes. Dehydrogenation is a major way to oxidize fatty acids, which needs NAD+ to accept the released H+ from fatty acids and form NADH, which increases the ratio of NADH/NAD+ and consequently inhibits FAO leading to the deposition of fat in the liver, which is termed fatty liver or steatosis. Consumption of alcohol (ethanol) initiates simple steatosis that progresses to alcoholic steatohepatitis, which constitutes a spectrum of liver disorders called alcohol-associated liver disease (ALD). ALD is linked to ethanol metabolism. Ethanol is metabolized by alcohol dehydrogenase (ADH), microsomal ethanol oxidation system (MEOS), mainly cytochrome P450 2E1 (CYP2E1), and catalase. ADH also requires NAD+ to accept the released H+ from ethanol. Thus, ethanol metabolism by ADH leads to increased ratio of NADH/NAD+, which inhibits FAO and induces steatosis. CYP2E1 directly consumes reducing equivalent NADPH to oxidize ethanol, which generates reactive oxygen species (ROS) that lead to cellular injury. Catalase is mainly present in peroxisomes, where very long-chain fatty acids and branched-chain fatty acids are oxidized, and the resultant short-chain fatty acids will be further oxidized in mitochondria. Peroxisomal FAO generates hydrogen peroxide (H2O2), which is locally decomposed by catalase. When ethanol is present, catalase uses H2O2 to oxidize ethanol. In this review, we introduce FAO (including α-, β-, and ω-oxidation) and ethanol metabolism (by ADH, CYP2E1, and catalase) followed by the interaction between FAO and ethanol metabolism in the liver and its pathophysiological significance.
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Affiliation(s)
- Yongke Lu
- Department of Biomedical Sciences, Joan C. Edwards College of Medicine, Marshall University, Huntington, West Virginia, United States
| | - Joseph George
- Department of Hepatology, Kanazawa Medical University, Uchinada, Ishikawa, Japan
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Gaussmann S, Peschel R, Ott J, Zak KM, Sastre J, Delhommel F, Popowicz GM, Boekhoven J, Schliebs W, Erdmann R, Sattler M. Modulation of peroxisomal import by the PEX13 SH3 domain and a proximal FxxxF binding motif. Nat Commun 2024; 15:3317. [PMID: 38632234 PMCID: PMC11024197 DOI: 10.1038/s41467-024-47605-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
Import of proteins into peroxisomes depends on PEX5, PEX13 and PEX14. By combining biochemical methods and structural biology, we show that the C-terminal SH3 domain of PEX13 mediates intramolecular interactions with a proximal FxxxF motif. The SH3 domain also binds WxxxF peptide motifs in the import receptor PEX5, demonstrating evolutionary conservation of such interactions from yeast to human. Strikingly, intramolecular interaction of the PEX13 FxxxF motif regulates binding of PEX5 WxxxF/Y motifs to the PEX13 SH3 domain. Crystal structures reveal how FxxxF and WxxxF/Y motifs are recognized by a non-canonical surface on the SH3 domain. The PEX13 FxxxF motif also mediates binding to PEX14. Surprisingly, the potential PxxP binding surface of the SH3 domain does not recognize PEX14 PxxP motifs, distinct from its yeast ortholog. Our data show that the dynamic network of PEX13 interactions with PEX5 and PEX14, mediated by diaromatic peptide motifs, modulates peroxisomal matrix import.
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Affiliation(s)
- Stefan Gaussmann
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Rebecca Peschel
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
| | - Julia Ott
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
| | - Krzysztof M Zak
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Judit Sastre
- Technical University of Munich, TUM School of Natural Sciences, Department of Chemistry, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Florent Delhommel
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Grzegorz M Popowicz
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Job Boekhoven
- Technical University of Munich, TUM School of Natural Sciences, Department of Chemistry, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany.
| | - Michael Sattler
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany.
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
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Garrelfs SF, Chornyi S, Te Brinke H, Ruiter J, Groothoff J, Wanders RJA. Glyoxylate reductase: Definitive identification in human liver mitochondria, its importance for the compartment-specific detoxification of glyoxylate. J Inherit Metab Dis 2024; 47:280-288. [PMID: 38200664 DOI: 10.1002/jimd.12711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 11/13/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024]
Abstract
Glyoxylate is a key metabolite generated from various precursor substrates in different subcellular compartments including mitochondria, peroxisomes, and the cytosol. The fact that glyoxylate is a good substrate for the ubiquitously expressed enzyme lactate dehydrogenase (LDH) requires the presence of efficient glyoxylate detoxification systems to avoid the formation of oxalate. Furthermore, this detoxification needs to be compartment-specific since LDH is actively present in multiple subcellular compartments including peroxisomes, mitochondria, and the cytosol. Whereas the identity of these protection systems has been established for both peroxisomes and the cytosol as concluded from the deficiency of alanine glyoxylate aminotransferase (AGT) in primary hyperoxaluria type 1 (PH1) and glyoxylate reductase (GR) in PH2, the glyoxylate protection system in mitochondria has remained less well defined. In this manuscript, we show that the enzyme glyoxylate reductase has a bimodal distribution in human embryonic kidney (HEK293), hepatocellular carcinoma (HepG2), and cervical carcinoma (HeLa) cells and more importantly, in human liver, and is actively present in both the mitochondrial and cytosolic compartments. We conclude that the metabolism of glyoxylate in humans requires the complicated interaction between different subcellular compartments within the cell and discuss the implications for the different primary hyperoxalurias.
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Affiliation(s)
- Sander F Garrelfs
- Departments of Pediatrics, Emma Children's Hospital, Section Pediatric Nephrology & Laboratory Division, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands
| | - Serhii Chornyi
- Departments of Pediatrics, Emma Children's Hospital, Section Pediatric Nephrology & Laboratory Division, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands
| | - Heleen Te Brinke
- Departments of Pediatrics, Emma Children's Hospital, Section Pediatric Nephrology & Laboratory Division, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands
| | - Jos Ruiter
- Departments of Pediatrics, Emma Children's Hospital, Section Pediatric Nephrology & Laboratory Division, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands
| | - Jaap Groothoff
- Departments of Pediatrics, Emma Children's Hospital, Section Pediatric Nephrology & Laboratory Division, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands
| | - Ronald J A Wanders
- Departments of Pediatrics, Emma Children's Hospital, Section Pediatric Nephrology & Laboratory Division, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centers, Academic Medical Center, Amsterdam, The Netherlands
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Parsons BD, Medina-Luna D, Scur M, Pinelli M, Gamage GS, Chilvers RA, Hamon Y, Ahmed IHI, Savary S, Makrigiannis AP, Braverman NE, Rodriguez-Alcazar JF, Latz E, Karakach TK, Di Cara F. Peroxisome deficiency underlies failures in hepatic immune cell development and antigen presentation in a severe Zellweger disease model. Cell Rep 2024; 43:113744. [PMID: 38329874 DOI: 10.1016/j.celrep.2024.113744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/21/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
Peroxisome biogenesis disorders (PBDs) represent a group of metabolic conditions that cause severe developmental defects. Peroxisomes are essential metabolic organelles, present in virtually every eukaryotic cell and mediating key processes in immunometabolism. To date, the full spectrum of PBDs remains to be identified, and the impact PBDs have on immune function is unexplored. This study presents a characterization of the hepatic immune compartment of a neonatal PBD mouse model at single-cell resolution to establish the importance and function of peroxisomes in developmental hematopoiesis. We report that hematopoietic defects are a feature in a severe PBD murine model. Finally, we identify a role for peroxisomes in the regulation of the major histocompatibility class II expression and antigen presentation to CD4+ T cells in dendritic cells. This study adds to our understanding of the mechanisms of PBDs and expands our knowledge of the role of peroxisomes in immunometabolism.
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Affiliation(s)
- Brendon D Parsons
- University of Alberta, Department of Laboratory Medicine and Pathology, Edmonton, AB T6G 1C9, Canada
| | - Daniel Medina-Luna
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Michal Scur
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Marinella Pinelli
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Gayani S Gamage
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Rebecca A Chilvers
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Yannick Hamon
- Aix Marseille University, CNRS, INSERM au Centre d'Immunologie de Marseille Luminy, 13288 Marseille, France
| | - Ibrahim H I Ahmed
- Dalhousie University, Department of Pharmacology, Halifax, NS B3H 4R2, Canada; Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Stéphane Savary
- University of Bourgogne, Laboratoire Bio-PeroxIL EA7270, Dijon, France
| | - Andrew P Makrigiannis
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada; Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Nancy E Braverman
- Research Institute of the McGill University Children's Hospital, Montreal, QC H4A 3J1, Canada
| | | | - Eicke Latz
- University of Bonn, Institute of Innate Immunity, Medical Faculty, 53127 Bonn, Germany
| | - Tobias K Karakach
- Dalhousie University, Department of Pharmacology, Halifax, NS B3H 4R2, Canada; Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Francesca Di Cara
- University of Alberta, Department of Laboratory Medicine and Pathology, Edmonton, AB T6G 1C9, Canada; Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada.
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5
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Doering LN, Gerling N, Linnenbrügger L, Lansing H, Baune MC, Fischer K, von Schaewen A. Evidence for dual targeting control of Arabidopsis 6-phosphogluconate dehydrogenase isoforms by N-terminal phosphorylation. J Exp Bot 2024:erae077. [PMID: 38412416 DOI: 10.1093/jxb/erae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Indexed: 02/29/2024]
Abstract
The oxidative pentose-phosphate pathway (OPPP) retrieves NADPH from glucose-6-phosphate, which is important in chloroplasts at night and in plastids of heterotrophic tissues. We previously studied how OPPP enzymes may transiently locate to peroxisomes, but how this is achieved for the 3rd enzyme remained unclear. By extending our genetic approach, we could demonstrate that Arabidopsis isoform 6-phosphogluconate dehydrogenase 2 (PGD2) is indispensable in peroxisomes during fertilization, and then studied why all PGD-reporter fusions show a mostly cytosolic pattern. Previously published interaction of a plant PGD with thioredoxin m was confirmed using Trxm2 for yeast-2-hybrid (Y2H) and bimolecular fluorescent complementation (BiFC) assays, and medial reporter fusions (with both ends accessible) turned out to be beneficial for studying peroxisomal targeting of PGD2. Of special importance were phosphomimetic changes at Thr6, resulting in a clear targeting switch to peroxisomes, while a similar change at position Ser7 in PGD1 conferred plastid import. Apparently, efficient subcellular localization can be achieved by activating an unknown kinase, either early after or during translation. N-terminal phosphorylation of PGD2 interfered with dimerization in the cytosol, thus allowing accessibility of the C-terminal peroxisomal targeting signal (PTS1). Notably, we identified amino-acid positions that are conserved among plant PGD homologs, with PTS1 motifs first appearing in ferns, suggesting a functional link to fertilization during the evolution of seed plants.
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Affiliation(s)
- Lennart Nico Doering
- University of Münster, Department of Biology, Institute of Plant Biology and Biotechnology, Molecular Physiology of Plants, Schlossplatz 7, D-48149 Münster, Germany
| | - Niklas Gerling
- University of Münster, Department of Biology, Institute of Plant Biology and Biotechnology, Molecular Physiology of Plants, Schlossplatz 7, D-48149 Münster, Germany
| | - Loreen Linnenbrügger
- University of Münster, Department of Biology, Institute of Plant Biology and Biotechnology, Molecular Physiology of Plants, Schlossplatz 7, D-48149 Münster, Germany
| | - Hannes Lansing
- University of Münster, Department of Biology, Institute of Plant Biology and Biotechnology, Molecular Physiology of Plants, Schlossplatz 7, D-48149 Münster, Germany
| | - Marie-Christin Baune
- University of Münster, Department of Biology, Institute of Plant Biology and Biotechnology, Molecular Physiology of Plants, Schlossplatz 7, D-48149 Münster, Germany
| | - Kerstin Fischer
- University of Münster, Department of Biology, Institute of Plant Biology and Biotechnology, Molecular Physiology of Plants, Schlossplatz 7, D-48149 Münster, Germany
| | - Antje von Schaewen
- University of Münster, Department of Biology, Institute of Plant Biology and Biotechnology, Molecular Physiology of Plants, Schlossplatz 7, D-48149 Münster, Germany
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Obara K, Nishimura K, Kamura T. E3 Ligases Regulate Organelle Inheritance in Yeast. Cells 2024; 13:292. [PMID: 38391905 PMCID: PMC10887072 DOI: 10.3390/cells13040292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/25/2024] [Accepted: 02/03/2024] [Indexed: 02/24/2024] Open
Abstract
Saccharomyces cerevisiae proliferates by budding, which includes the formation of a cytoplasmic protrusion called the 'bud', into which DNA, RNA, proteins, organelles, and other materials are transported. The transport of organelles into the growing bud must be strictly regulated for the proper inheritance of organelles by daughter cells. In yeast, the RING-type E3 ubiquitin ligases, Dma1 and Dma2, are involved in the proper inheritance of mitochondria, vacuoles, and presumably peroxisomes. These organelles are transported along actin filaments toward the tip of the growing bud by the myosin motor protein, Myo2. During organelle transport, organelle-specific adaptor proteins, namely Mmr1, Vac17, and Inp2 for mitochondria, vacuoles, and peroxisomes, respectively, bridge the organelles and myosin. After reaching the bud, the adaptor proteins are ubiquitinated by the E3 ubiquitin ligases and degraded by the proteasome. Targeted degradation of the adaptor proteins is necessary to unload vacuoles, mitochondria, and peroxisomes from the actin-myosin machinery. Impairment of the ubiquitination of adaptor proteins results in the failure of organelle release from myosin, which, in turn, leads to abnormal dynamics, morphology, and function of the inherited organelles, indicating the significance of proper organelle unloading from myosin. Herein, we summarize the role and regulation of E3 ubiquitin ligases during organelle inheritance in yeast.
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Affiliation(s)
- Keisuke Obara
- Department of Biological Science, Graduate School of Science, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya 464-8602, Japan;
| | | | - Takumi Kamura
- Department of Biological Science, Graduate School of Science, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya 464-8602, Japan;
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Osei D, Baumgart-Vogt E, Ahlemeyer B, Herden C. Tumor Necrosis Factor-α Receptor 1 Mediates Borna Disease Virus 1-Induced Changes in Peroxisomal and Mitochondrial Dynamics in Neurons. Int J Mol Sci 2024; 25:1849. [PMID: 38339126 PMCID: PMC10855776 DOI: 10.3390/ijms25031849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Borna disease virus 1 (BoDV1) causes a persistent infection in the mammalian brain. Peroxisomes and mitochondria play essential roles in the cellular antiviral immune response, but the effect of BoDV1 infection on peroxisomal and mitochondrial dynamics and their respective antioxidant capacities is still not clear. Using different mouse lines-i.e., tumor necrosis factor-α transgenic (TNFTg; to pro-inflammatory status), TNF receptor-1 knockout (TNFR1ko), and TNFR2ko mice in comparison to wild-type (Wt) mice-we analyzed the abundances of both organelles and their main antioxidant enzymes, catalase and superoxide dismutase 2 (SOD2), in neurons of the hippocampal, cerebral, and cerebellar cortices. In TNFTg mice, a strong increase in mitochondrial (6.9-fold) and SOD2 (12.1-fold) abundances was detected; meanwhile, peroxisomal abundance increased slightly (1.5-fold), but that of catalase decreased (2.9-fold). After BoDV1 infection, a strong decrease in mitochondrial (2.1-6.5-fold), SOD2 (2.7-9.1-fold), and catalase (2.7-10.3-fold) abundances, but a slight increase in peroxisomes (1.3-1.6-fold), were detected in Wt and TNFR2ko mice, whereas no changes occurred in TNFR1ko mice. Our data suggest that the TNF system plays a crucial role in the biogenesis of both subcellular organelles. Moreover, TNFR1 signaling mediated the changes in peroxisomal and mitochondrial dynamics after BoDV1 infection, highlighting new mechanisms by which BoDV1 may achieve immune evasion and viral persistence.
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Affiliation(s)
- Dominic Osei
- Institute for Anatomy and Cell Biology, Justus Liebig University Giessen, 35392 Giessen, Germany; (D.O.); (E.B.-V.)
- Institute of Veterinary Pathology, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Eveline Baumgart-Vogt
- Institute for Anatomy and Cell Biology, Justus Liebig University Giessen, 35392 Giessen, Germany; (D.O.); (E.B.-V.)
| | - Barbara Ahlemeyer
- Institute for Anatomy and Cell Biology, Justus Liebig University Giessen, 35392 Giessen, Germany; (D.O.); (E.B.-V.)
| | - Christiane Herden
- Institute of Veterinary Pathology, Justus Liebig University Giessen, 35392 Giessen, Germany
- Center for Mind, Brain and Behavior, Justus Liebig University Giessen, 35392 Giessen, Germany
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Landowski M, Gogoi P, Ikeda S, Ikeda A. Roles of transmembrane protein 135 in mitochondrial and peroxisomal functions - implications for age-related retinal disease. Front Ophthalmol (Lausanne) 2024; 4:1355379. [PMID: 38576540 PMCID: PMC10993500 DOI: 10.3389/fopht.2024.1355379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Aging is the most significant risk factor for age-related diseases in general, which is true for age-related diseases in the eye including age-related macular degeneration (AMD). Therefore, in order to identify potential therapeutic targets for these diseases, it is crucial to understand the normal aging process and how its mis-regulation could cause age-related diseases at the molecular level. Recently, abnormal lipid metabolism has emerged as one major aspect of age-related symptoms in the retina. Animal models provide excellent means to identify and study factors that regulate lipid metabolism in relation to age-related symptoms. Central to this review is the role of transmembrane protein 135 (TMEM135) in the retina. TMEM135 was identified through the characterization of a mutant mouse strain exhibiting accelerated retinal aging and positional cloning of the responsible mutation within the gene, indicating the crucial role of TMEM135 in regulating the normal aging process in the retina. Over the past decade, the molecular functions of TMEM135 have been explored in various models and tissues, providing insights into the regulation of metabolism, particularly lipid metabolism, through its action in multiple organelles. Studies indicated that TMEM135 is a significant regulator of peroxisomes, mitochondria, and their interaction. Here, we provide an overview of the molecular functions of TMEM135 which is crucial for regulating mitochondria, peroxisomes, and lipids. The review also discusses the age-dependent phenotypes in mice with TMEM135 perturbations, emphasizing the importance of a balanced TMEM135 function for the health of the retina and other tissues including the heart, liver, and adipose tissue. Finally, we explore the potential roles of TMEM135 in human age-related retinal diseases, connecting its functions to the pathobiology of AMD.
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Affiliation(s)
- Michael Landowski
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, United States
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Purnima Gogoi
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, United States
| | - Sakae Ikeda
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, United States
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Akihiro Ikeda
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, United States
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, United States
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Martín JF, Liras P. Targeting of Specialized Metabolites Biosynthetic Enzymes to Membranes and Vesicles by Posttranslational Palmitoylation: A Mechanism of Non-Conventional Traffic and Secretion of Fungal Metabolites. Int J Mol Sci 2024; 25:1224. [PMID: 38279221 PMCID: PMC10816013 DOI: 10.3390/ijms25021224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/30/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024] Open
Abstract
In nature, the formation of specialized (secondary) metabolites is associated with the late stages of fungal development. Enzymes involved in the biosynthesis of secondary metabolites in fungi are located in distinct subcellular compartments including the cytosol, peroxisomes, endosomes, endoplasmic reticulum, different types of vesicles, the plasma membrane and the cell wall space. The enzymes traffic between these subcellular compartments and the secretion through the plasma membrane are still unclear in the biosynthetic processes of most of these metabolites. Recent reports indicate that some of these enzymes initially located in the cytosol are later modified by posttranslational acylation and these modifications may target them to membrane vesicle systems. Many posttranslational modifications play key roles in the enzymatic function of different proteins in the cell. These modifications are very important in the modulation of regulatory proteins, in targeting of proteins, intracellular traffic and metabolites secretion. Particularly interesting are the protein modifications by palmitoylation, prenylation and miristoylation. Palmitoylation is a thiol group-acylation (S-acylation) of proteins by palmitic acid (C16) that is attached to the SH group of a conserved cysteine in proteins. Palmitoylation serves to target acylated proteins to the cytosolic surface of cell membranes, e.g., to the smooth endoplasmic reticulum, whereas the so-called toxisomes are formed in trichothecene biosynthesis. Palmitoylation of the initial enzymes involved in the biosynthesis of melanin serves to target them to endosomes and later to the conidia, whereas other non-palmitoylated laccases are secreted directly by the conventional secretory pathway to the cell wall space where they perform the last step(s) of melanin biosynthesis. Six other enzymes involved in the biosynthesis of endocrosin, gliotoxin and fumitremorgin believed to be cytosolic are also targeted to vesicles, although it is unclear if they are palmitoylated. Bioinformatic analysis suggests that palmitoylation may be frequent in the modification and targeting of polyketide synthetases and non-ribosomal peptide synthetases. The endosomes may integrate other small vesicles with different cargo proteins, forming multivesicular bodies that finally fuse with the plasma membrane during secretion. Another important effect of palmitoylation is that it regulates calcium metabolism by posttranslational modification of the phosphatase calcineurin. Mutants defective in the Akr1 palmitoyl transferase in several fungi are affected in calcium transport and homeostasis, thus impacting on the biosynthesis of calcium-regulated specialized metabolites. The palmitoylation of secondary metabolites biosynthetic enzymes and their temporal distribution respond to the conidiation signaling mechanism. In summary, this posttranslational modification drives the spatial traffic of the biosynthetic enzymes between the subcellular organelles and the plasma membrane. This article reviews the molecular mechanism of palmitoylation and the known fungal palmitoyl transferases. This novel information opens new ways to improve the biosynthesis of the bioactive metabolites and to increase its secretion in fungi.
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Affiliation(s)
- Juan F. Martín
- Departamento de Biología Molecular, Área de Microbiología, Universidad de León, 24071 León, Spain;
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Singin Ö, Astapenka A, Costina V, Kühl S, Bonekamp N, Drews O, Islinger M. Analysis of the Mouse Hepatic Peroxisome Proteome-Identification of Novel Protein Constituents Using a Semi-Quantitative SWATH-MS Approach. Cells 2024; 13:176. [PMID: 38247867 PMCID: PMC10814758 DOI: 10.3390/cells13020176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024] Open
Abstract
Ongoing technical and bioinformatics improvements in mass spectrometry (MS) allow for the identifying and quantifying of the enrichment of increasingly less-abundant proteins in individual fractions. Accordingly, this study reassessed the proteome of mouse liver peroxisomes by the parallel isolation of peroxisomes from a mitochondria- and a microsome-enriched prefraction, combining density-gradient centrifugation with a semi-quantitative SWATH-MS proteomics approach to unveil novel peroxisomal or peroxisome-associated proteins. In total, 1071 proteins were identified using MS and assessed in terms of their distribution in either high-density peroxisomal or low-density gradient fractions, containing the bulk of organelle material. Combining the data from both fractionation approaches allowed for the identification of specific protein profiles characteristic of mitochondria, the ER and peroxisomes. Among the proteins significantly enriched in the peroxisomal cluster were several novel peroxisomal candidates. Five of those were validated by colocalization in peroxisomes, using confocal microscopy. The peroxisomal import of HTATIP2 and PAFAH2, which contain a peroxisome-targeting sequence 1 (PTS1), could be confirmed by overexpression in HepG2 cells. The candidates SAR1B and PDCD6, which are known ER-exit-site proteins, did not directly colocalize with peroxisomes, but resided at ER sites, which frequently surrounded peroxisomes. Hence, both proteins might concentrate at presumably co-purified peroxisome-ER membrane contacts. Intriguingly, the fifth candidate, OCIA domain-containing protein 1, was previously described as decreasing mitochondrial network formation. In this work, we confirmed its peroxisomal localization and further observed a reduction in peroxisome numbers in response to OCIAD1 overexpression. Hence, OCIAD1 appears to be a novel protein, which has an impact on both mitochondrial and peroxisomal maintenance.
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Affiliation(s)
- Öznur Singin
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
| | - Artur Astapenka
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
| | - Victor Costina
- Institute of Clinical Chemistry, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (V.C.); (O.D.)
| | - Sandra Kühl
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
| | - Nina Bonekamp
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
| | - Oliver Drews
- Institute of Clinical Chemistry, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (V.C.); (O.D.)
- Biomedical Mass Spectrometry, Center for Medical Research, Johannes Kepler University Linz, 4020 Linz, Austria
| | - Markus Islinger
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
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11
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Aguirre-López B, Suaste-Olmos F, Peraza-Reyes L. The peroxisome protein translocation machinery is developmentally regulated in the fungus Podospora anserina. Microbiol Spectr 2024; 12:e0213923. [PMID: 38088545 PMCID: PMC10782954 DOI: 10.1128/spectrum.02139-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 11/11/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Sexual reproduction allows eukaryotic organisms to produce genetically diverse progeny. This process relies on meiosis, a reductional division that enables ploidy maintenance and genetic recombination. Meiotic differentiation also involves the renewal of cell functioning to promote offspring rejuvenation. Research in the model fungus Podospora anserina has shown that this process involves a complex regulation of the function and dynamics of different organelles, including peroxisomes. These organelles are critical for meiosis induction and play further significant roles in meiotic development. Here we show that PEX13-a key constituent of the protein conduit through which the proteins defining peroxisome function reach into the organelle-is subject to a developmental regulation that almost certainly involves its selective ubiquitination-dependent removal and that modulates its abundance throughout meiotic development and at different sexual differentiation processes. Our results show that meiotic development involves a complex developmental regulation of the peroxisome protein translocation system.
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Affiliation(s)
- Beatriz Aguirre-López
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Coyoacán, Mexico
| | - Fernando Suaste-Olmos
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Coyoacán, Mexico
| | - Leonardo Peraza-Reyes
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Coyoacán, Mexico
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12
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Miner GE, Smith SY, Showalter WK, So CM, Ragusa JV, Powers AE, Zanellati MC, Hsu CH, Marchan MF, Cohen S. Contact-FP: A Dimerization-Dependent Fluorescent Protein Toolkit for Visualizing Membrane Contact Site Dynamics. Contact (Thousand Oaks) 2024; 7:25152564241228911. [PMID: 38327561 PMCID: PMC10846013 DOI: 10.1177/25152564241228911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/11/2024] [Indexed: 02/09/2024]
Abstract
Membrane contact sites (MCSs) are sites of close apposition between two organelles used to exchange ions, lipids, and information. Cells respond to changing environmental or developmental conditions by modulating the number, extent, or duration of MCSs. Because of their small size and dynamic nature, tools to study the dynamics of MCSs in live cells have been limited. Dimerization-dependent fluorescent proteins (ddFPs) targeted to organelle membranes are an ideal tool for studying MCS dynamics because they reversibly interact to fluoresce specifically at the interface between two organelles. Here, we build on previous work using ddFPs as sensors to visualize the morphology and dynamics of MCSs. We engineered a suite of ddFPs called Contact-FP that targets ddFP monomers to lipid droplets (LDs), the endoplasmic reticulum (ER), mitochondria, peroxisomes, lysosomes, plasma membrane, caveolae, and the cytoplasm. We show that these probes correctly localize to their target organelles. Using LDs as a test case, we demonstrate that Contact-FP pairs specifically localize to the interface between two target organelles. Titration of LD-mitochondria ddFPs revealed that these sensors can be used at high concentrations to drive MCSs or can be titrated down to minimally perturb and visualize endogenous MCSs. We show that Contact-FP probes can be used to: (1) visualize LD-mitochondria MCS dynamics, (2) observe changes in LD-mitochondria MCS dynamics upon overexpression of PLIN5, a known LD-mitochondrial tether, and (3) visualize two MCSs that share one organelle simultaneously (e.g., LD-mitochondria and LD-ER MCSs). Contact-FP probes can be optimized to visualize MCSs between any pair of organelles represented in the toolkit.
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Affiliation(s)
- Gregory E. Miner
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sidney Y. Smith
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Wendy K. Showalter
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Christina M. So
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joey V. Ragusa
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alex E. Powers
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Maria Clara Zanellati
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Chih-Hsuan Hsu
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Michelle F. Marchan
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah Cohen
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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13
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Koenig AM, Liu B, Hu J. Visualizing the dynamics of plant energy organelles. Biochem Soc Trans 2023; 51:2029-2040. [PMID: 37975429 PMCID: PMC10754284 DOI: 10.1042/bst20221093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023]
Abstract
Plant organelles predominantly rely on the actin cytoskeleton and the myosin motors for long-distance trafficking, while using microtubules and the kinesin motors mostly for short-range movement. The distribution and motility of organelles in the plant cell are fundamentally important to robust plant growth and defense. Chloroplasts, mitochondria, and peroxisomes are essential organelles in plants that function independently and coordinately during energy metabolism and other key metabolic processes. In response to developmental and environmental stimuli, these energy organelles modulate their metabolism, morphology, abundance, distribution and motility in the cell to meet the need of the plant. Consistent with their metabolic links in processes like photorespiration and fatty acid mobilization is the frequently observed inter-organellar physical interaction, sometimes through organelle membranous protrusions. The development of various organelle-specific fluorescent protein tags has allowed the simultaneous visualization of organelle movement in living plant cells by confocal microscopy. These energy organelles display an array of morphology and movement patterns and redistribute within the cell in response to changes such as varying light conditions, temperature fluctuations, ROS-inducible treatments, and during pollen tube development and immune response, independently or in association with one another. Although there are more reports on the mechanism of chloroplast movement than that of peroxisomes and mitochondria, our knowledge of how and why these three energy organelles move and distribute in the plant cell is still scarce at the functional and mechanistic level. It is critical to identify factors that control organelle motility coupled with plant growth, development, and stress response.
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Affiliation(s)
- Amanda M. Koenig
- Michigan State University-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
| | - Bo Liu
- Department of Plant Biology, University of California, Davis, CA, U.S.A
| | - Jianping Hu
- Michigan State University-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
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14
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Kunze M, Alder NN, Hwang I, Roussel G, Karamyshev AL. Editorial: Targeting signals in protein trafficking and transport. Front Physiol 2023; 14:1338852. [PMID: 38143916 PMCID: PMC10748493 DOI: 10.3389/fphys.2023.1338852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023] Open
Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Nathan N. Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Guillaume Roussel
- Laboratory of Molecular Bacteriology, Department of Microbiology, Immunology, and Transplantation, Rega Institute, Katholieke Universiteit-Leuven, Leuven, Belgium
| | - Andrey L. Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, United States
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15
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Hunt LC, Pagala V, Stephan A, Xie B, Kodali K, Kavdia K, Wang YD, Shirinifard A, Curley M, Graca FA, Fu Y, Poudel S, Li Y, Wang X, Tan H, Peng J, Demontis F. An adaptive stress response that confers cellular resilience to decreased ubiquitination. Nat Commun 2023; 14:7348. [PMID: 37963875 PMCID: PMC10646096 DOI: 10.1038/s41467-023-43262-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 11/02/2023] [Indexed: 11/16/2023] Open
Abstract
Ubiquitination is a post-translational modification initiated by the E1 enzyme UBA1, which transfers ubiquitin to ~35 E2 ubiquitin-conjugating enzymes. While UBA1 loss is cell lethal, it remains unknown how partial reduction in UBA1 activity is endured. Here, we utilize deep-coverage mass spectrometry to define the E1-E2 interactome and to determine the proteins that are modulated by knockdown of UBA1 and of each E2 in human cells. These analyses define the UBA1/E2-sensitive proteome and the E2 specificity in protein modulation. Interestingly, profound adaptations in peroxisomes and other organelles are triggered by decreased ubiquitination. While the cargo receptor PEX5 depends on its mono-ubiquitination for binding to peroxisomal proteins and importing them into peroxisomes, we find that UBA1/E2 knockdown induces the compensatory upregulation of other PEX proteins necessary for PEX5 docking to the peroxisomal membrane. Altogether, this study defines a homeostatic mechanism that sustains peroxisomal protein import in cells with decreased ubiquitination capacity.
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Affiliation(s)
- Liam C Hunt
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Department of Biology, Rhodes College, 2000 North Pkwy, Memphis, TN, 38112, USA
| | - Vishwajeeth Pagala
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Anna Stephan
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Boer Xie
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kiran Kodali
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kanisha Kavdia
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yong-Dong Wang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Abbas Shirinifard
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Michelle Curley
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Flavia A Graca
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yingxue Fu
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Suresh Poudel
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Junmin Peng
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Fabio Demontis
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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16
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Svensson CM, Reglinski K, Schliebs W, Erdmann R, Eggeling C, Figge MT. Quantitative analysis of peroxisome tracks using a Hidden Markov Model. Sci Rep 2023; 13:19694. [PMID: 37951993 PMCID: PMC10640649 DOI: 10.1038/s41598-023-46812-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023] Open
Abstract
Diffusion and mobility are essential for cellular functions, as molecules are usually distributed throughout the cell and have to meet to interact and perform their function. This also involves the cytosolic migration of cellular organelles. However, observing such diffusion and interaction dynamics is challenging due to the high spatial and temporal resolution required and the accurate analysis of the diffusional tracks. The latter is especially important when identifying anomalous diffusion events, such as directed motions, which are often rare. Here, we investigate the migration modes of peroxisome organelles in the cytosol of living cells. Peroxisomes predominantly migrate randomly, but occasionally they bind to the cell's microtubular network and perform directed migration, which is difficult to quantify, and so far, accurate analysis of switching between these migration modes is missing. We set out to solve this limitation by experiments and analysis with high statistical accuracy. Specifically, we collect temporal diffusion tracks of thousands of individual peroxisomes in the HEK 293 cell line using two-dimensional spinning disc fluorescence microscopy at a high acquisition rate of 10 frames/s. We use a Hidden Markov Model with two hidden states to (1) automatically identify directed migration segments of the tracks and (2) quantify the migration properties for comparison between states and between different experimental conditions. Comparing different cellular conditions, we show that the knockout of the peroxisomal membrane protein PEX14 leads to a decrease in the directed movement due to a lowered binding probability to the microtubule. However, it does not eradicate binding, highlighting further microtubule-binding mechanisms of peroxisomes than via PEX14. In contrast, structural changes of the microtubular network explain perceived eradication of directed movement by disassembly of microtubules by Nocodazole-treatment.
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Affiliation(s)
- Carl-Magnus Svensson
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Katharina Reglinski
- Leibniz-Institute of Photonic Technologies, Jena, Germany
- Institute of Applied Optics and Biophysics, Friedrich-Schiller University Jena, Jena, Germany
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- University Hospital Jena, Jena, Germany
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Christian Eggeling
- Leibniz-Institute of Photonic Technologies, Jena, Germany.
- Institute of Applied Optics and Biophysics, Friedrich-Schiller University Jena, Jena, Germany.
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Jena Center for Soft Matter (JCSM), Jena, Germany.
| | - Marc Thilo Figge
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany.
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich-Schiller University Jena, Jena, Germany.
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17
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Mishra S, Spaccarotella K, Gido J, Samanta I, Chowdhary G. Effects of Heat Stress on Plant-Nutrient Relations: An Update on Nutrient Uptake, Transport, and Assimilation. Int J Mol Sci 2023; 24:15670. [PMID: 37958654 PMCID: PMC10649217 DOI: 10.3390/ijms242115670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
As a consequence of global climate change, the frequency, severity, and duration of heat stress are increasing, impacting plant growth, development, and reproduction. While several studies have focused on the physiological and molecular aspects of heat stress, there is growing concern that crop quality, particularly nutritional content and phytochemicals important for human health, is also negatively impacted. This comprehensive review aims to provide profound insights into the multifaceted effects of heat stress on plant-nutrient relationships, with a particular emphasis on tissue nutrient concentration, the pivotal nutrient-uptake proteins unique to both macro- and micronutrients, and the effects on dietary phytochemicals. Finally, we propose a new approach to investigate the response of plants to heat stress by exploring the possible role of plant peroxisomes in the context of heat stress and nutrient mobilization. Understanding these complex mechanisms is crucial for developing strategies to improve plant nutrition and resilience during heat stress.
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Affiliation(s)
- Sasmita Mishra
- Department of Biology, Kean University, 1000 Morris Avenue, Union, NJ 07083, USA
| | - Kim Spaccarotella
- Department of Biology, Kean University, 1000 Morris Avenue, Union, NJ 07083, USA
| | - Jaclyn Gido
- Department of Biology, Kean University, 1000 Morris Avenue, Union, NJ 07083, USA
| | - Ishita Samanta
- Plant Molecular Biology Laboratory, School of Biotechnology, KIIT—Kalinga Institute of Industrial Technology, Bhubaneswar 751024, Odisha, India (G.C.)
| | - Gopal Chowdhary
- Plant Molecular Biology Laboratory, School of Biotechnology, KIIT—Kalinga Institute of Industrial Technology, Bhubaneswar 751024, Odisha, India (G.C.)
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18
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Kocherlakota S, Das Y, Swinkels D, Vanmunster M, Callens M, Vinckier S, Vaz FM, Sinha D, Van Veldhoven PP, Fransen M, Baes M. The murine retinal pigment epithelium requires peroxisomal β-oxidation to maintain lysosomal function and prevent dedifferentiation. Proc Natl Acad Sci U S A 2023; 120:e2301733120. [PMID: 37862382 PMCID: PMC10614831 DOI: 10.1073/pnas.2301733120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 08/14/2023] [Indexed: 10/22/2023] Open
Abstract
Retinal pigment epithelium (RPE) cells have to phagocytose shed photoreceptor outer segments (POS) on a daily basis over the lifetime of an organism, but the mechanisms involved in the digestion and recycling of POS lipids are poorly understood. Although it was frequently assumed that peroxisomes may play an essential role, this was never investigated. Here, we show that global as well as RPE-selective loss of peroxisomal β-oxidation in multifunctional protein 2 (MFP2) knockout mice impairs the digestive function of lysosomes in the RPE at a very early age, followed by RPE degeneration. This was accompanied by prolonged mammalian target of rapamycin activation, lipid deregulation, and mitochondrial structural anomalies without, however, causing oxidative stress or energy shortage. The RPE degeneration caused secondary photoreceptor death. Notably, the deterioration of the RPE did not occur in an Mfp2/rd1 mutant mouse line, characterized by absent POS shedding. Our findings prove that peroxisomal β-oxidation in the RPE is essential for handling the polyunsaturated fatty acids present in ingested POS and shed light on retinopathy in patients with peroxisomal disorders. Our data also have implications for gene therapy development as they highlight the importance of targeting the RPE in addition to the photoreceptor cells.
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Affiliation(s)
- Sai Kocherlakota
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Leuven3000, Belgium
| | - Yannick Das
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Leuven3000, Belgium
| | - Daniëlle Swinkels
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Leuven3000, Belgium
| | - Maarten Vanmunster
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Leuven3000, Belgium
| | - Manon Callens
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Leuven3000, Belgium
| | - Stefan Vinckier
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Insituut voor Biotechnologie, Leuven3000, Belgium
- Department of Oncology, Leuven Cancer Institute, Katholieke Universiteit Leuven, Leuven3000, Belgium
| | - Frédéric M. Vaz
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Center, University of Amsterdam, Amsterdam1105AZ, The Netherlands
- Core Facility Metabolomics, Amsterdam University Medical Center, Amsterdam1105AZ, The Netherlands
| | - Debasish Sinha
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Paul P. Van Veldhoven
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven, Leuven3000, Belgium
| | - Marc Fransen
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven, Leuven3000, Belgium
| | - Myriam Baes
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Leuven3000, Belgium
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19
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Hu J, Pan R, Weber APM, Whelan J. Editorial: Photosynthetic and photorespiratory organelles: metabolism, dynamics, and signaling. Front Plant Sci 2023; 14:1293246. [PMID: 37920721 PMCID: PMC10619851 DOI: 10.3389/fpls.2023.1293246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 09/22/2023] [Indexed: 11/04/2023]
Affiliation(s)
- Jianping Hu
- Michigan State University-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Ronghui Pan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Andreas P. M. Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-University, Düsseldorf, Germany
| | - James Whelan
- College of Life Science, Zhejiang University, Hangzhou, China
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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Rüttermann M, Koci M, Lill P, Geladas ED, Kaschani F, Klink BU, Erdmann R, Gatsogiannis C. Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a substrate. Nat Commun 2023; 14:5942. [PMID: 37741838 PMCID: PMC10518020 DOI: 10.1038/s41467-023-41640-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 09/12/2023] [Indexed: 09/25/2023] Open
Abstract
The double-ring AAA+ ATPase Pex1/Pex6 is required for peroxisomal receptor recycling and is essential for peroxisome formation. Pex1/Pex6 mutations cause severe peroxisome associated developmental disorders. Despite its pathophysiological importance, mechanistic details of the heterohexamer are not yet available. Here, we report cryoEM structures of Pex1/Pex6 from Saccharomyces cerevisiae, with an endogenous protein substrate trapped in the central pore of the catalytically active second ring (D2). Pairs of Pex1/Pex6(D2) subdomains engage the substrate via a staircase of pore-1 loops with distinct properties. The first ring (D1) is catalytically inactive but undergoes significant conformational changes resulting in alternate widening and narrowing of its pore. These events are fueled by ATP hydrolysis in the D2 ring and disengagement of a "twin-seam" Pex1/Pex6(D2) heterodimer from the staircase. Mechanical forces are propagated in a unique manner along Pex1/Pex6 interfaces that are not available in homo-oligomeric AAA-ATPases. Our structural analysis reveals the mechanisms of how Pex1 and Pex6 coordinate to achieve substrate translocation.
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Affiliation(s)
- Maximilian Rüttermann
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany
| | - Michelle Koci
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Pascal Lill
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Ermis Dionysios Geladas
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany
| | - Farnusch Kaschani
- Analytics Core Facility Essen, Center of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Björn Udo Klink
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany
| | - Ralf Erdmann
- Institute for Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Christos Gatsogiannis
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany.
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany.
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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22
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Weindel CG, Ellzey LM, Martinez EL, Watson RO, Patrick KL. Gasdermins gone wild: new roles for GSDMs in regulating cellular homeostasis. Trends Cell Biol 2023; 33:773-787. [PMID: 37062616 PMCID: PMC10611448 DOI: 10.1016/j.tcb.2023.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/13/2023] [Accepted: 02/24/2023] [Indexed: 04/18/2023]
Abstract
Since their discovery, members of the gasdermin (GSDM) family of proteins have been firmly established as executors of pyroptosis, with the N-terminal fragment of most GSDMs capable of forming pores in the plasma membrane. More recent findings suggest that some GSDMs can drive additional cell death pathways, such as apoptosis and necroptosis, through mechanisms independent of plasma membrane perforation. There is also emerging evidence that by associating with cellular compartments such as mitochondria, peroxisomes, endosomes, and the nucleus, GSDMs regulate cell death-independent aspects of cellular homeostasis. Here, we review the diversity of GSDM function across several cell types and explore how various cellular stresses can promote relocalization - and thus refunctionalization - of GSDMs.
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Affiliation(s)
- Chi G Weindel
- Texas A&M University School of Medicine, Bryan, TX, USA
| | - Lily M Ellzey
- Texas A&M University School of Medicine, Bryan, TX, USA
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23
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Trammell SAJ, Gamon LF, Gotfryd K, Michler KT, Alrehaili BD, Rix I, Knop FK, Gourdon P, Lee YK, Davies MJ, Gillum MP, Grevengoed TJ. Identification of bile acid-CoA:amino acid N-acyltransferase as the hepatic N-acyl taurine synthase for polyunsaturated fatty acids. J Lipid Res 2023; 64:100361. [PMID: 36958721 PMCID: PMC10470208 DOI: 10.1016/j.jlr.2023.100361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 03/25/2023] Open
Abstract
N-acyl taurines (NATs) are bioactive lipids with emerging roles in glucose homeostasis and lipid metabolism. The acyl chains of hepatic and biliary NATs are enriched in polyunsaturated fatty acids (PUFAs). Dietary supplementation with a class of PUFAs, the omega-3 fatty acids, increases their cognate NATs in mice and humans. However, the synthesis pathway of the PUFA-containing NATs remains undiscovered. Here, we report that human livers synthesize NATs and that the acyl-chain preference is similar in murine liver homogenates. In the mouse, we found that hepatic NAT synthase activity localizes to the peroxisome and depends upon an active-site cysteine. Using unbiased metabolomics and proteomics, we identified bile acid-CoA:amino acid N-acyltransferase (BAAT) as the likely hepatic NAT synthase in vitro. Subsequently, we confirmed that BAAT knockout livers lack up to 90% of NAT synthase activity and that biliary PUFA-containing NATs are significantly reduced compared with wildtype. In conclusion, we identified the in vivo PUFA-NAT synthase in the murine liver and expanded the known substrates of the bile acid-conjugating enzyme, BAAT, beyond classic bile acids to the synthesis of a novel class of bioactive lipids.
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Affiliation(s)
- Samuel A J Trammell
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Luke F Gamon
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kamil Gotfryd
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Katja Thorøe Michler
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bandar D Alrehaili
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, OH, USA; Department of Pharmacology and Toxicology, Pharmacy College, Taibah University, Medina, Saudi Arabia
| | - Iben Rix
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Filip K Knop
- Center for Clinical Metabolic Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Steno Diabetes Center Copenhagen, Herlev, Denmark; Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Pontus Gourdon
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Yoon-Kwang Lee
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, OH, USA
| | - Michael J Davies
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthew P Gillum
- Global Obesity and Liver Disease Research, Novo Nordisk A/S, Måløv, Denmark
| | - Trisha J Grevengoed
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.
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24
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Zhang W, Zhang L, Yao H, Wang Y, Zhang X, Shang L, Chen X, Zeng J. Long-chain dicarboxylic acids play a critical role in inducing peroxisomal β-oxidation and hepatic triacylglycerol accumulation. J Biol Chem 2023; 299:105174. [PMID: 37599002 PMCID: PMC10494467 DOI: 10.1016/j.jbc.2023.105174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/13/2023] [Accepted: 08/15/2023] [Indexed: 08/22/2023] Open
Abstract
Recent studies provide evidence that peroxisomal β-oxidation negatively regulates mitochondrial fatty acid oxidation, and induction of peroxisomal β-oxidation causes hepatic lipid accumulation. However, whether there exists a triggering mechanism inducing peroxisomal β-oxidation is not clear. Long-chain dicarboxylic acids (LCDAs) are the product of mono fatty acids subjected to ω-oxidation, and both fatty acid ω-oxidation and peroxisomal β-oxidation are induced under ketogenic conditions, indicating there might be a crosstalk between. Here, we revealed that administration of LCDAs strongly induces peroxisomal fatty acid β-oxidation and causes hepatic steatosis in mice through the metabolites acetyl-CoA and hydrogen peroxide. Under ketogenic conditions, upregulation of fatty acid ω-oxidation resulted in increased generation of LCDAs and induction of peroxisomal β-oxidation, which causes hepatic accumulation of lipid droplets in animals. Inhibition of fatty acid ω-oxidation reduced LCDA formation and significantly lowered peroxisomal β-oxidation and improved hepatic steatosis. Our results suggest that endogenous LCDAs act as triggering molecules inducing peroxisomal β-oxidation and hepatic triacylglycerol deposition. Targeting fatty acid ω-oxidation might be an effective pathway in treating fatty liver and related metabolic diseases through regulating peroxisomal β-oxidation.
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Affiliation(s)
- Wei Zhang
- School of Life Science, Hunan University of Science and Technology, Xiangtan, Hunan, P. R. China
| | - Lina Zhang
- School of Life Science, Hunan University of Science and Technology, Xiangtan, Hunan, P. R. China
| | - Haoya Yao
- School of Life Science, Hunan University of Science and Technology, Xiangtan, Hunan, P. R. China
| | - Yaoqing Wang
- School of Life Science, Hunan University of Science and Technology, Xiangtan, Hunan, P. R. China
| | - Xiao Zhang
- School of Life Science, Hunan University of Science and Technology, Xiangtan, Hunan, P. R. China
| | - Lin Shang
- School of Life Science, Hunan University of Science and Technology, Xiangtan, Hunan, P. R. China
| | - Xiaocui Chen
- School of Life Science, Hunan University of Science and Technology, Xiangtan, Hunan, P. R. China
| | - Jia Zeng
- School of Life Science, Hunan University of Science and Technology, Xiangtan, Hunan, P. R. China.
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25
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Honsho M, Fujiki Y. Asymmetric Distribution of Plasmalogens and Their Roles-A Mini Review. Membranes (Basel) 2023; 13:764. [PMID: 37755186 PMCID: PMC10534842 DOI: 10.3390/membranes13090764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/03/2023] [Accepted: 08/25/2023] [Indexed: 09/28/2023]
Abstract
Plasmalogens are a unique family of cellular glycerophospholipids that contain a vinyl-ether bond. The synthesis of plasmalogens is initiated in peroxisomes and completed in the endoplasmic reticulum. Plasmalogens are transported to the post-Golgi compartment, including endosomes and plasma membranes, in a manner dependent on ATP, but not vesicular transport. Plasmalogens are preferentially localized in the inner leaflet of the plasma membrane in a manner dependent on P4-type ATPase ATP8B2, that associates with the CDC50 subunit. Plasmalogen biosynthesis is spatiotemporally regulated by a feedback mechanism that senses the amount of plasmalogens in the inner leaflet of the plasma membrane and controls the stability of fatty acyl-CoA reductase 1 (FAR1), the rate-limiting enzyme for plasmalogen biosynthesis. The physiological consequences of such asymmetric localization and homeostasis of plasmalogens are discussed in this review.
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Affiliation(s)
- Masanori Honsho
- Department of Neuroinflammation and Brain Fatigue Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8581, Japan
| | - Yukio Fujiki
- Institute of Rheological Functions of Food-Kyushu University Collaboration Program, Kyushu University, Fukuoka 811-2501, Japan
- Graduate School of Science, University of Hyogo, Himeji 671-2280, Japan
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26
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Costello JL, Koster J, Silva BSC, Worthy HL, Schrader TA, Hacker C, Passmore J, Kuypers FA, Waterham HR, Schrader M. Differential roles for ACBD4 and ACBD5 in peroxisome-ER interactions and lipid metabolism. J Biol Chem 2023; 299:105013. [PMID: 37414147 PMCID: PMC10410513 DOI: 10.1016/j.jbc.2023.105013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/09/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023] Open
Abstract
Peroxisomes and the endoplasmic reticulum (ER) are intimately linked subcellular organelles, physically connected at membrane contact sites. While collaborating in lipid metabolism, for example, of very long-chain fatty acids (VLCFAs) and plasmalogens, the ER also plays a role in peroxisome biogenesis. Recent work identified tethering complexes on the ER and peroxisome membranes that connect the organelles. These include membrane contacts formed via interactions between the ER protein VAPB (vesicle-associated membrane protein-associated protein B) and the peroxisomal proteins ACBD4 and ACBD5 (acyl-coenzyme A-binding domain protein). Loss of ACBD5 has been shown to cause a significant reduction in peroxisome-ER contacts and accumulation of VLCFAs. However, the role of ACBD4 and the relative contribution these two proteins make to contact site formation and recruitment of VLCFAs to peroxisomes remain unclear. Here, we address these questions using a combination of molecular cell biology, biochemical, and lipidomics analyses following loss of ACBD4 or ACBD5 in HEK293 cells. We show that the tethering function of ACBD5 is not absolutely required for efficient peroxisomal β-oxidation of VLCFAs. We demonstrate that loss of ACBD4 does not reduce peroxisome-ER connections or result in the accumulation of VLCFAs. Instead, the loss of ACBD4 resulted in an increase in the rate of β-oxidation of VLCFAs. Finally, we observe an interaction between ACBD5 and ACBD4, independent of VAPB binding. Overall, our findings suggest that ACBD5 may act as a primary tether and VLCFA recruitment factor, whereas ACBD4 may have regulatory functions in peroxisomal lipid metabolism at the peroxisome-ER interface.
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Affiliation(s)
| | - Janet Koster
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Center Location University of Amsterdam, Amsterdam, The Netherlands
| | - Beatriz S C Silva
- Department of Biosciences, University of Exeter, Exeter, UK; Luxembourg Centre for Systems Biomedicine, Campus Belval | House of Biomedicine II, Université du Luxembourg, Belvaux, Luxembourg
| | | | | | | | - Josiah Passmore
- Department of Biosciences, University of Exeter, Exeter, UK; Division of Cell Biology, Utrecht University, Utrecht, The Netherlands
| | | | - Hans R Waterham
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Center Location University of Amsterdam, Amsterdam, The Netherlands.
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27
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Enkler L, Szentgyörgyi V, Pennauer M, Prescianotto-Baschong C, Riezman I, Wiesyk A, Avraham RE, Spiess M, Zalckvar E, Kucharczyk R, Riezman H, Spang A. Arf1 coordinates fatty acid metabolism and mitochondrial homeostasis. Nat Cell Biol 2023; 25:1157-1172. [PMID: 37400497 PMCID: PMC10415182 DOI: 10.1038/s41556-023-01180-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/05/2023] [Indexed: 07/05/2023]
Abstract
Lipid mobilization through fatty acid β-oxidation is a central process essential for energy production during nutrient shortage. In yeast, this catabolic process starts in the peroxisome from where β-oxidation products enter mitochondria and fuel the tricarboxylic acid cycle. Little is known about the physical and metabolic cooperation between these organelles. Here we found that expression of fatty acid transporters and of the rate-limiting enzyme involved in β-oxidation is decreased in cells expressing a hyperactive mutant of the small GTPase Arf1, leading to an accumulation of fatty acids in lipid droplets. Consequently, mitochondria became fragmented and ATP synthesis decreased. Genetic and pharmacological depletion of fatty acids phenocopied the arf1 mutant mitochondrial phenotype. Although β-oxidation occurs in both mitochondria and peroxisomes in mammals, Arf1's role in fatty acid metabolism is conserved. Together, our results indicate that Arf1 integrates metabolism into energy production by regulating fatty acid storage and utilization, and presumably organelle contact sites.
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Affiliation(s)
| | | | | | | | - Isabelle Riezman
- Department of Biochemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Aneta Wiesyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Reut Ester Avraham
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | | | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Howard Riezman
- Department of Biochemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Anne Spang
- Biozentrum, University of Basel, Basel, Switzerland.
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28
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Collington E, Lobb B, Mazen NA, Doxey AC, Glerum DM. Phylogenomic analysis of 155 helminth species reveals widespread absence of oxygen metabolic capacity. Genome Biol Evol 2023:evad135. [PMID: 37481257 PMCID: PMC10400150 DOI: 10.1093/gbe/evad135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 07/11/2023] [Accepted: 07/16/2023] [Indexed: 07/24/2023] Open
Abstract
The terminal electron acceptor of most aerobic respiratory chains, cytochrome c oxidase (COX), has been highly conserved throughout evolution, from aerobic prokaryotes to complex eukaryotes. Oxygen metabolism in parasitic helminths differs significantly from that of most aerobic eukaryotes, as these organisms can switch between aerobic and anaerobic metabolisms throughout their life cycles. Early studies suggested a lack of COX activity in certain parasitic helminths, and the role of COX in helminth mitochondria remains unclear. To determine whether a functional COX is widely present in helminths, we analyzed the phylogenetic distribution of oxygen metabolism systems across 155 helminth genomes, investigating three distinct sets of protein-coding genes involved in different aspects of oxygen metabolism: COX and its assembly factors, peroxisomes, and the most abundant reactive oxygen species (ROS)-metabolizing proteins. While glycolytic and citric acid cycle enzymes are highly conserved in helminthic species, we observed an apparent widespread absence of essential COX genes across 52% of helminth species investigated. While the most common proteins involved in the defense against ROS are highly maintained across virtually all lineages, we also observed an apparent absence of essential peroxisomal protein-coding genes in 42% of species investigated. Our results suggest that a subset of parasitic helminths utilize oxygen differently from related, non-parasitic species such as C. elegans, with significant differences in their mitochondrial electron transport chains and peroxisomes. The identification of substantive differences between parasite and host metabolism offers a new avenue for the development of anthelmintic agents that could target these divergent pathways.
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Affiliation(s)
- Emma Collington
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo ON, N2L 3G1, Canada
| | - Briallen Lobb
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo ON, N2L 3G1, Canada
| | - Nooran Abu Mazen
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo ON, N2L 3G1, Canada
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo ON, N2L 3G1, Canada
| | - D Moira Glerum
- Department of Biology, University of Waterloo, 200 University Ave W., Waterloo ON, N2L 3G1, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo ON, Canada
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29
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Palma JM, Rodríguez-Ruiz M, Foyer CH, Corpas FJ. Editorial: Subcellular compartmentalization of plant antioxidants and ROS generating systems, volume II. Front Plant Sci 2023; 14:1224289. [PMID: 37534285 PMCID: PMC10393032 DOI: 10.3389/fpls.2023.1224289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/07/2023] [Indexed: 08/04/2023]
Affiliation(s)
- José M. Palma
- Dpt. Stress, Development and Signalling in Plants, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
| | - Marta Rodríguez-Ruiz
- Dpt. Stress, Development and Signalling in Plants, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
| | - Christine H. Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Francisco J. Corpas
- Dpt. Stress, Development and Signalling in Plants, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
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30
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Zhou P, Zhou X, Yuan D, Fang X, Pang X, Yuan K, Li A, Wang X. Combining Protein and Organelle Engineering for Linalool Overproduction in Saccharomyces cerevisiae. J Agric Food Chem 2023. [PMID: 37350414 DOI: 10.1021/acs.jafc.2c08416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
Abstract
Linalool, a plant-derived high-value monoterpene, is widely used in the perfume, cosmetic, and pharmaceutical industries. Recently, engineering microbes to produce linalool has become an attractive alternative to plant extraction or chemical synthesis approaches. However, the low catalytic activity of linalool synthase and the shortage of precursor pools have been considered as two key factors for low yields of linalool. In this study, we rationally engineered the entrance of the substrate-binding pocket of linalool synthase (t67OMcLISM) and successfully increased the catalytic efficiency of this enzyme toward geranyl pyrophosphate. Specifically, F447E and F447A, with decreased entrance hydrophobicity and steric hindrance, increased linalool production by 2.2 and 1.9 folds, respectively. Subsequently, cytoplasm and peroxisomes were harnessed to boost linalool synthesis in Saccharomyces cerevisiae, achieving a high titer of linalool (219.1 mg/L) in shake-flask cultivation. Finally, the engineered diploid strain produced 2.6 g/L of linalool by 5 L fed-batch fermentation, which was the highest production in yeast to date. The protein engineering and biosynthetic pathway compartmentalization in the peroxisome provide references for the microbial production of other monoterpenes.
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Affiliation(s)
- Pingping Zhou
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, PR China
| | - Xiuqi Zhou
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, PR China
| | - Doudou Yuan
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, PR China
| | - Xin Fang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, PR China
| | - Xueqing Pang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, PR China
| | - Ke Yuan
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, PR China
| | - Aipeng Li
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Xiqing Wang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, PR China
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, PR China
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Dolman NJ, Kilgore JA. A Review of Reagents for Fluorescence Microscopy of Cellular Compartments and Structures, Part I: BacMam Labeling and Reagents for Vesicular Structures. Curr Protoc 2023; 3:e751. [PMID: 37311031 DOI: 10.1002/cpz1.751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fluorescent labeling of vesicular structures in cultured cells, particularly for live cells, can be challenging for a number of reasons. The first challenge is to identify a reagent that will be specific enough where some structures have a number of potential reagents and others very few options. The emergence of BacMam constructs has provided more easy-to-use choices. Presented here is a discussion of BacMam constructs as well as a review of commercially available reagents for labeling vesicular structures in cells, including endosomes, peroxisomes, lysosomes, and autophagosomes, complete with a featured reagent, recommended protocol, troubleshooting guide, and example image for each structure. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Delivering targeted fluorescent proteins using pre-made, high-titer BacMam constructs Alternate Protocol 1: Non-pseudo-typed BacMam viruses in standard cell types and pseudo-typed BacMam viruses in hard-to-transduce cell types Basic Protocol 2: Labeling endosomes: pHrodo™-10k-dextran Basic Protocol 3: Labeling peroxisomes: BacMam 2.0 CellLight™ Peroxisome-GFP Alternate Protocol 2: Labeling peroxisomes using antibodies Basic Protocol 4: Labeling autophagosomes: Transduction of cells with Premo™ Autophagy Sensor GFP-LC3B Alternate Protocol 3: Labeling autophagosomes using antibodies Basic Protocol 5: Labeling lysosomes: LysoTracker Red DND-99.
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Aleksic M, Golic I, Jankovic A, Cvoro A, Korac A. ACOX-driven peroxisomal heterogeneity and functional compartmentalization in brown adipocytes of hypothyroid rats. R Soc Open Sci 2023; 10:230109. [PMID: 37153362 PMCID: PMC10154930 DOI: 10.1098/rsos.230109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/11/2023] [Indexed: 05/09/2023]
Abstract
We previously demonstrated that hypothyroidism increases peroxisomal biogenesis in rat brown adipose tissue (BAT). We also showed heterogeneity in peroxisomal origin and their unique structural association with mitochondria and/or lipid bodies to carry out β-oxidation, contributing thus to BAT thermogenesis. Distinctive heterogeneity creates structural compartmentalization within peroxisomal population, raising the question of whether it is followed by their functional compartmentalization regarding localization/colocalization of two main acyl-CoA oxidase (ACOX) isoforms, ACOX1 and ACOX3. ACOX is the first and rate-limiting enzyme of peroxisomal β-oxidation, and, to date, their protein expression patterns in BAT have not been fully defined. Therefore, we used methimazole-induced hypothyroidism to study ACOX1 and ACOX3 protein expression and their tissue immunolocalization. Additionally, we analysed their specific peroxisomal localization and colocalization in parallel with peroxisomal structural compartmentalization in brown adipocytes. Hypothyroidism caused a linear increase in ACOX1 expression, while a temporary decrease in ACOX3 levels is only recovered to the control level at day 21. Peroxisomal ACOX1 and ACOX3 localization and colocalization patterns entirely mirrored heterogeneous peroxisomal biogenesis pathways and structural compartmentalization, e.g. associations with mitochondria and/or lipid bodies. Hence, different ACOX isoforms localization/colocalization creates distinct functional heterogeneity of peroxisomes and drives their functional compartmentalization in rat brown adipocytes.
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Affiliation(s)
- Marija Aleksic
- Center for Electron Microscopy, Faculty of Biology, University of Belgrade, Belgrade 11000, Serbia
| | - Igor Golic
- Center for Electron Microscopy, Faculty of Biology, University of Belgrade, Belgrade 11000, Serbia
| | - Aleksandra Jankovic
- Institute for Biological Research 'Sinisa Stankovic'—National Institute of Republic of Serbia, University of Belgrade, Belgrade 11000, Serbia
| | - Aleksandra Cvoro
- Center for Electron Microscopy, Faculty of Biology, University of Belgrade, Belgrade 11000, Serbia
| | - Aleksandra Korac
- Center for Electron Microscopy, Faculty of Biology, University of Belgrade, Belgrade 11000, Serbia
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Carmichael RE, Richards DM, Fahimi HD, Schrader M. Organelle Membrane Extensions in Mammalian Cells. Biology (Basel) 2023; 12:biology12050664. [PMID: 37237478 DOI: 10.3390/biology12050664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023]
Abstract
Organelles within eukaryotic cells are not isolated static compartments, instead being morphologically diverse and highly dynamic in order to respond to cellular needs and carry out their diverse and cooperative functions. One phenomenon exemplifying this plasticity, and increasingly gaining attention, is the extension and retraction of thin tubules from organelle membranes. While these protrusions have been observed in morphological studies for decades, their formation, properties and functions are only beginning to be understood. In this review, we provide an overview of what is known and still to be discovered about organelle membrane protrusions in mammalian cells, focusing on the best-characterised examples of these membrane extensions arising from peroxisomes (ubiquitous organelles involved in lipid metabolism and reactive oxygen species homeostasis) and mitochondria. We summarise the current knowledge on the diversity of peroxisomal/mitochondrial membrane extensions, as well as the molecular mechanisms by which they extend and retract, necessitating dynamic membrane remodelling, pulling forces and lipid flow. We also propose broad cellular functions for these membrane extensions in inter-organelle communication, organelle biogenesis, metabolism and protection, and finally present a mathematical model that suggests that extending protrusions is the most efficient way for an organelle to explore its surroundings.
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Affiliation(s)
- Ruth E Carmichael
- Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - David M Richards
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
- Department of Physics and Astronomy, University of Exeter, Exeter EX4 4QL, UK
| | - H Dariush Fahimi
- Institute for Anatomy and Cell Biology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Michael Schrader
- Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter EX4 4QD, UK
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Dhingra A, Tobias JW, Philp NJ, Boesze-Battaglia K. Transcriptomic Changes Predict Metabolic Alterations in LC3 Associated Phagocytosis in Aged Mice. Int J Mol Sci 2023; 24:ijms24076716. [PMID: 37047689 PMCID: PMC10095460 DOI: 10.3390/ijms24076716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
LC3b (Map1lc3b) plays an essential role in canonical autophagy and is one of several components of the autophagy machinery that mediates non-canonical autophagic functions. Phagosomes are often associated with lipidated LC3b to promote phagosome maturation in a process called LC3-associated phagocytosis (LAP). Specialized phagocytes, such as mammary epithelial cells, retinal pigment epithelial (RPE) cells, and sertoli cells, utilize LAP for optimal degradation of phagocytosed material, including debris. In the visual system, LAP is critical to maintain retinal function, lipid homeostasis, and neuroprotection. In a mouse model of retinal lipid steatosis-mice lacking LC3b (LC3b-/-), we observed increased lipid deposition, metabolic dysregulation, and enhanced inflammation. Herein, we present a non-biased approach to determine if loss of LAP mediated processes modulate the expression of various genes related to metabolic homeostasis, lipid handling, and inflammation. A comparison of the RPE transcriptome of WT and LC3b-/- mice revealed 1533 DEGs, with ~73% upregulated and 27% downregulated. Enriched gene ontology (GO) terms included inflammatory response (upregulated DEGs), fatty acid metabolism, and vascular transport (downregulated DEGs). Gene set enrichment analysis (GSEA) identified 34 pathways; 28 were upregulated (dominated by inflammation/related pathways) and 6 were downregulated (dominated by metabolic pathways). Analysis of additional gene families identified significant differences for genes in the solute carrier family, RPE signature genes, and genes with a potential role in age-related macular degeneration. These data indicate that loss of LC3b induces robust changes in the RPE transcriptome contributing to lipid dysregulation and metabolic imbalance, RPE atrophy, inflammation, and disease pathophysiology.
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Affiliation(s)
- Anuradha Dhingra
- Department of Basic and Translational Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John W Tobias
- Penn Genomics and Sequencing Core, Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nancy J Philp
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Kathleen Boesze-Battaglia
- Department of Basic and Translational Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
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Ivanov S, Daniels DA, Harrison MJ. A Medicago truncatula Cell Biology Resource: Transgenic Lines Expressing Fluorescent Protein-Based Markers of Membranes, Organelles, and Subcellular Compartments. Mol Plant Microbe Interact 2023; 36:256-259. [PMID: 36401845 DOI: 10.1094/mpmi-01-22-0023-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Sergey Ivanov
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, U.S.A
| | | | - Maria J Harrison
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, U.S.A
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Watermann C, Meyer MT, Wagner S, Wittekindt C, Klussmann JP, Erguen S, Baumgart-Vogt E, Karnati S. Peroxisomes Are Highly Abundant and Heterogeneous in Human Parotid Glands. Int J Mol Sci 2023; 24. [PMID: 36902220 DOI: 10.3390/ijms24054783] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
The parotid gland is one of the major salivary glands producing a serous secretion, and it plays an essential role in the digestive and immune systems. Knowledge of peroxisomes in the human parotid gland is minimal; furthermore, the peroxisomal compartment and its enzyme composition in the different cell types of the human parotid gland have never been subjected to a detailed investigation. Therefore, we performed a comprehensive analysis of peroxisomes in the human parotid gland's striated duct and acinar cells. We combined biochemical techniques with various light and electron microscopy techniques to determine the localization of parotid secretory proteins and different peroxisomal marker proteins in parotid gland tissue. Moreover, we analyzed the mRNA of numerous gene encoding proteins localized in peroxisomes using real-time quantitative PCR. The results confirm the presence of peroxisomes in all striated duct and acinar cells of the human parotid gland. Immunofluorescence analyses for various peroxisomal proteins showed a higher abundance and more intense staining in striated duct cells compared to acinar cells. Moreover, human parotid glands comprise high quantities of catalase and other antioxidative enzymes in discrete subcellular regions, suggesting their role in protection against oxidative stress. This study provides the first thorough description of parotid peroxisomes in different parotid cell types of healthy human tissue.
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Blum D, Reuter M, Schliebs W, Tomaschewski J, Erdmann R, Wagner R. Membrane binding and pore forming insertion of PEX5 into horizontal lipid bilayer. Biol Chem 2023; 404:157-167. [PMID: 36260915 DOI: 10.1515/hsz-2022-0183] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/29/2022] [Indexed: 11/15/2022]
Abstract
The assembly of the peroxisomal translocon involves the transition of a soluble form of the peroxisomal targeting receptor PEX5 into a membrane-bound form, which becomes an integral membrane component of the import pore for peroxisomal matrix proteins. How this transition occurs is still a mystery. We addressed this question using a artificial horizontal bilayer in combination with fluorescence time-correlated single photon counting (TCSPC) and electrophysiological channel recording. Purified human isoform PEX5L and truncated PEX5L(1-335) lacking the cargo binding domain were selectively labeled with thiol-reactive Atto-dyes. Diffusion coefficients of labeled protein in solution show that PEX5L is monomeric with a rather compact spherical conformation, while the truncated protein appeared in a more extended conformation. Labeled PEX5L and the truncated PEX5L(1-335) bind stably to horizontal bilayer thereby accumulating around 100-fold. The diffusion coefficients of the membrane-bound PEX5L forms are 3-4 times lower than in solution, indicating the formation of larger complexes. Electrophysiological single channel recording shows that membrane-bound labeled and non-labeled PEX5L, but not the truncated PEX5L(1-335), can form ion conducting membrane channels. The data suggest that PEX5L is the pore-forming component of the oligomeric peroxisomal translocon and that spontaneous PEX5L membrane surface binding might be an important step in its assembly.
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Affiliation(s)
- Daniel Blum
- MOLIFE Research Center, Jacobs, University Bremen, D-28759 Bremen, Germany
| | - Maren Reuter
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Medizinische Fakultät, Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Wolfgang Schliebs
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Medizinische Fakultät, Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Jana Tomaschewski
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Medizinische Fakultät, Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Ralf Erdmann
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Medizinische Fakultät, Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Richard Wagner
- MOLIFE Research Center, Jacobs, University Bremen, D-28759 Bremen, Germany
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Abstract
Fluorescence microscopy is an important tool for studying cellular structures such as organelles. Unfortunately, many details in the corresponding images are hidden due to the resolution limit of conventional lens-based far-field microscopy. An example is the study of peroxisomes, where important processes such as molecular organization during protein important can simply not be studied with conventional far-field microscopy methods. A remedy is super-resolution fluorescence microscopy, which is nowadays a well-established technique for the investigation of inner-cellular structures but has so far to a lesser extent been applied to the study of peroxisomes. To help advancing the latter, we here give an overview over the different super-resolution microscopy approaches and their potentials and challenges in cell-biological research, including labelling issues and a focus on studies on peroxisomes. Here, we also highlight experiments beyond simple imaging such as observations of diffusion dynamics of peroxisomal proteins.
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Affiliation(s)
- Silvia Galiani
- Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, UK
| | - Christian Eggeling
- Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, UK.,Leibniz Institute of Photonic Technology e.V., Albert-Einstein Strasse 9, D-07745 Jena, Germany, Member of the Leibniz Centre for Photonics in Infection Research (LPI), Jena, Germany.,Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Max-Wien-Platz 1, D-07743 Jena, Germany.,Jena Center for Soft Matter, Philosophenweg 7, D-07743 Jena, Germany
| | - Katharina Reglinski
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein Strasse 9, D-07745 Jena, Germany, Member of the Leibniz Centre for Photonics in Infection Research (LPI), Jena, Germany.,Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Max-Wien-Platz 1, D-07743 Jena, Germany.,University Clinics Jena, Bachstraße 18, D-07743 Jena, Germany
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Demoor A, Lacaze I, Ferrari R, Lalanne C, Silar P, Brun S. GUN Mutants: New Weapons To Unravel Ascospore Germination Regulation in the Model Fungus Podospora anserina. Microbiol Spectr 2023; 11:e0146122. [PMID: 36786590 PMCID: PMC10100959 DOI: 10.1128/spectrum.01461-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/14/2022] [Indexed: 02/15/2023] Open
Abstract
In Podospora anserina as in many other Ascomycetes, ascospore germination is a regulated process that requires the breaking of dormancy. Despite its importance in survival and dispersal, ascospore germination in filamentous fungi has been poorly investigated, and little is known about its regulation and genetic control. We have designed a positive genetic screen that led to the isolation of mutants showing uncontrolled germination, the GUN (Germination UNcontrolled) mutants. Here, we report on the characterization of the gun1SG (Spontaneous Germination) mutant. We show that gun1SG is mutated in Pa_6_1340, the ortholog of Magnaporthe oryzae Pth2, which encodes a carnitine-acetyltransferase (CAT) involved in the shuttling of acetyl coenzyme A between peroxisomes and mitochondria and which is required for appressorium development. Bioinformatic analysis revealed that the mutated residue (I441) is highly conserved among Fungi and that the mutation has a deleterious impact on the protein function. We show that GUN1 is essential for ascospore germination and that the protein is localized both in mitochondria and in peroxisomes. Finally, epistasis studies allowed us to place GUN1 together with the PaMpk2 MAPK pathway upstream of the PaNox2/PaPls1 complex in the regulation of ascospore germination. In addition, we show that GUN1 plays a role in appressorium functioning. The pivotal role of GUN1, the ortholog of Pth2, in ascospore germination and in appressorium functioning reinforces the idea of a common genetic regulation governing both appressorium development and melanized ascospore germination. Furthermore, we characterize the second CAT encoded in P. anserina genome, Pa_3_7660/GUP1, and we show that the function of both CATs is conserved in P. anserina. IMPORTANCE The regulation of ascospore germination in filamentous fungi has been poorly investigated so far. To unravel new genes involved in this regulation pathway, we conducted a genetic screen in Podospora anserina, and we isolated 57 mutants affected in ascospore germination. Here, we describe the Germination UNcontrolled One (gun1SG) mutant, and we characterize the gene affected. GUN1 is a peroxisomal/mitochondrial carnitine-acetyltransferase required for acetyl coenzyme A shuttling between both organelles, and we show that GUN1 is a pleiotropic gene also involved in appressorium functioning similarly to its ortholog, the pathogenesis factor Pth2, in the plant pathogen Magnaporthe oryzae. Given the similarities in the regulation of appressorium development and ascospore germination, we speculate that discovering new genes controlling ascospore germination in P. anserina may lead to the discovery of new pathogenesis factors in pathogenic fungi. The characterization of GUN1, the ortholog of M. oryzae Pth2, represents a proof of concept.
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Affiliation(s)
- Alexander Demoor
- Université Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain/UMR 8236, Paris, France
| | - Isabelle Lacaze
- Université Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain/UMR 8236, Paris, France
| | - Roselyne Ferrari
- Université Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain/UMR 8236, Paris, France
| | - Christophe Lalanne
- Université Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain/UMR 8236, Paris, France
| | - Philippe Silar
- Université Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain/UMR 8236, Paris, France
| | - Sylvain Brun
- Université Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain/UMR 8236, Paris, France
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Makdissi S, Parsons BD, Di Cara F. Towards early detection of neurodegenerative diseases: A gut feeling. Front Cell Dev Biol 2023; 11:1087091. [PMID: 36824371 PMCID: PMC9941184 DOI: 10.3389/fcell.2023.1087091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/20/2023] [Indexed: 02/10/2023] Open
Abstract
The gastrointestinal tract communicates with the nervous system through a bidirectional network of signaling pathways called the gut-brain axis, which consists of multiple connections, including the enteric nervous system, the vagus nerve, the immune system, endocrine signals, the microbiota, and its metabolites. Alteration of communications in the gut-brain axis is emerging as an overlooked cause of neuroinflammation. Neuroinflammation is a common feature of the pathogenic mechanisms involved in various neurodegenerative diseases (NDs) that are incurable and debilitating conditions resulting in progressive degeneration and death of neurons, such as in Alzheimer and Parkinson diseases. NDs are a leading cause of global death and disability, and the incidences are expected to increase in the following decades if prevention strategies and successful treatment remain elusive. To date, the etiology of NDs is unclear due to the complexity of the mechanisms of diseases involving genetic and environmental factors, including diet and microbiota. Emerging evidence suggests that changes in diet, alteration of the microbiota, and deregulation of metabolism in the intestinal epithelium influence the inflammatory status of the neurons linked to disease insurgence and progression. This review will describe the leading players of the so-called diet-microbiota-gut-brain (DMGB) axis in the context of NDs. We will report recent findings from studies in model organisms such as rodents and fruit flies that support the role of diets, commensals, and intestinal epithelial functions as an overlooked primary regulator of brain health. We will finish discussing the pivotal role of metabolisms of cellular organelles such as mitochondria and peroxisomes in maintaining the DMGB axis and how alteration of the latter can be used as early disease makers and novel therapeutic targets.
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Affiliation(s)
- Stephanie Makdissi
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS, Canada
- IWK Health Centre, Department of Pediatrics, Halifax, Canada
| | - Brendon D. Parsons
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS, Canada
| | - Francesca Di Cara
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS, Canada
- IWK Health Centre, Department of Pediatrics, Halifax, Canada
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Wu N, Ma YC, Gong XQ, Zhao PJ, Jia YJ, Zhao Q, Duan JH, Zou CG. The metabolite alpha-ketobutyrate extends lifespan by promoting peroxisomal function in C. elegans. Nat Commun 2023; 14:240. [PMID: 36646719 DOI: 10.1038/s41467-023-35899-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023] Open
Abstract
Metabolism is intimately linked to aging. There is a growing number of studies showing that endogenous metabolites may delay aging and improve healthspan. Through the analysis of existing transcriptome data, we discover a link between activation of the transsulfuration pathway and a transcriptional program involved in peroxisome function and biogenesis in long-lived glp-1(e2141ts) mutant Caenorhabditis elegans worms. Subsequently, we show that supplementation with α-ketobutyrate, an intermediate of the transsulfuration pathway, extends lifespan in wild-type worms. Alpha-ketobutyrate augments the production of NAD+ via the lactate dehydrogenase LDH-1, leading to SIR-2.1/SIRT1-mediated enhanced peroxisome function and biogenesis, along with a concomitant increase in the expression of acox-1.2/ACOX1 in the peroxisomal fatty acid β-oxidation pathway. ACOX-1.2/ACOX1 promotes H2O2 formation, thereby resulting in activation of SKN-1/NRF2. This transcription factor in turn extends the lifespan of worms by driving expression of autophagic and lysosomal genes. Finally, we show that α-ketobutyrate also delays the cellular senescence in fibroblast cells through the SIRT1-ACOX1-H2O2-NRF2 pathway. This finding uncovers a previously unknown role for α-ketobutyrate in organismal lifespan and healthspan by coordinating the NAD+-SIRT1 signaling and peroxisomal function.
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Kataya A, Fedosejevs E, Ye Y. Editorial: Post-translational mechanisms involved in regulating peroxisome biogenesis, functions and organelle-crosstalk. Front Cell Dev Biol 2023; 11:1136992. [PMID: 36711036 PMCID: PMC9877304 DOI: 10.3389/fcell.2023.1136992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Affiliation(s)
- Amr Kataya
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada,*Correspondence: Amr Kataya, ,
| | - Eric Fedosejevs
- Harrow Research and Development Centre, Agriculture and Agri-Food Canada, Harrow, ON, Canada
| | - Yajin Ye
- College of Forestry, Nanjing Forestry University, Nanjing, China
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Morito K, Shimizu R, Ali H, Shimada A, Miyazaki T, Takahashi N, Rahman MM, Tsuji K, Shimozawa N, Nakao M, Sano S, Azuma M, Nanjundan M, Kogure K, Tanaka T. Molecular species profiles of plasma ceramides in different clinical types of X-linked adrenoleukodystrophy. J Med Invest 2023; 70:403-410. [PMID: 37940524 DOI: 10.2152/jmi.70.403] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
X-linked adrenoleukodystrophy (X-ALD) is a genetic disorder associated with peroxisomal dysfunction. Patients with this rare disease accumulate very long-chain fatty acids (VLCFAs) in their bodies because of impairment of peroxisomal VLCFA ?-oxidation. Several clinical types of X-ALD, ranging from mild (axonopathy in the spinal cord) to severe (cerebral demyelination), are known. However, the molecular basis for this phenotypic variability remains largely unknown. In this study, we determined plasma ceramide (CER) profile using liquid chromatography-tandem mass spectrometry. We characterized the molecular species profile of CER in the plasma of patients with mild (adrenomyeloneuropathy;AMN) and severe (cerebral) X-ALD. Eleven X-ALD patients (five cerebral, five AMN, and one carrier) and 10 healthy volunteers participated in this study. Elevation of C26:0 CER was found to be a common feature regardless of the clinical types. The level of C26:1 CER was significantly higher in AMN but not in cerebral type, than that in healthy controls. The C26:1 CER level in the cerebral type was significantly lower than that in the AMN type. These results suggest that a high level of C26:0 CER, along with a control level of C26:1 CER, is a characteristic feature of the cerebral type X-ALD. J. Med. Invest. 70 : 403-410, August, 2023.
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Affiliation(s)
- Katsuya Morito
- Department of Pharmaceutical Health Chemistry, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8505, Japan
| | - Ryota Shimizu
- Department of Pharmaceutical Health Chemistry, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8505, Japan
| | - Hanif Ali
- Department of Medical Pharmacology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8505, Japan
| | - Akina Shimada
- Department of Pharmaceutical Health Chemistry, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8505, Japan
| | - Tohru Miyazaki
- Department of Pharmaceutical Health Chemistry, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8505, Japan
| | - Naoko Takahashi
- Department of Pharmaceutical Health Chemistry, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8505, Japan
| | - M Motiur Rahman
- Department of Pharmaceutical Health Chemistry, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8505, Japan
| | - Kazuki Tsuji
- Department of Pharmaceutical Health Chemistry, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8505, Japan
| | - Nobuyuki Shimozawa
- Division of Genomics Research, Life Science Research Center, Gifu University, Gifu 501-1193, Japan
| | - Michiyasu Nakao
- Depertment of Molecular Medicinal Chemistry, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8505, Japan
| | - Shigeki Sano
- Depertment of Molecular Medicinal Chemistry, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8505, Japan
| | - Momoyo Azuma
- Department of Infection Control and Prevention, Tokushima University Hospital, Tokushima 770-8503, Japan
| | - Meera Nanjundan
- Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima 770-8513, Japan
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida 33647, U.S.A
| | - Kentaro Kogure
- Department of Pharmaceutical Health Chemistry, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8505, Japan
| | - Tamotsu Tanaka
- Department of Pharmaceutical Health Chemistry, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8505, Japan
- Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima 770-8513, Japan
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44
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Yao H, Wang Y, Zhang X, Li P, Shang L, Chen X, Zeng J. Targeting peroxisomal fatty acid oxidation improves hepatic steatosis and insulin resistance in obese mice. J Biol Chem 2022; 299:102845. [PMID: 36586435 PMCID: PMC9898756 DOI: 10.1016/j.jbc.2022.102845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/17/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Obesity and diabetes normally cause mitochondrial dysfunction and hepatic lipid accumulation, while fatty acid synthesis is suppressed and malonyl-CoA is depleted in the liver of severe obese or diabetic animals. Therefore, a negative regulatory mechanism might work for the control of mitochondrial fatty acid metabolism that is independent of malonyl-CoA in the diabetic animals. As mitochondrial β-oxidation is controlled by the acetyl-CoA/CoA ratio, and the acetyl-CoA generated in peroxisomal β-oxidation could be transported into mitochondria via carnitine shuttles, we hypothesize that peroxisomal β-oxidation might play a role in regulating mitochondrial fatty acid oxidation and inducing hepatic steatosis under the condition of obesity or diabetes. This study reveals a novel mechanism by which peroxisomal β-oxidation controls mitochondrial fatty acid oxidation in diabetic animals. We determined that excessive oxidation of fatty acids by peroxisomes generates considerable acetyl-carnitine in the liver of diabetic mice, which significantly elevates the mitochondrial acetyl-CoA/CoA ratio and causes feedback suppression of mitochondrial β-oxidation. Additionally, we found that specific suppression of peroxisomal β-oxidation enhances mitochondrial fatty acid oxidation by reducing acetyl-carnitine formation in the liver of obese mice. In conclusion, we suggest that induction of peroxisomal fatty acid oxidation serves as a mechanism for diabetes-induced hepatic lipid accumulation. Targeting peroxisomal β-oxidation might be a promising pathway in improving hepatic steatosis and insulin resistance as induced by obesity or diabetes.
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Affiliation(s)
| | | | | | | | | | | | - Jia Zeng
- School of Life Science, Hunan University of Science and Technology, Xiangtan, Hunan, PR China.
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45
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Feng P, Skowyra ML, Rapoport TA. Structure and function of the peroxisomal ubiquitin ligase complex. Biochem Soc Trans 2022; 50:1921-1930. [PMID: 36421406 PMCID: PMC9788354 DOI: 10.1042/bst20221393] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 09/26/2023]
Abstract
Peroxisomes are membrane-bounded organelles that exist in most eukaryotic cells and are involved in the oxidation of fatty acids and the destruction of reactive oxygen species. Depending on the organism, they house additional metabolic reactions that range from glycolysis in parasitic protozoa to the production of ether lipids in animals and antibiotics in fungi. The importance of peroxisomes for human health is revealed by various disorders - notably the Zellweger spectrum - that are caused by defects in peroxisome biogenesis and are often fatal. Most peroxisomal metabolic enzymes reside in the lumen, but are synthesized in the cytosol and imported into the organelle by mobile receptors. The receptors accompany cargo all the way into the lumen and must return to the cytosol to start a new import cycle. Recycling requires receptor monoubiquitination by a membrane-embedded ubiquitin ligase complex composed of three RING finger (RF) domain-containing proteins: PEX2, PEX10, and PEX12. A recent cryo-electron microscopy (cryo-EM) structure of the complex reveals its function as a retro-translocation channel for peroxisomal import receptors. Each subunit of the complex contributes five transmembrane segments that assemble into an open channel. The N terminus of a receptor likely inserts into the pore from the lumenal side, and is then monoubiquitinated by one of the RFs to enable extraction into the cytosol. If recycling is compromised, receptors are polyubiquitinated by the concerted action of the other two RFs and ultimately degraded. The new data provide mechanistic insight into a crucial step of peroxisomal protein import.
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Affiliation(s)
- Peiqiang Feng
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, U.S.A
| | - Michael L. Skowyra
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, U.S.A
| | - Tom A. Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, U.S.A
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46
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Wilhelm LP, Zapata-Muñoz J, Villarejo-Zori B, Pellegrin S, Freire CM, Toye AM, Boya P, Ganley IG. BNIP3L/NIX regulates both mitophagy and pexophagy. EMBO J 2022; 41:e111115. [PMID: 36215693 PMCID: PMC9753467 DOI: 10.15252/embj.2022111115] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 01/15/2023] Open
Abstract
Mitochondria and peroxisomes are closely related metabolic organelles, both in terms of origin and in terms of function. Mitochondria and peroxisomes can also be turned over by autophagy, in processes termed mitophagy and pexophagy, respectively. However, despite their close relationship, it is not known if both organelles are turned over under similar conditions, and if so, how this might be coordinated molecularly. Here, we find that multiple selective autophagy pathways are activated upon iron chelation and show that mitophagy and pexophagy occur in a BNIP3L/NIX-dependent manner. We reveal that the outer mitochondrial membrane-anchored NIX protein, previously described as a mitophagy receptor, also independently localises to peroxisomes and drives pexophagy. We show this process happens in vivo, with mouse tissue that lacks NIX having a higher peroxisomal content. We further show that pexophagy is stimulated under the same physiological conditions that activate mitophagy, including cardiomyocyte and erythrocyte differentiation. Taken together, our work uncovers a dual role for NIX, not only in mitophagy but also in pexophagy, thus illustrating the interconnection between selective autophagy pathways.
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Affiliation(s)
- Léa P Wilhelm
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Juan Zapata-Muñoz
- Department of Cellular and Molecular Biology, Margarita Salas Center for Biological Research, CSIC, Madrid, Spain
| | - Beatriz Villarejo-Zori
- Department of Cellular and Molecular Biology, Margarita Salas Center for Biological Research, CSIC, Madrid, Spain
| | - Stephanie Pellegrin
- School of Biochemistry, Biomedical Sciences Building, University Walk, Bristol, UK.,National Institute for Health Research (NIHR) Blood and Transplant Research Unit in Red Blood Cell Products, University of Bristol, Bristol, UK
| | | | - Ashley M Toye
- School of Biochemistry, Biomedical Sciences Building, University Walk, Bristol, UK.,National Institute for Health Research (NIHR) Blood and Transplant Research Unit in Red Blood Cell Products, University of Bristol, Bristol, UK
| | - Patricia Boya
- Department of Cellular and Molecular Biology, Margarita Salas Center for Biological Research, CSIC, Madrid, Spain
| | - Ian G Ganley
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
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47
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Yao C, Xu Y, Tang J, Hu P, Qi H, Yang D. Dynamic assembly of DNA-ceria nanocomplex in living cells generates artificial peroxisome. Nat Commun 2022; 13:7739. [PMID: 36517520 DOI: 10.1038/s41467-022-35472-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
Intracellular accumulation of reactive oxygen species (ROS) leads to oxidative stress, which is closely associated with many diseases. Introducing artificial organelles to ROS-imbalanced cells is a promising solution, but this route requires nanoscale particles for efficient cell uptake and micro-scale particles for long-term cell retention, which meets a dilemma. Herein, we report a deoxyribonucleic acid (DNA)-ceria nanocomplex-based dynamic assembly system to realize the intracellular in-situ construction of artificial peroxisomes (AP). The DNA-ceria nanocomplex is synthesized from branched DNA with i-motif structure that responds to the acidic lysosomal environment, triggering transformation from the nanoscale into bulk-scale AP. The initial nanoscale of the nanocomplex facilitates cellular uptake, and the bulk-scale of AP supports cellular retention. AP exhibits enzyme-like catalysis activities, serving as ROS eliminator, scavenging ROS by decomposing H2O2 into O2 and H2O. In living cells, AP efficiently regulates intracellular ROS level and resists GSH consumption, preventing cells from redox dyshomeostasis. With the protection of AP, cytoskeleton integrity, mitochondrial membrane potential, calcium concentration and ATPase activity are maintained under oxidative stress, and thus the energy of cell migration is preserved. As a result, AP inhibits cell apoptosis, reducing cell mortality through ROS elimination.
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48
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Vickers SD, Shumar SA, Saporito DC, Kunovac A, Hathaway QA, Mintmier B, King JA, King RD, Rajendran VM, Infante AM, Hollander JM, Leonardi R. NUDT7 regulates total hepatic CoA levels and the composition of the intestinal bile acid pool in male mice fed a Western diet. J Biol Chem 2022; 299:102745. [PMID: 36436558 PMCID: PMC9792899 DOI: 10.1016/j.jbc.2022.102745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/25/2022] [Accepted: 11/22/2022] [Indexed: 11/26/2022] Open
Abstract
Nudix hydrolase 7 (NUDT7) is an enzyme that hydrolyzes CoA species, is highly expressed in the liver, and resides in the peroxisomes. Peroxisomes are organelles where the preferential oxidation of dicarboxylic fatty acids occurs and where the hepatic synthesis of the primary bile acids cholic acid and chenodeoxycholic acid is completed. We previously showed that liver-specific overexpression of NUDT7 affects peroxisomal lipid metabolism but does not prevent the increase in total liver CoA levels that occurs during fasting. We generated Nudt7-/- mice to further characterize the role that peroxisomal (acyl-)CoA degradation plays in the modulation of the size and composition of the acyl-CoA pool and in the regulation of hepatic lipid metabolism. Here, we show that deletion of Nudt7 alters the composition of the hepatic acyl-CoA pool in mice fed a low-fat diet, but only in males fed a Western diet does the lack of NUDT7 activity increase total liver CoA levels. This effect is driven by the male-specific accumulation of medium-chain dicarboxylic acyl-CoAs, which are produced from the β-oxidation of dicarboxylic fatty acids. We also show that, under conditions of elevated synthesis of chenodeoxycholic acid derivatives, Nudt7 deletion promotes the production of tauromuricholic acid, decreasing the hydrophobicity index of the intestinal bile acid pool and increasing fecal cholesterol excretion in male mice. These findings reveal that NUDT7-mediated hydrolysis of acyl-CoA pathway intermediates in liver peroxisomes contributes to the regulation of dicarboxylic fatty acid metabolism and the composition of the bile acid pool.
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Affiliation(s)
- Schuyler D Vickers
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Stephanie A Shumar
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Dominique C Saporito
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Amina Kunovac
- Division of Exercise Physiology, West Virginia University, Morgantown, West Virginia, USA
| | - Quincy A Hathaway
- Division of Exercise Physiology, West Virginia University, Morgantown, West Virginia, USA
| | - Breeanna Mintmier
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Judy A King
- Department of Pathology and Translational Pathobiology, LSU Health Shreveport, Shreveport, Louisiana, USA
| | - Rachel D King
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Vazhaikkurichi M Rajendran
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Aniello M Infante
- Genomics Core Facility, West Virginia University, Morgantown, West Virginia, USA
| | - John M Hollander
- Division of Exercise Physiology, West Virginia University, Morgantown, West Virginia, USA
| | - Roberta Leonardi
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA.
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49
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Bari KA, Berg MD, Genereaux J, Brandl CJ, Lajoie P. Tra1 controls the transcriptional landscape of the aging cell. G3 (Bethesda) 2022; 13:6782959. [PMID: 36315064 PMCID: PMC9836359 DOI: 10.1093/g3journal/jkac287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/25/2022] [Indexed: 11/07/2022]
Abstract
Gene expression undergoes considerable changes during the aging process. The mechanisms regulating the transcriptional response to cellular aging remain poorly understood. Here, we employ the budding yeast Saccharomyces cerevisiae to better understand how organisms adapt their transcriptome to promote longevity. Chronological lifespan assays in yeast measure the survival of nondividing cells at stationary phase over time, providing insights into the aging process of postmitotic cells. Tra1 is an essential component of both the yeast Spt-Ada-Gcn5 acetyltransferase/Spt-Ada-Gcn5 acetyltransferase-like and nucleosome acetyltransferase of H4 complexes, where it recruits these complexes to acetylate histones at targeted promoters. Importantly, Tra1 regulates the transcriptional response to multiple stresses. To evaluate the role of Tra1 in chronological aging, we took advantage of a previously characterized mutant allele that carries mutations in the TRA1 PI3K domain (tra1Q3). We found that loss of functions associated with tra1Q3 sensitizes cells to growth media acidification and shortens lifespan. Transcriptional profiling reveals that genes differentially regulated by Tra1 during the aging process are enriched for components of the response to stress. Notably, expression of catalases (CTA1, CTT1) involved in hydrogen peroxide detoxification decreases in chronologically aged tra1Q3 cells. Consequently, they display increased sensitivity to oxidative stress. tra1Q3 cells are unable to grow on glycerol indicating a defect in mitochondria function. Aged tra1Q3 cells also display reduced expression of peroxisomal genes, exhibit decreased numbers of peroxisomes, and cannot grow on media containing oleate. Thus, Tra1 emerges as an important regulator of longevity in yeast via multiple mechanisms.
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Affiliation(s)
- Khaleda Afrin Bari
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Matthew D Berg
- Present address for Matthew D Berg: Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Julie Genereaux
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada,Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Christopher J Brandl
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Patrick Lajoie
- Corresponding author: Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada.
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50
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Viñegra de la Torre N, Vayssières A, Obeng-Hinneh E, Neumann U, Zhou Y, Lázaro A, Roggen A, Sun H, Stolze SC, Nakagami H, Schneeberger K, Timmers T, Albani MC. FLOWERING REPRESSOR AAA + ATPase 1 is a novel regulator of perennial flowering in Arabis alpina. New Phytol 2022; 236:729-744. [PMID: 35832005 DOI: 10.1111/nph.18374] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Arabis alpina is a polycarpic perennial, in which PERPETUAL FLOWERING1 (PEP1) regulates flowering and perennial traits in a vernalization-dependent manner. Mutagenesis screens of the pep1 mutant established the role of other flowering time regulators in PEP1-parallel pathways. Here we characterized three allelic enhancers of pep1 (eop002, 085 and 091) which flower early. We mapped the causal mutations and complemented mutants with the identified gene. Using quantitative reverse transcriptase PCR and reporter lines, we determined the protein spatiotemporal expression patterns and localization within the cell. We also characterized its role in Arabidopsis thaliana using CRISPR and in A. alpina by introgressing mutant alleles into a wild-type background. These mutants carried lesions in an AAA+ ATPase of unknown function, FLOWERING REPRESSOR AAA+ ATPase 1 (AaFRAT1). AaFRAT1 was detected in the vasculature of young leaf primordia and the rib zone of flowering shoot apical meristems. At the subcellular level, AaFRAT1 was localized at the interphase between the endoplasmic reticulum and peroxisomes. Introgression lines carrying Aafrat1 alleles required less vernalization to flower and reduced number of vegetative axillary branches. By contrast, A. thaliana CRISPR lines showed weak flowering phenotypes. AaFRAT1 contributes to flowering time regulation and the perennial growth habit of A. alpina.
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Affiliation(s)
- Natanael Viñegra de la Torre
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225, Düsseldorf, Germany
| | - Alice Vayssières
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225, Düsseldorf, Germany
| | - Evelyn Obeng-Hinneh
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225, Düsseldorf, Germany
| | - Ulla Neumann
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Yanhao Zhou
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225, Düsseldorf, Germany
| | - Ana Lázaro
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225, Düsseldorf, Germany
| | - Adrian Roggen
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Hequan Sun
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Sara C Stolze
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Hirofumi Nakagami
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Korbinian Schneeberger
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Ton Timmers
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Maria C Albani
- Institute for Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences "From Complex Traits towards Synthetic Modules", 40225, Düsseldorf, Germany
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