1
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Knoblach B, Rachubinski RA. Peroxisome population control by phosphoinositide signaling at the endoplasmic reticulum-plasma membrane interface. Traffic 2024; 25:e12923. [PMID: 37926951 DOI: 10.1111/tra.12923] [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: 06/15/2023] [Revised: 09/21/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
Phosphoinositides are lipid signaling molecules acting at the interface of membranes and the cytosol to regulate membrane trafficking, lipid transport and responses to extracellular stimuli. Peroxisomes are multicopy organelles that are highly responsive to changes in metabolic and environmental conditions. In yeast, peroxisomes are tethered to the cell cortex at defined focal structures containing the peroxisome inheritance protein, Inp1p. We investigated the potential impact of changes in cortical phosphoinositide levels on the peroxisome compartment of the yeast cell. Here we show that the phosphoinositide, phosphatidylinositol-4-phosphate (PI4P), found at the junction of the cortical endoplasmic reticulum and plasma membrane (cER-PM) acts to regulate the cell's peroxisome population. In cells lacking a cER-PM tether or the enzymatic activity of the lipid phosphatase Sac1p, cortical PI4P is elevated, peroxisome numbers and motility are increased, and peroxisomes are no longer firmly tethered to Inp1p-containing foci. Reattachment of the cER to the PM through an artificial ER-PM "staple" in cells lacking the cER-PM tether does not restore peroxisome populations to the wild-type condition, demonstrating that integrity of PI4P signaling at the cell cortex is required for peroxisome homeostasis.
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Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, Canada
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2
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Di Cara F, Savary S, Kovacs WJ, Kim P, Rachubinski RA. The peroxisome: an up-and-coming organelle in immunometabolism. Trends Cell Biol 2023; 33:70-86. [PMID: 35788297 DOI: 10.1016/j.tcb.2022.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [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: 04/06/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 12/27/2022]
Abstract
Peroxisomes are essential metabolic organelles, well known for their roles in the metabolism of complex lipids and reactive ionic species. In the past 10 years, peroxisomes have also been cast as central regulators of immunity. Lipid metabolites of peroxisomes, such as polyunsaturated fatty acids (PUFAs), are precursors for important immune mediators, including leukotrienes (LTs) and resolvins. Peroxisomal redox metabolism modulates cellular immune signaling such as nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation. Additionally, peroxisomal β-oxidation and ether lipid synthesis control the development and aspects of the activation of both innate and adaptive immune cells. Finally, peroxisome number and metabolic activity have been linked to inflammatory diseases. These discoveries have opened avenues of investigation aimed at targeting peroxisomes for therapeutic intervention in immune disorders, inflammation, and cancer.
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Affiliation(s)
- Francesca Di Cara
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada.
| | - Stéphane Savary
- Lab. Bio-PeroxIL EA7270, University of Bourgogne Franche-Comté, 6 Bd Gabriel, 21000 Dijon, France
| | - Werner J Kovacs
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology in Zurich (ETH Zürich), Zurich, Switzerland
| | - Peter Kim
- Cell Biology Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada; Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, South Korea
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3
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Nath AS, Parsons BD, Makdissi S, Chilvers RL, Mu Y, Weaver CM, Euodia I, Fitze KA, Long J, Scur M, Mackenzie DP, Makrigiannis AP, Pichaud N, Boudreau LH, Simmonds AJ, Webber CA, Derfalvi B, Hammon Y, Rachubinski RA, Di Cara F. Modulation of the cell membrane lipid milieu by peroxisomal β-oxidation induces Rho1 signaling to trigger inflammatory responses. Cell Rep 2022; 38:110433. [PMID: 35235794 DOI: 10.1016/j.celrep.2022.110433] [Citation(s) in RCA: 8] [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: 03/22/2021] [Revised: 12/21/2021] [Accepted: 02/01/2022] [Indexed: 12/11/2022] Open
Abstract
Phagocytosis, signal transduction, and inflammatory responses require changes in lipid metabolism. Peroxisomes have key roles in fatty acid homeostasis and in regulating immune function. We find that Drosophila macrophages lacking peroxisomes have perturbed lipid profiles, which reduce host survival after infection. Using lipidomic, transcriptomic, and genetic screens, we determine that peroxisomes contribute to the cell membrane glycerophospholipid composition necessary to induce Rho1-dependent signals, which drive cytoskeletal remodeling during macrophage activation. Loss of peroxisome function increases membrane phosphatidic acid (PA) and recruits RhoGAPp190 during infection, inhibiting Rho1-mediated responses. Peroxisome-glycerophospholipid-Rho1 signaling also controls cytoskeleton remodeling in mouse immune cells. While high levels of PA in cells without peroxisomes inhibit inflammatory phenotypes, large numbers of peroxisomes and low amounts of cell membrane PA are features of immune cells from patients with inflammatory Kawasaki disease and juvenile idiopathic arthritis. Our findings reveal potential metabolic markers and therapeutic targets for immune diseases and metabolic disorders.
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Affiliation(s)
- Anu S Nath
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Brendon D Parsons
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Stephanie Makdissi
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Rebecca L Chilvers
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Yizhu Mu
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Ceileigh M Weaver
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Irene Euodia
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Katherine A Fitze
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Juyang Long
- 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
| | - Duncan P Mackenzie
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Andrew P Makrigiannis
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada
| | - Nicolas Pichaud
- Université de Moncton, Department of Chemistry and Biochemistry, Moncton, NB E1A 3E9, Canada; New Brunswick Centre for Precision Medicine (NBCPM), Moncton, NB E1A 3E9, Canada
| | - Luc H Boudreau
- Université de Moncton, Department of Chemistry and Biochemistry, Moncton, NB E1A 3E9, Canada; New Brunswick Centre for Precision Medicine (NBCPM), Moncton, NB E1A 3E9, Canada
| | - Andrew J Simmonds
- University of Alberta, Department of Cell Biology, Edmonton, AB T6G 2H7, Canada
| | - Christine A Webber
- University of Alberta, Department of Cell Biology, Edmonton, AB T6G 2H7, Canada
| | - Beata Derfalvi
- Dalhousie University, Department of Pediatrics, Halifax, NS B3K 6R8, Canada
| | - Yannick Hammon
- INSERM au Centre d'Immunologie de Marseille Luminy, Marseille 13288, France
| | | | - Francesca Di Cara
- Dalhousie University, Department of Microbiology and Immunology, Halifax, NS B3K 6R8, Canada; Dalhousie University, Department of Pediatrics, Halifax, NS B3K 6R8, Canada.
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4
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Liu Y, Weaver CM, Sen Y, Eitzen G, Simmonds AJ, Linchieh L, Lurette O, Hebert-Chatelain E, Rachubinski RA, Di Cara F. The Nitric Oxide Donor, S-Nitrosoglutathione, Rescues Peroxisome Number and Activity Defects in PEX1G843D Mild Zellweger Syndrome Fibroblasts. Front Cell Dev Biol 2021; 9:714710. [PMID: 34434934 PMCID: PMC8382563 DOI: 10.3389/fcell.2021.714710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/20/2021] [Indexed: 02/04/2023] Open
Abstract
Peroxisome biogenesis disorders (PBDs) are a group of metabolic developmental diseases caused by mutations in one or more genes encoding peroxisomal proteins. Zellweger syndrome spectrum (PBD-ZSS) results from metabolic dysfunction caused by damaged or non-functional peroxisomes and manifests as a multi-organ syndrome with significant morbidity and mortality for which there is no current drug therapy. Mild PBD-ZSS patients can exhibit a more progressive disease course and could benefit from the identification of drugs to improve the quality of life and extend the lifespan of affected individuals. Our study used a high-throughput screen of FDA-approved compounds to identify compounds that improve peroxisome function and biogenesis in human fibroblast cells carrying the mild PBD-ZSS variant, PEX1G843D. Our screen identified the nitrogen oxide donor, S-nitrosoglutathione (GSNO), as a potential therapeutic for this mild form of PBD-ZSS. Further biochemical characterization showed that GSNO enhances both peroxisome number and function in PEX1G843D mutant fibroblasts and leads to increased survival and longer lifespan in an in vivo humanized Drosophila model carrying the PEX1G843D mutation. GSNO is therefore a strong candidate to be translated to clinical trials as a potential therapeutic for mild PBD-ZSS.
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Affiliation(s)
- Yidi Liu
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Ceileigh M Weaver
- Department of Microbiology and Immunology, IWK Research Centre, Dalhousie University, Halifax, NS, Canada
| | - Yarina Sen
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Gary Eitzen
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Lilliana Linchieh
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Olivier Lurette
- Department of Biology, University of Moncton, Moncton, NB, Canada
| | | | | | - Francesca Di Cara
- Department of Microbiology and Immunology, IWK Research Centre, Dalhousie University, Halifax, NS, Canada
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5
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Banerjee H, LaPointe P, Eitzen G, Rachubinski RA. A Small Molecule Inhibitor of Pex3-Pex19 Interaction Disrupts Glycosome Biogenesis and Causes Lethality in Trypanosoma brucei. Front Cell Dev Biol 2021; 9:703603. [PMID: 34350186 PMCID: PMC8326762 DOI: 10.3389/fcell.2021.703603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/22/2021] [Indexed: 11/29/2022] Open
Abstract
Trypanosomatid parasites, including Trypanosoma and Leishmania, are infectious zoonotic agents for a number of severe diseases such as African sleeping sickness and American trypanosomiasis (Chagas disease) that affect millions of people, mostly in the emergent world. The glycosome is a specialized member of the peroxisome family of organelles found in trypanosomatids. These organelles compartmentalize essential enzymes of the glycolytic pathway, making them a prime target for drugs that can kill these organisms by interfering with either their biochemical functions or their formation. Glycosome biogenesis, like peroxisome biogenesis, is controlled by a group of proteins called peroxins (Pex). Pex3 is an early acting peroxin that docks Pex19, the receptor for peroxisomal membrane proteins, to initiate biogenesis of peroxisomes from the endoplasmic reticulum. Identification of Pex3 as the essential master regulator of glycosome biogenesis has implications in developing small molecule inhibitors that can impede Pex3–Pex19 interaction. Low amino acid sequence conservation between trypanosomatid Pex3 and human Pex3 (HsPex3) would aid in the identification of small molecule inhibitors that selectively interfere with the trypanosomatid Pex3–Pex19 interaction. We tested a library of pharmacologically active compounds in a modified yeast two-hybrid assay and identified a compound that preferentially inhibited the interaction of Trypanosoma brucei Pex3 and Pex19 versus HsPex3 and Pex19. Addition of this compound to either the insect or bloodstream form of T. brucei disrupted glycosome biogenesis, leading to mislocalization of glycosomal enzymes to the cytosol and lethality for the parasite. Our results show that preferential disruption of trypanosomal Pex3 function by small molecule inhibitors could help in the accelerated development of drugs for the treatment of trypanosomiases.
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Affiliation(s)
- Hiren Banerjee
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Paul LaPointe
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Gary Eitzen
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
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6
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Knoblach B, Ishida R, Hobman TC, Rachubinski RA. Peroxisomes exhibit compromised structure and matrix protein content in SARS-CoV-2-infected cells. Mol Biol Cell 2021; 32:1273-1282. [PMID: 34010015 PMCID: PMC8351553 DOI: 10.1091/mbc.e21-02-0074] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that has triggered global health and economic crises. Here we report the effects of SARS-CoV-2 infection on peroxisomes of human cell lines Huh-7 and SK-N-SH. Peroxisomes undergo dramatic changes in morphology in SARS-CoV-2-infected cells. Rearrangement of peroxisomal membranes is followed by redistribution of peroxisomal matrix proteins to the cytosol, resulting in a dramatic decrease in the number of mature peroxisomes. The SARS-CoV-2 ORF14 protein was shown to interact physically with human PEX14, a peroxisomal membrane protein required for matrix protein import and peroxisome biogenesis. Given the important roles of peroxisomes in innate immunity, SARS-CoV-2 may directly target peroxisomes, resulting in loss of peroxisome structural integrity, matrix protein content and ability to function in antiviral signaling.
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Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Ray Ishida
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Tom C Hobman
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Richard A Rachubinski
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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7
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Mast FD, Rachubinski RA, Aitchison JD. Peroxisome prognostications: Exploring the birth, life, and death of an organelle. J Cell Biol 2020; 219:133827. [PMID: 32211898 PMCID: PMC7054992 DOI: 10.1083/jcb.201912100] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 02/07/2023] Open
Abstract
Peroxisomes play a central role in human health and have biochemical properties that promote their use in many biotechnology settings. With a primary role in lipid metabolism, peroxisomes share a niche with lipid droplets within the endomembrane-secretory system. Notably, factors in the ER required for the biogenesis of peroxisomes also impact the formation of lipid droplets. The dynamic interface between peroxisomes and lipid droplets, and also between these organelles and the ER and mitochondria, controls their metabolic flux and their dynamics. Here, we review our understanding of peroxisome biogenesis to propose and reframe models for understanding how peroxisomes are formed in cells. To more fully understand the roles of peroxisomes and to take advantage of their many properties that may prove useful in novel therapeutics or biotechnology applications, we recast mechanisms controlling peroxisome biogenesis in a framework that integrates inference from these models with experimental data.
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Affiliation(s)
- Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA
| | | | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA.,Department of Pediatrics, University of Washington, Seattle, WA
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8
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Boycott KM, Campeau PM, Howley HE, Pavlidis P, Rogic S, Oriel C, Berman JN, Hamilton RM, Hicks GG, Lipshitz HD, Masson JY, Shoubridge EA, Junker A, Leroux MR, McMaster CR, Michaud JL, Turvey SE, Dyment D, Innes AM, van Karnebeek CD, Lehman A, Cohn RD, MacDonald IM, Rachubinski RA, Frosk P, Vandersteen A, Wozniak RW, Pena IA, Wen XY, Lacaze-Masmonteil T, Rankin C, Hieter P. The Canadian Rare Diseases Models and Mechanisms (RDMM) Network: Connecting Understudied Genes to Model Organisms. Am J Hum Genet 2020; 106:143-152. [PMID: 32032513 DOI: 10.1016/j.ajhg.2020.01.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 11/07/2019] [Accepted: 01/10/2020] [Indexed: 01/14/2023] Open
Abstract
Advances in genomics have transformed our ability to identify the genetic causes of rare diseases (RDs), yet we have a limited understanding of the mechanistic roles of most genes in health and disease. When a novel RD gene is first discovered, there is minimal insight into its biological function, the pathogenic mechanisms of disease-causing variants, and how therapy might be approached. To address this gap, the Canadian Rare Diseases Models and Mechanisms (RDMM) Network was established to connect clinicians discovering new disease genes with Canadian scientists able to study equivalent genes and pathways in model organisms (MOs). The Network is built around a registry of more than 500 Canadian MO scientists, representing expertise for over 7,500 human genes. RDMM uses a committee process to identify and evaluate clinician-MO scientist collaborations and approve 25,000 Canadian dollars in catalyst funding. To date, we have made 85 clinician-MO scientist connections and funded 105 projects. These collaborations help confirm variant pathogenicity and unravel the molecular mechanisms of RD, and also test novel therapies and lead to long-term collaborations. To expand the impact and reach of this model, we made the RDMM Registry open-source, portable, and customizable, and we freely share our committee structures and processes. We are currently working with emerging networks in Europe, Australia, and Japan to link international RDMM networks and registries and enable matches across borders. We will continue to create meaningful collaborations, generate knowledge, and advance RD research locally and globally for the benefit of patients and families living with RD.
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Affiliation(s)
- Kym M Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada.
| | - Philippe M Campeau
- Centre de Recherche du CHU Ste-Justine, Department of Pediatrics, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Heather E Howley
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sanja Rogic
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Christine Oriel
- Maternal Infant Child and Youth Research Network (MICYRN), Vancouver, BC V5Z 4H4, Canada
| | - Jason N Berman
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Robert M Hamilton
- Labatt Family Heart Centre and Translational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Geoffrey G Hicks
- Regenerative Medicine Program, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P5, Canada; Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P5, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jean-Yves Masson
- Oncology Division, CHU de Québec-Université Laval, Laval University Cancer Research Center, Quebec City, QC, G1R 3S3, Canada
| | - Eric A Shoubridge
- Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Anne Junker
- Department of Pediatrics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Michel R Leroux
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | | | - Jaques L Michaud
- Centre de Recherche du CHU Ste-Justine, Department of Pediatrics, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Stuart E Turvey
- Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - David Dyment
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - A Micheil Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Alberta Children's Hospital, Calgary, AB T2N 4N1, Canada
| | - Clara D van Karnebeek
- Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada; Department of Pediatrics, Amsterdam University Medical Centres, Amsterdam, the Netherlands; Department of Clinical Genetics, Amsterdam University Medical Centres, Amsterdam, the Netherlands
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Ronald D Cohn
- Genetics and Genome Biology Program, SickKids Research Institute, Department of Paediatrics and Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Ian M MacDonald
- Department of Ophthalmology and Visual Sciences, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R7, Canada
| | - Richard A Rachubinski
- Genetics and Genome Biology Program, SickKids Research Institute, Department of Paediatrics and Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Patrick Frosk
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3A 1S1, Canada
| | - Anthony Vandersteen
- Department of Pediatrics, Maritime Medical Genetics Service, Dalhousie University, IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Richard W Wozniak
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Izabella A Pena
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Xiao-Yan Wen
- Zebrafish Centre for Advanced Drug Discovery, Keenan Research Centre for Biomedical Science, St Michael's Hospital, Unity Health Toronto, Department of Medicine, University of Toronto, Toronto, ON M5B 1T8
| | - Thierry Lacaze-Masmonteil
- Maternal Infant Child and Youth Research Network (MICYRN), Vancouver, BC V5Z 4H4, Canada; Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Catharine Rankin
- Department of Psychology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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9
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Banerjee H, Knoblach B, Rachubinski RA. The early-acting glycosome biogenic protein Pex3 is essential for trypanosome viability. Life Sci Alliance 2019; 2:2/4/e201900421. [PMID: 31341002 PMCID: PMC6658674 DOI: 10.26508/lsa.201900421] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 11/24/2022] Open
Abstract
This study reports the identification of trypanosome Pex3, the master regulator of glycosome biogenesis. Trypanosome Pex3 is essential for glycosome assembly and trypanosome viability and is distinct from human Pex3. Trypanosomatid parasites are infectious agents for diseases such as African sleeping sickness, Chagas disease, and leishmaniasis that threaten millions of people, mostly in the emerging world. Trypanosomes compartmentalize glycolytic enzymes to an organelle called the glycosome, a specialized peroxisome. Functionally intact glycosomes are essential for trypanosomatid viability, making glycosomal proteins as potential drug targets against trypanosomatid diseases. Peroxins (Pex), of which Pex3 is the master regulator, control glycosome biogenesis. Although Pex3 has been found throughout the eukaryota, its identity has remained stubbornly elusive in trypanosomes. We used bioinformatics predictive of protein secondary structure to identify trypanosomal Pex3. Microscopic and biochemical analyses showed trypanosomal Pex3 to be glycosomal. Interaction of Pex3 with the peroxisomal membrane protein receptor Pex19 observed for other eukaryotes is replicated by trypanosomal Pex3 and Pex19. Depletion of Pex3 leads to mislocalization of glycosomal proteins to the cytosol, reduced glycosome numbers, and trypanosomatid death. Our findings are consistent with Pex3 being an essential gene in trypanosomes.
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Affiliation(s)
- Hiren Banerjee
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, Canada
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10
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Chang J, Rachubinski RA. Pex20p functions as the receptor for non‐PTS1/non‐PTS2 acyl‐CoA oxidase import into peroxisomes of the yeast
Yarrowia lipolytica. Traffic 2019; 20:504-515. [DOI: 10.1111/tra.12652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/29/2019] [Accepted: 04/29/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Jinlan Chang
- Department of Cell BiologyUniversity of Alberta Edmonton Alberta Canada
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11
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Knoblach B, Rachubinski RA. Determinants of the assembly, integrity and maintenance of the endoplasmic reticulum-peroxisome tether. Traffic 2019; 20:213-225. [PMID: 30597694 DOI: 10.1111/tra.12635] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 06/01/2018] [Revised: 12/24/2018] [Accepted: 12/26/2018] [Indexed: 11/29/2022]
Abstract
Organelle tethering and intercommunication are crucial for proper cell function. We previously described a tether between peroxisomes and the endoplasmic reticulum (ER) that acts in peroxisome population control in the yeast, Saccharomyces cerevisiae. Components of this tether are Pex3p, an integral membrane protein of both peroxisomes and the ER and Inp1p, a connector that links peroxisomes to the ER. Here, we report the analysis of random Inp1p mutants that enabled identification of regions in Inp1p required for the assembly and maintenance of the ER-peroxisome tether. Interaction analysis between Inp1p mutants and known Inp1p-binding proteins demonstrated that Pex3p and Inp1p do not constitute the sole components of the ER-peroxisome tether. Deletion of these Inp1p interactors whose steady-state localization is outside of ER-peroxisome tethers affected peroxisome dynamics. Our findings are consistent with the presence of regulatory cues that act on ER-peroxisome tethers and point to the existence of membrane contact sites between peroxisomes and organelles other than the ER.
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Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
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12
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Knoblach B, Rachubinski RA. Reconstitution of human peroxisomal β-oxidation in yeast. FEMS Yeast Res 2018; 18:5075582. [PMID: 30124827 DOI: 10.1093/femsyr/foy092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/14/2018] [Indexed: 11/14/2022] Open
Abstract
We report the permanent introduction of the human peroxisomal β-oxidation enzymatic machinery required for straight chain degradation of fatty acids into the yeast, Saccharomyces cerevisiae. Peroxisomal β-oxidation encompasses four sequential reactions that are confined to three enzymes. The genes encoding human acyl-CoA oxidase 1, peroxisomal multifunctional enzyme type 2 and 3-ketoacyl-CoA thiolase were introduced into the genomic loci of their yeast gene equivalents. The human β-oxidation genes were individually tagged with sequence coding for GFP and expression of the protein chimeras as well as their targeting to peroxisomes was confirmed. Functional complementation of the β-oxidation pathway was assessed by growth on media containing fatty acids of different chain lengths. Yeast cells exhibited distinctive substrate specificities depending on whether they expressed the human or their endogenous β-oxidation machinery. The genetic engineering of yeast to contain a 'humanized' organelle is a first step for the in vivo study of human peroxisome disorders in a model organism.
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Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, MSB 5-14, Edmonton, Alberta T6G 2H7, Canada
| | - Richard A Rachubinski
- Department of Cell Biology, University of Alberta, Edmonton, MSB 5-14, Edmonton, Alberta T6G 2H7, Canada
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13
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Marcus SL, Miyata KS, Rachubinski RA, Capone JP. Transactivation by PPAR/RXR heterodimers in yeast is potentiated by exogenous fatty acid via a pathway requiring intact peroxisomes. Gene Expr 2018; 4:227-39. [PMID: 7787415 PMCID: PMC6134384] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Peroxisome proliferator-activated receptors (PPARs) are orphan members of the nuclear hormone receptor superfamily. PPARs bind to cognate response elements through heterodimerization with retinoid X receptors (RXRs). Together PPAR/RXR regulate the transcription of genes for which products are involved in lipid homeostasis, cell growth, and differentiation. PPARs are activated by fatty acids and by nongenotoxic rodent hepatocarcinogens called peroxisome proliferators through as of yet undefined signal transduction pathways. In an effort to elucidate the requirements for PPAR function and the pathways of its activation, we expressed mouse PPAR alpha and human RXR alpha in the yeast Saccharomyces cerevisiae. Mouse PPAR alpha and human RXR alpha had little activity individually in yeast; however, when cosynthesized, they were able to synergistically activate transcription via cognate response elements. Transactivation was independent of exogenously added activators of either receptor but was potentiated by the addition of petroselinic acid, a fatty acid shown to activate PPARs in mammalian cells. Similar experiments were carried out in a mutant yeast strain lacking peroxisomes entirely or in a mutant strain deficient for 3-ketoacyl-CoA thiolase, the final enzyme of the peroxisomal beta-oxidation cascade. The findings showed that constitutive transactivation by PPAR/RXR did not require the complete beta-oxidation pathway or intact peroxisomes but required intact peroxisomes for potentiation by exogenously added petroselinic acid. This study demonstrates that at least part of the mammalian peroxisome proliferator-signaling pathway can be faithfully reconstituted in yeast and that activation of PPAR by at least one particular fatty acid requires the integrity of peroxisomes.
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Affiliation(s)
- S L Marcus
- Department of Anatomy and Cell Biology, University of Alberta, Edmonton, Canada
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14
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Di Cara F, Bülow MH, Simmonds AJ, Rachubinski RA. Dysfunctional peroxisomes compromise gut structure and host defense by increased cell death and Tor-dependent autophagy. Mol Biol Cell 2018; 29:2766-2783. [PMID: 30188767 PMCID: PMC6249834 DOI: 10.1091/mbc.e18-07-0434] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The gut has a central role in digestion and nutrient absorption, but it also serves in defending against pathogens, engages in mutually beneficial interactions with commensals, and is a major source of endocrine signals. Gut homeostasis is necessary for organismal health and changes to the gut are associated with conditions like obesity and diabetes and inflammatory illnesses like Crohn's disease. We report that peroxisomes, organelles involved in lipid metabolism and redox balance, are required to maintain gut epithelium homeostasis and renewal in Drosophila and for survival and development of the organism. Dysfunctional peroxisomes in gut epithelial cells activate Tor kinase-dependent autophagy that increases cell death and epithelial instability, which ultimately alter the composition of the intestinal microbiota, compromise immune pathways in the gut in response to infection, and affect organismal survival. Peroxisomes in the gut effectively function as hubs that coordinate responses from stress, metabolic, and immune signaling pathways to maintain enteric health and the functionality of the gut-microbe interface.
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Affiliation(s)
- Francesca Di Cara
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Margret H Bülow
- Development, Genetics and Molecular Physiology, LIMES (Life and Medical Sciences), University of Bonn, D-53115 Bonn, Germany
| | - Andrew J Simmonds
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
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15
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Weill U, Yofe I, Sass E, Stynen B, Davidi D, Natarajan J, Ben-Menachem R, Avihou Z, Goldman O, Harpaz N, Chuartzman S, Kniazev K, Knoblach B, Laborenz J, Boos F, Kowarzyk J, Ben-Dor S, Zalckvar E, Herrmann JM, Rachubinski RA, Pines O, Rapaport D, Michnick SW, Levy ED, Schuldiner M. Genome-wide SWAp-Tag yeast libraries for proteome exploration. Nat Methods 2018; 15:617-622. [PMID: 29988094 PMCID: PMC6076999 DOI: 10.1038/s41592-018-0044-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/10/2018] [Indexed: 12/31/2022]
Abstract
Yeast libraries revolutionized the systematic study of cell biology. To extensively increase the number of such libraries and the type of information that can be gleaned from them, we previously devised the SWAp-Tag (SWAT) approach that enables rapid, easy and efficient creation of yeast strain collections. Here we present the construction and investigation of a full genome library of ~5500 strains carrying the SWAT NOP1promoter-GFP module at the N terminus of proteins, as well as its use in creating six additional libraries that either restore the native regulation, create an overexpression library with a Cherry tag or enable protein complementation assays from two fragments of an enzyme or fluorophore. We show methods to utilize these SWAT collections to systematically characterize the yeast proteome on multiple levels spanning protein abundance, localization, topology and interactions. Our findings demonstrate how diverse full-genome SWAT libraries facilitate obtaining insights into numerous aspects of the proteome.
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Affiliation(s)
- Uri Weill
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ido Yofe
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ehud Sass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Bram Stynen
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
| | - Dan Davidi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Janani Natarajan
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Reut Ben-Menachem
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zohar Avihou
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Omer Goldman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Nofar Harpaz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Silvia Chuartzman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Kiril Kniazev
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Janina Laborenz
- Department of Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Felix Boos
- Department of Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jacqueline Kowarzyk
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Johannes M Herrmann
- Department of Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | | | - Ophry Pines
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Stephen W Michnick
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
| | - Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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16
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Mast FD, Herricks T, Strehler KM, Miller LR, Saleem RA, Rachubinski RA, Aitchison JD. ESCRT-III is required for scissioning new peroxisomes from the endoplasmic reticulum. J Cell Biol 2018; 217:2087-2102. [PMID: 29588378 PMCID: PMC5987711 DOI: 10.1083/jcb.201706044] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 01/23/2018] [Accepted: 03/05/2018] [Indexed: 12/11/2022] Open
Abstract
Dynamic control of peroxisome proliferation is integral to the peroxisome's many functions. The endoplasmic reticulum (ER) serves as a source of preperoxisomal vesicles (PPVs) that mature into peroxisomes during de novo peroxisome biogenesis and support growth and division of existing peroxisomes. However, the mechanism of PPV formation and release from the ER remains poorly understood. In this study, we show that endosomal sorting complexes required for transport (ESCRT)-III are required to release PPVs budding from the ER into the cytosol. Absence of ESCRT-III proteins impedes de novo peroxisome formation and results in an aberrant peroxisome population in vivo. Using a cell-free PPV budding assay, we show that ESCRT-III proteins Vps20 and Snf7 are necessary to release PPVs from the ER. ESCRT-III is therefore a positive effector of membrane scission for vesicles budding both away from and toward the cytosol. These findings have important implications for the evolutionary timing of emergence of peroxisomes and the rest of the internal membrane architecture of the eukaryotic cell.
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Affiliation(s)
- Fred D Mast
- Center for Infectious Disease Research, Seattle, WA.,Institute for Systems Biology, Seattle, WA
| | - Thurston Herricks
- Center for Infectious Disease Research, Seattle, WA.,Institute for Systems Biology, Seattle, WA
| | - Kathleen M Strehler
- Center for Infectious Disease Research, Seattle, WA.,Institute for Systems Biology, Seattle, WA
| | - Leslie R Miller
- Center for Infectious Disease Research, Seattle, WA.,Institute for Systems Biology, Seattle, WA
| | - Ramsey A Saleem
- Center for Infectious Disease Research, Seattle, WA.,Institute for Systems Biology, Seattle, WA
| | | | - John D Aitchison
- Center for Infectious Disease Research, Seattle, WA.,Institute for Systems Biology, Seattle, WA.,Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
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17
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Banerjee H, Rachubinski RA. Involvement of SNARE protein Ykt6 in glycosome biogenesis in Trypanosoma brucei. Mol Biochem Parasitol 2017; 218:28-37. [PMID: 29107734 DOI: 10.1016/j.molbiopara.2017.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 04/20/2017] [Revised: 10/02/2017] [Accepted: 10/21/2017] [Indexed: 11/30/2022]
Abstract
The kinetoplastid parasites Trypanosoma and Leishmania are etiologic agents of diseases like African sleeping sickness, Chagas and leishmaniasis that inflict many tropical and subtropical parts of the world. These parasites are distinctive in that they compartmentalize most of the usually cytosolic enzymes of the glycolytic pathway within a peroxisome-like organelle called the glycosome. Functional glycosomes are essential in both the procyclic and bloodstream forms of trypanosomatid parasites, and mislocalization of glycosomal enzymes to the cytosol is fatal for the parasite. The life cycle of these parasites is intimately linked to their efficient protein and vesicular trafficking machinery that helps them in immune evasion, host-pathogen interaction and organelle biogenesis and integrity. Soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) proteins play important roles in vesicular trafficking and mediate a wide range of protein-protein interactions in eukaryotes. We show here that the SNARE protein Ykt6 is necessary for glycosome biogenesis and function in Trypanosoma brucei. RNAi-mediated depletion of Ykt6 in both the procyclic and bloodstream forms of T. brucei leads to mislocalization of glycosomal matrix proteins to the cytosol, pronounced reduction in glycosome number, and cell death. GFP-tagged Ykt6 appears as punctate structures in the T. brucei cell and colocalizes in part to glycosomes. Our results constitute the first demonstration of a role for SNARE proteins in the biogenesis of peroxisomal organelles.
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Affiliation(s)
- Hiren Banerjee
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Richard A Rachubinski
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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18
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Di Cara F, Sheshachalam A, Braverman NE, Rachubinski RA, Simmonds AJ. Peroxisome-Mediated Metabolism Is Required for Immune Response to Microbial Infection. Immunity 2017; 47:93-106.e7. [PMID: 28723556 DOI: 10.1016/j.immuni.2017.06.016] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [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: 12/06/2016] [Revised: 04/20/2017] [Accepted: 06/22/2017] [Indexed: 12/21/2022]
Abstract
The innate immune response is critical for animal homeostasis and is conserved from invertebrates to vertebrates. This response depends on specialized cells that recognize, internalize, and destroy microbial invaders through phagocytosis. This is coupled to autonomous or non-autonomous cellular signaling via reactive oxygen species (ROS) and cytokine production. Lipids are known signaling factors in this process, as the acute phase response of macrophages is accompanied by systemic lipid changes that help resolve inflammation. We found that peroxisomes, membrane-enclosed organelles central to lipid metabolism and ROS turnover, were necessary for the engulfment of bacteria by Drosophila and mouse macrophages. Peroxisomes were also required for resolution of bacterial infection through canonical innate immune signaling. Reduced peroxisome function impaired the turnover of the oxidative burst necessary to fight infection. This impaired response to bacterial challenge affected cell and organism survival and revealed a previously unknown requirement for peroxisomes in phagocytosis and innate immunity.
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Affiliation(s)
- Francesca Di Cara
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
| | - Avinash Sheshachalam
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Nancy E Braverman
- Research Institute of the McGill University Children's Hospital, Montreal, Quebec H4A 3J1, Canada
| | - Richard A Rachubinski
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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19
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Gentekaki E, Curtis BA, Stairs CW, Klimeš V, Eliáš M, Salas-Leiva DE, Herman EK, Eme L, Arias MC, Henrissat B, Hilliou F, Klute MJ, Suga H, Malik SB, Pightling AW, Kolisko M, Rachubinski RA, Schlacht A, Soanes DM, Tsaousis AD, Archibald JM, Ball SG, Dacks JB, Clark CG, van der Giezen M, Roger AJ. Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis. PLoS Biol 2017; 15:e2003769. [PMID: 28892507 PMCID: PMC5608401 DOI: 10.1371/journal.pbio.2003769] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/21/2017] [Accepted: 08/25/2017] [Indexed: 12/11/2022] Open
Abstract
Blastocystis is the most prevalent eukaryotic microbe colonizing the human gut, infecting approximately 1 billion individuals worldwide. Although Blastocystis has been linked to intestinal disorders, its pathogenicity remains controversial because most carriers are asymptomatic. Here, the genome sequence of Blastocystis subtype (ST) 1 is presented and compared to previously published sequences for ST4 and ST7. Despite a conserved core of genes, there is unexpected diversity between these STs in terms of their genome sizes, guanine-cytosine (GC) content, intron numbers, and gene content. ST1 has 6,544 protein-coding genes, which is several hundred more than reported for ST4 and ST7. The percentage of proteins unique to each ST ranges from 6.2% to 20.5%, greatly exceeding the differences observed within parasite genera. Orthologous proteins also display extreme divergence in amino acid sequence identity between STs (i.e., 59%-61% median identity), on par with observations of the most distantly related species pairs of parasite genera. The STs also display substantial variation in gene family distributions and sizes, especially for protein kinase and protease gene families, which could reflect differences in virulence. It remains to be seen to what extent these inter-ST differences persist at the intra-ST level. A full 26% of genes in ST1 have stop codons that are created on the mRNA level by a novel polyadenylation mechanism found only in Blastocystis. Reconstructions of pathways and organellar systems revealed that ST1 has a relatively complete membrane-trafficking system and a near-complete meiotic toolkit, possibly indicating a sexual cycle. Unlike some intestinal protistan parasites, Blastocystis ST1 has near-complete de novo pyrimidine, purine, and thiamine biosynthesis pathways and is unique amongst studied stramenopiles in being able to metabolize α-glucans rather than β-glucans. It lacks all genes encoding heme-containing cytochrome P450 proteins. Predictions of the mitochondrion-related organelle (MRO) proteome reveal an expanded repertoire of functions, including lipid, cofactor, and vitamin biosynthesis, as well as proteins that may be involved in regulating mitochondrial morphology and MRO/endoplasmic reticulum (ER) interactions. In sharp contrast, genes for peroxisome-associated functions are absent, suggesting Blastocystis STs lack this organelle. Overall, this study provides an important window into the biology of Blastocystis, showcasing significant differences between STs that can guide future experimental investigations into differences in their virulence and clarifying the roles of these organisms in gut health and disease.
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Affiliation(s)
- Eleni Gentekaki
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Bruce A. Curtis
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Courtney W. Stairs
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Vladimír Klimeš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Dayana E. Salas-Leiva
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Emily K. Herman
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Laura Eme
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Maria C. Arias
- Université des Sciences et Technologies de Lille, Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 CNRS-USTL, Cité Scientifique, Villeneuve d’Ascq Cedex, France
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Mary J. Klute
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Hiroshi Suga
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Nanatsuka 562, Shobara, Hiroshima, Japan
| | - Shehre-Banoo Malik
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Arthur W. Pightling
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Martin Kolisko
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Alexander Schlacht
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Darren M. Soanes
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Anastasios D. Tsaousis
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - John M. Archibald
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
- Canadian Institute for Advanced Research, CIFAR Program in Integrated Microbial Biodiversity, Toronto, Canada
| | - Steven G. Ball
- Université des Sciences et Technologies de Lille, Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576 CNRS-USTL, Cité Scientifique, Villeneuve d’Ascq Cedex, France
| | - Joel B. Dacks
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - C. Graham Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Andrew J. Roger
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
- Canadian Institute for Advanced Research, CIFAR Program in Integrated Microbial Biodiversity, Toronto, Canada
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20
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Mast FD, Jamakhandi A, Saleem RA, Dilworth DJ, Rogers RS, Rachubinski RA, Aitchison JD. Peroxins Pex30 and Pex29 Dynamically Associate with Reticulons to Regulate Peroxisome Biogenesis from the Endoplasmic Reticulum. J Biol Chem 2016; 291:15408-27. [PMID: 27129769 DOI: 10.1074/jbc.m116.728154] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [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: 03/18/2016] [Indexed: 12/11/2022] Open
Abstract
Peroxisome proliferation occurs by at least two routes, division of existing peroxisomes and de novo biogenesis from the endoplasmic reticulum (ER). The proteins and molecular mechanisms governing peroxisome emergence from the ER are poorly characterized. In this study, we report that two integral membrane peroxins (proteins required for peroxisome biogenesis) in Saccharomyces cerevisiae, Pex29 and Pex30, reside in distinct regions of the ER and associate with Rtn1 and Yop1, reticulon family members that contribute to ER morphology, to govern peroxisome emergence from the ER. In vivo and in vitro analyses reveal that peroxisome proliferation is therefore not restricted to the peroxisome but begins at the level of the ER.
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Affiliation(s)
- Fred D Mast
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - Arvind Jamakhandi
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - Ramsey A Saleem
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - David J Dilworth
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - Richard S Rogers
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - Richard A Rachubinski
- the Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - John D Aitchison
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
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21
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Baron MN, Klinger CM, Rachubinski RA, Simmonds AJ. A Systematic Cell-Based Analysis of Localization of PredictedDrosophilaPeroxisomal Proteins. Traffic 2016; 17:536-53. [DOI: 10.1111/tra.12384] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/29/2016] [Accepted: 01/29/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Matthew N. Baron
- Department of Cell Biology; University of Alberta; Medical Sciences Building 5-14 Edmonton AB T6G 2H7 Canada
| | - Christen M. Klinger
- Department of Cell Biology; University of Alberta; Medical Sciences Building 5-14 Edmonton AB T6G 2H7 Canada
| | - Richard A. Rachubinski
- Department of Cell Biology; University of Alberta; Medical Sciences Building 5-14 Edmonton AB T6G 2H7 Canada
| | - Andrew J. Simmonds
- Department of Cell Biology; University of Alberta; Medical Sciences Building 5-14 Edmonton AB T6G 2H7 Canada
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22
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Knoblach B, Rachubinski RA. Sharing with your children: Mechanisms of peroxisome inheritance. Biochim Biophys Acta 2015; 1863:1014-8. [PMID: 26620799 DOI: 10.1016/j.bbamcr.2015.11.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 10/22/2022]
Abstract
Organelle inheritance is the process by which eukaryotic cells actively replicate and equitably partition their organelles between mother cell and daughter cell at cytokinesis to maintain the benefits of subcellular compartmentalization. The budding yeast Saccharomyces cerevisiae has proven invaluable in helping to define the factors involved in the inheritance of different organelles and in understanding how these factors act and interact to maintain balance in the organelle populations of actively dividing cells. Inheritance factors can be classified as motors that transport organelles, tethers that retain organelles, and connectors (receptors) that mediate the attachment of organelles to motors and anchors. This article will review how peroxisomes are inherited by cells, with a focus on budding yeast, and will discuss common themes and mechanisms of action that underlie the inheritance of all membrane-enclosed organelles.
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Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Richard A Rachubinski
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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23
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Abstract
Organelle inheritance is a process whereby organelles are actively distributed between dividing cells at cytokinesis. Much valuable insight into the molecular mechanisms of organelle inheritance has come from the analysis of asymmetrically dividing cells, which transport a portion of their organelles to the bud while retaining another portion in the mother cell. Common principles apply to the inheritance of all organelles, although individual organelles use specific factors for their partitioning. Inheritance factors can be classified as motors, which are required for organelle transport; anchors, which immobilize organelles at distinct cell structures; or connectors, which mediate the attachment of organelles to motors and anchors. Here, we provide an overview of recent advances in the field of organelle inheritance and highlight how motor, anchor, and connector molecules choreograph the segregation of a multicopy organelle, the peroxisome. We also discuss the role of organelle population control in the generation of cellular diversity.
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Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada;
| | - Richard A Rachubinski
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada;
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24
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Abstract
Peroxisomes are remarkably responsive organelles. Their composition, abundance and even their mechanism of biogenesis are influenced strongly by cell type and the environment. This plasticity underlies peroxisomal functions in metabolism and the detoxification of dangerous reactive oxygen species. However, peroxisomes are integrated into the cellular system as a whole such that they communicate intimately with other organelles, control signaling dynamics as in the case of innate immune responses to infectious disease, and contribute to processes as fundamental as longevity. The increasing evidence for peroxisomes having roles in various cellular and organismal functions, combined with their malleability, suggests complex mechanisms operate to control cellular dynamics and the specificity of cellular responses and functions extending well beyond the peroxisome itself. A deeper understanding of the functions of peroxisomes and the mechanisms that control their plasticity could offer opportunities for exploiting changes in peroxisome abundance to control cellular function.
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Affiliation(s)
- Fred D Mast
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, USA; Institute for Systems Biology, Seattle, USA
| | | | - John D Aitchison
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, USA; Institute for Systems Biology, Seattle, USA.
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25
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Chang J, Klute MJ, Tower RJ, Mast FD, Dacks JB, Rachubinski RA. An ancestral role in peroxisome assembly is retained by the divisional peroxin Pex11 in the yeast Yarrowia lipolytica. J Cell Sci 2015; 128:1327-40. [PMID: 25663700 DOI: 10.1242/jcs.157743] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [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: 02/04/2023] Open
Abstract
The peroxin Pex11 has a recognized role in peroxisome division. Pex11p remodels and elongates peroxisomal membranes prior to the recruitment of dynamin-related GTPases that act in membrane scission to divide peroxisomes. We performed a comprehensive comparative genomics survey to understand the significance of the evolution of the Pex11 protein family in yeast and other eukaryotes. Pex11p is highly conserved and ancestral, and has undergone numerous lineage-specific duplications, whereas other Pex11 protein family members are fungal-specific innovations. Functional characterization of the in-silico-predicted Pex11 protein family members of the yeast Yarrowia lipolytica, i.e. Pex11p, Pex11Cp and Pex11/25p, demonstrated that Pex11Cp and Pex11/25p have a role in the regulation of peroxisome size and number characteristic of Pex11 protein family members. Unexpectedly, deletion of PEX11 in Y. lipolytica produces cells that lack morphologically identifiable peroxisomes, mislocalize peroxisomal matrix proteins and preferentially degrade peroxisomal membrane proteins, i.e. they exhibit the classical pex mutant phenotype, which has not been observed previously in cells deleted for the PEX11 gene. Our results are consistent with an unprecedented role for Pex11p in de novo peroxisome assembly.
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Affiliation(s)
- Jinlan Chang
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Mary J Klute
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Robert J Tower
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Fred D Mast
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Joel B Dacks
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
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26
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Abstract
Eukaryotic cells replicate and partition their organelles between the mother cell and the daughter cell at cytokinesis. Polarized cells, notably the budding yeast Saccharomyces cerevisiae, are well suited for the study of organelle inheritance, as they facilitate an experimental dissection of organelle transport and retention processes. Much progress has been made in defining the molecular players involved in organelle partitioning in yeast. Each organelle uses a distinct set of factors - motor, anchor and adaptor proteins - that ensures its inheritance by future generations of cells. We propose that all organelles, regardless of origin or copy number, are partitioned by the same fundamental mechanism involving division and segregation. Thus, the mother cell keeps, and the daughter cell receives, their fair and equitable share of organelles. This mechanism of partitioning moreover facilitates the segregation of organelle fragments that are not functionally equivalent. In this Commentary, we describe how this principle of organelle population control affects peroxisomes and other organelles, and outline its implications for yeast life span and rejuvenation.
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Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, AL T6G 2H7, Canada
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27
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Knoblach B, Rachubinski RA. Transport and retention mechanisms govern lipid droplet inheritance in Saccharomyces cerevisiae. Traffic 2015; 16:298-309. [PMID: 25524182 DOI: 10.1111/tra.12247] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [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: 07/15/2014] [Revised: 11/25/2014] [Accepted: 11/28/2014] [Indexed: 01/26/2023]
Abstract
Lipid droplets are ubiquitous cellular structures involved in energy homeostasis and metabolism that have long been considered as simple inert deposits of lipid. Here, we show that lipid droplets are bona fide organelles that are actively partitioned between mother cell and daughter cell in Saccharomyces cerevisiae. Video microscopy revealed that a subset of lipid droplets moves from mother cell to bud in an ordered, vectorial process, while the remaining lipid droplets are retained by the mother cell. Bud-directed movement of lipid droplets is mediated by the molecular motor Myo2p, while retention of lipid droplets occurs at the perinuclear endoplasmic reticulum. Lipid droplets are thus apportioned between mother cell and daughter cell at cell division rather than being made anew.
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Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
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28
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Titorenko VI, Rachubinski RA. Origin and spatiotemporal dynamics of the peroxisomal endomembrane system. Front Physiol 2014; 5:493. [PMID: 25566090 PMCID: PMC4267184 DOI: 10.3389/fphys.2014.00493] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 11/30/2014] [Indexed: 11/13/2022] Open
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29
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Sasvari Z, Gonzalez PA, Rachubinski RA, Nagy PD. Tombusvirus replication depends on Sec39p endoplasmic reticulum-associated transport protein. Virology 2013; 447:21-31. [PMID: 24210096 DOI: 10.1016/j.virol.2013.07.039] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [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: 06/07/2013] [Revised: 07/03/2013] [Accepted: 07/31/2013] [Indexed: 10/26/2022]
Abstract
Positive-stranded RNA viruses subvert subcellular membranes to built viral replicases complexes (VRCs) in infected cells. Tombusviruses use peroxisomal membranes for the assembly of their VRCs and they can efficiently switch to the endoplasmic reticulum membrane in the absence of peroxisomes. In this paper, we show that the ER-resident Sec39p vesicular transport protein is critical for the formation of active VRCs in yeast model host. Repression of Sec39p expression in yeast or in plants resulted in greatly reduced tombusvirus accumulation. Moreover, the purified tombusvirus replicase from Sec39p-depleted yeast cells showed low in vitro activity. Also, tombusvirus RNA replication was poor in cell-free extracts or in isolated ER membranes from yeast with repressed Sec39p expression. The tombusvirus p33 replication protein was mislocalized to the ER when Sec39p was depleted in yeast. Overall, Sec39p is the first peroxisomal biogenesis protein characterized that is critical for tombusvirus replication in yeast and plants.
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Affiliation(s)
- Zsuzsanna Sasvari
- Department of Plant Pathology, University of Kentucky, Lexington, 201F Plant Science Building, KY 40546, USA
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30
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Knoblach B, Rachubinski RA. Doing the math: How yeast cells maintain their peroxisome populations. Commun Integr Biol 2013; 6:e26901. [PMID: 24567780 PMCID: PMC3925452 DOI: 10.4161/cib.26901] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 10/22/2013] [Indexed: 01/31/2023] Open
Abstract
The formation of membrane contact sites between cellular organelles is required for proper organelle communication and maintenance in the compartmentalized eukaryotic cell. We recently identified a tether that links peroxisomes to the cortical ER in the yeast, Saccharomyces cerevisiae. The tether is made up of the peroxisome biogenic protein Pex3p and the peroxisome inheritance factor Inp1p, and is formed by Inp1p-mediated linkage of ER-bound Pex3p and peroxisomal Pex3p. Here we discuss how this tether is fine-tuned to ensure that peroxisomes are stably maintained over generations of yeast cells.
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Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology; University of Alberta; Edmonton, AB Canada
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31
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Chang J, Tower RJ, Lancaster DL, Rachubinski RA. Dynein light chain interaction with the peroxisomal import docking complex modulates peroxisome biogenesis in yeast. J Cell Sci 2013; 126:4698-706. [PMID: 23943868 DOI: 10.1242/jcs.129056] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [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: 11/20/2022] Open
Abstract
Dynein is a large macromolecular motor complex that moves cargo along microtubules. A motor-independent role for the light chain of dynein, Dyn2p, in peroxisome biology in Saccharomyces cerevisiae was suggested from its interaction with Pex14p, a component of the peroxisomal matrix protein import docking complex. Here we show that cells of the yeast Yarrowia lipolytica deleted for the gene encoding the homologue of Dyn2p are impaired in peroxisome function and biogenesis. These cells exhibit compromised growth on medium containing oleic acid as the carbon source, the metabolism of which requires functional peroxisomes. Their peroxisomes have abnormal morphology, atypical matrix protein localization, and an absence of proteolytic processing of the matrix enzyme thiolase, which normally occurs upon its import into the peroxisome. We also show physical and genetic interactions between Dyn2p and members of the docking complex, particularly Pex17p. Together, our results demonstrate a role for Dyn2p in the assembly of functional peroxisomes and provide evidence that Dyn2p acts in cooperation with the peroxisomal matrix protein import docking complex to effect optimal matrix protein import.
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Affiliation(s)
- Jinlan Chang
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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32
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Knoblach B, Sun X, Coquelle N, Fagarasanu A, Poirier RL, Rachubinski RA. An ER-peroxisome tether exerts peroxisome population control in yeast. EMBO J 2013; 32:2439-53. [PMID: 23900285 DOI: 10.1038/emboj.2013.170] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 07/02/2013] [Indexed: 01/08/2023] Open
Abstract
Eukaryotic cells compartmentalize biochemical reactions into membrane-enclosed organelles that must be faithfully propagated from one cell generation to the next. Transport and retention processes balance the partitioning of organelles between mother and daughter cells. Here we report the identification of an ER-peroxisome tether that links peroxisomes to the ER and ensures peroxisome population control in the yeast Saccharomyces cerevisiae. The tether consists of the peroxisome biogenic protein, Pex3p, and the peroxisome inheritance factor, Inp1p. Inp1p bridges the two compartments by acting as a molecular hinge between ER-bound Pex3p and peroxisomal Pex3p. Asymmetric peroxisome division leads to the formation of Inp1p-containing anchored peroxisomes and Inp1p-deficient mobile peroxisomes that segregate to the bud. While peroxisomes in mother cells are not released from tethering, de novo formation of tethers in the bud assists in the directionality of peroxisome transfer. Peroxisomes are thus stably maintained over generations of cells through their continued interaction with tethers.
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Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
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33
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Loughran PA, Stolz DB, Barrick SR, Wheeler DS, Friedman PA, Rachubinski RA, Watkins SC, Billiar TR. PEX7 and EBP50 target iNOS to the peroxisome in hepatocytes. Nitric Oxide 2013; 31:9-19. [PMID: 23474170 DOI: 10.1016/j.niox.2013.02.084] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 02/08/2013] [Accepted: 02/25/2013] [Indexed: 10/27/2022]
Abstract
iNOS localizes to both the cytosol and peroxisomes in hepatocytes in vitro and in vivo. The structural determinants for iNOS localization are not known. One plausible mechanism for iNOS localization to the peroxisome is through the interaction with peroxisomal import proteins PEX5 or PEX7. siRNA knockdown of PEX7 reduced iNOS colocalization with the peroxisomal protein PMP70. Proteomic studies using MALDI-MS identified iNOS association with the 50-kD ezrin binding PDZ protein (EBP50). Confocal microscopy studies and immunoelectron microscopy confirmed iNOS association with EBP50, with greatest colocalization occurring at 8h of cytokine exposure. EBP50 associated with peroxisomes in a PEX5 and PEX7-dependent manner. iNOS localization to peroxisomes was contingent on EBP50 expression in LPS-treated mice. Thus, iNOS targeting to peroxisomes in hepatocytes involves interaction with PEX7 and EBP50. The targeting of iNOS protein to the peroxisome may shift the balance of metabolic processes that rely on heme proteins susceptible to modification by radical oxygen and nitrogen radicals.
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Affiliation(s)
- Patricia A Loughran
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.
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34
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Lancaster DL, Dobson CM, Rachubinski RA. Chaperone proteins select and maintain [PIN+] prion conformations in Saccharomyces cerevisiae. J Biol Chem 2012; 288:1266-76. [PMID: 23148221 DOI: 10.1074/jbc.m112.377564] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prions are proteins that can adopt different infectious conformations known as "strains" or "variants," each with a distinct, epigenetically inheritable phenotype. Mechanisms by which prion variants are determined remain unclear. Here we use the Saccharomyces cerevisiae prion Rnq1p/[PIN(+)] as a model to investigate the effects of chaperone proteins upon prion variant determination. We show that deletion of specific chaperone genes alters [PIN(+)] variant phenotypes, including [PSI(+)] induction efficiency, Rnq1p aggregate morphology/size and variant dominance. Mating assays demonstrate that gene deletion-induced phenotypic changes are stably inherited in a non-Mendelian manner even after restoration of the deleted gene, confirming that they are due to a bona fide change in the [PIN(+)] variant. Together, our results demonstrate a role for chaperones in regulating the prion variant complement of a cell.
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Affiliation(s)
- David L Lancaster
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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35
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Mast FD, Li J, Virk MK, Hughes SC, Simmonds AJ, Rachubinski RA. A Drosophila model for the Zellweger spectrum of peroxisome biogenesis disorders. Dis Model Mech 2011; 4:659-72. [PMID: 21669930 PMCID: PMC3180231 DOI: 10.1242/dmm.007419] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Human peroxisome biogenesis disorders are lethal genetic diseases in which abnormal peroxisome assembly compromises overall peroxisome and cellular function. Peroxisomes are ubiquitous membrane-bound organelles involved in several important biochemical processes, notably lipid metabolism and the use of reactive oxygen species for detoxification. Using cultured cells, we systematically characterized the peroxisome assembly phenotypes associated with dsRNA-mediated knockdown of 14 predicted Drosophila homologs of PEX genes (encoding peroxins; required for peroxisome assembly and linked to peroxisome biogenesis disorders), and confirmed that at least 13 of them are required for normal peroxisome assembly. We also demonstrate the relevance of Drosophila as a genetic model for the early developmental defects associated with the human peroxisome biogenesis disorders. Mutation of the PEX1 gene is the most common cause of peroxisome biogenesis disorders and is one of the causes of the most severe form of the disease, Zellweger syndrome. Inherited mutations in Drosophila Pex1 correlate with reproducible defects during early development. Notably, Pex1 mutant larvae exhibit abnormalities that are analogous to those exhibited by Zellweger syndrome patients, including developmental delay, poor feeding, severe structural abnormalities in the peripheral and central nervous systems, and early death. Finally, microarray analysis defined several clusters of genes whose expression varied significantly between wild-type and mutant larvae, implicating peroxisomal function in neuronal development, innate immunity, lipid and protein metabolism, gamete formation, and meiosis.
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Affiliation(s)
- Fred D Mast
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
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36
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Abstract
Eukaryotic cells are characterized by their varied complement of organelles. One set of membrane-bound, usually spherical compartments are commonly grouped together under the term peroxisomes. Peroxisomes function in regulating the synthesis and availability of many diverse lipids by harnessing the power of oxidative reactions and contribute to a number of metabolic processes essential for cellular differentiation and organismal development.
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Affiliation(s)
- Fred D Mast
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
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37
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Tower RJ, Fagarasanu A, Aitchison JD, Rachubinski RA. The peroxin Pex34p functions with the Pex11 family of peroxisomal divisional proteins to regulate the peroxisome population in yeast. Mol Biol Cell 2011; 22:1727-38. [PMID: 21441307 PMCID: PMC3093324 DOI: 10.1091/mbc.e11-01-0084] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Peroxisomes are ubiquitous organelles involved in diverse metabolic processes, most notably the metabolism of lipids and the detoxification of reactive oxygen species. Peroxisomes are highly dynamic and change in size and number in response to both intra- and extracellular cues. In the yeast Saccharomyces cerevisiae, peroxisome growth and division are controlled by both the differential import of soluble matrix proteins and a specialized divisional machinery that includes peroxisome-specific factors, such as members of the Pex11 protein family, and general organelle divisional factors, such as the dynamin-related protein Vps1p. Global yeast two-hybrid analyses have demonstrated interactions between the product of the S. cerevisiae gene of unknown function, YCL056c, and Pex proteins involved in peroxisome biogenesis. Here we show that the protein encoded by YCL056c, renamed Pex34p, is a peroxisomal integral membrane protein that acts independently and also in concert with the Pex11 protein family members Pex11p, Pex25p, and Pex27p to control the peroxisome populations of cells under conditions of both peroxisome proliferation and constitutive peroxisome division. Yeast two-hybrid analysis showed that Pex34p interacts physically with itself and with Pex11p, Pex25p, and Pex27p but not with Vps1p. Pex34p can act as a positive effector of peroxisome division as its overexpression leads to increased numbers of peroxisomes in wild type and pex34Δ cells. Pex34p requires the Pex11 family proteins to promote peroxisome division. Our discovery of Pex34p as a protein involved in the already complex control of peroxisome populations emphasizes the necessity of cells to strictly regulate their peroxisome populations to be able to respond appropriately to changing environmental conditions.
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Affiliation(s)
- Robert J Tower
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada Institute for Systems Biology, Seattle, WA 98103, USA
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38
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Vinh DBN, Ko DC, Rachubinski RA, Aitchison JD, Miller SI. Expression of the Salmonella spp. virulence factor SifA in yeast alters Rho1 activity on peroxisomes. Mol Biol Cell 2010; 21:3567-77. [PMID: 20739463 PMCID: PMC2954121 DOI: 10.1091/mbc.e10-06-0482] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 08/02/2010] [Accepted: 08/17/2010] [Indexed: 11/11/2022] Open
Abstract
The Salmonella typhimurium effector protein SifA regulates the assembly and tubulation of the Salmonella phagosome. SifA localizes to the phagosome and interacts with the membrane via its prenylated tail. SifA is a structural homologue of another bacterial effector that acts as a GTP-exchange factor for Rho family GTPases and can bind GDP-RhoA. When coexpressed with a bacterial lipase that is activated by RhoA, SifA can induce tubulation of mammalian endosomes. In an effort to develop a genetic system to study SifA function, we expressed SifA and characterized its activity in yeast. GFP-SifA predominantly localized to yeast peroxisomal membranes. Under peroxisome-inducing conditions, GFP-SifA reduced the number of free peroxisomes and promoted the formation of large peroxisomes with membrane invaginations. GFP-SifA activity depended on the recruitment to peroxisomes of wild-type Rho1p and Pex25p, a receptor for Rho1p. GFP-SifA could also rescue the actin organization defects in pex25Δ and rho1 mutants, suggesting that SifA may recruit and potentiate Rho1p activity. We reexamined the distribution of GFP-SifA in mammalian cells and found the majority colocalizing with LAMP1-positive compartment and not with the peroxisomal marker PMP70. Together, these data suggest that SifA may use a similar mode of action via Rho proteins to alter yeast peroxisomal and mammalian endosomal membranes. Further definition of SifA activity on yeast peroxisomes could provide more insight into its role in regulating host membrane dynamics and small GTPases.
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Affiliation(s)
| | | | - Richard A. Rachubinski
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada; and
| | | | - Samuel I. Miller
- Departments of *Medicine
- Immunology
- Microbiology, and
- Genome Sciences, University of Washington, Seattle, WA 98195
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39
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Saleem RA, Long-O'Donnell R, Dilworth DJ, Armstrong AM, Jamakhandi AP, Wan Y, Knijnenburg TA, Niemistö A, Boyle J, Rachubinski RA, Shmulevich I, Aitchison JD. Genome-wide analysis of effectors of peroxisome biogenesis. PLoS One 2010; 5:e11953. [PMID: 20694151 PMCID: PMC2915925 DOI: 10.1371/journal.pone.0011953] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 07/12/2010] [Indexed: 11/19/2022] Open
Abstract
Peroxisomes are intracellular organelles that house a number of diverse metabolic processes, notably those required for beta-oxidation of fatty acids. Peroxisomes biogenesis can be induced by the presence of peroxisome proliferators, including fatty acids, which activate complex cellular programs that underlie the induction process. Here, we used multi-parameter quantitative phenotype analyses of an arrayed mutant collection of yeast cells induced to proliferate peroxisomes, to establish a comprehensive inventory of genes required for peroxisome induction and function. The assays employed include growth in the presence of fatty acids, and confocal imaging and flow cytometry through the induction process. In addition to the classical phenotypes associated with loss of peroxisomal functions, these studies identified 169 genes required for robust signaling, transcription, normal peroxisomal development and morphologies, and transmission of peroxisomes to daughter cells. These gene products are localized throughout the cell, and many have indirect connections to peroxisome function. By integration with extant data sets, we present a total of 211 genes linked to peroxisome biogenesis and highlight the complex networks through which information flows during peroxisome biogenesis and function.
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Affiliation(s)
- Ramsey A. Saleem
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Rose Long-O'Donnell
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - David J. Dilworth
- Institute for Systems Biology, Seattle, Washington, United States of America
| | | | | | - Yakun Wan
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Theo A. Knijnenburg
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Antti Niemistö
- Institute for Systems Biology, Seattle, Washington, United States of America
- Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - John Boyle
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Richard A. Rachubinski
- Department of Cell Biology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Ilya Shmulevich
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - John D. Aitchison
- Institute for Systems Biology, Seattle, Washington, United States of America
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Saleem RA, Rogers RS, Ratushny AV, Dilworth DJ, Shannon PT, Shteynberg D, Wan Y, Moritz RL, Nesvizhskii AI, Rachubinski RA, Aitchison JD. Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction. Mol Cell Proteomics 2010; 9:2076-88. [PMID: 20395639 DOI: 10.1074/mcp.m000116-mcp201] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Phosphorylation of proteins is a key posttranslational modification in cellular signaling, regulating many aspects of cellular responses. We used a quantitative, integrated, phosphoproteomics approach to characterize the cellular responses of the yeast Saccharomyces cerevisiae to the fatty acid oleic acid, a molecule with broad human health implications and a potent inducer of peroxisomes. A combination of cryolysis and urea solubilization was used to minimize the opportunity for reorientation of the phosphoproteome, and hydrophilic interaction liquid chromatography and IMAC chemistries were used to fractionate and enrich for phosphopeptides. Using these approaches, numerous phosphorylated peptides specific to oleate-induced and glucose-repressed conditions were identified and mapped to known signaling pathways. These include several transcription factors, two of which, Pip2p and Cst6p, must be phosphorylated for the normal transcriptional response of fatty acid-responsive loci encoding peroxisomal proteins. The phosphoproteome data were integrated with results from genome-wide assays studying the effects of signaling molecule deletions and known protein-protein interactions to generate a putative fatty acid-responsive signaling network. In this network, the most highly connected nodes are those with the largest effects on cellular responses to oleic acid. These properties are consistent with a scale-free topology, demonstrating that scale-free properties are conserved in condition-specific networks.
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Affiliation(s)
- Ramsey A Saleem
- Institute for Systems Biology, Seattle, Washington 98103, USA
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41
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Knoblach B, Rachubinski RA. Phosphorylation-dependent activation of peroxisome proliferator protein PEX11 controls peroxisome abundance. J Biol Chem 2009; 285:6670-80. [PMID: 20028986 DOI: 10.1074/jbc.m109.094805] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Peroxisomes are dynamic organelles that divide continuously in growing cell cultures and expand extensively in lipid-rich medium. Peroxisome population control is achieved in part by Pex11p-dependent regulation of peroxisome size and number. Although the production of Pex11p in yeast is tightly linked to peroxisome biogenesis by transcriptional regulation of the PEX11 gene, it remains unclear if and how Pex11p activity could be modulated by rapid signaling. We report the reversible phosphorylation of Saccharomyces cerevisiae Pex11p in response to nutritional cues and delineate a mechanism for phosphorylation-dependent activation of Pex11p through the analysis of phosphomimicking mutants. Peroxisomal phenotypes in the PEX11-A and PEX11-D strains expressing constitutively dephosphorylated and phosphorylated forms of Pex11p resemble those of PEX11 gene knock-out and overexpression mutants, although PEX11 transcript and Pex11 protein levels remain unchanged. We demonstrate functional inequality and differences in subcellular localization of the Pex11p forms. Pex11Dp promotes peroxisome fragmentation when reexpressed in cells containing induced peroxisomes. Pex11p translocates between endoplasmic reticulum and peroxisomes in a phosphorylation-dependent manner, whereas Pex11Ap and Pex11Dp are impaired in trafficking and constitutively associated with mature and proliferating peroxisomes, respectively. Overexpression of cyclin-dependent kinase Pho85p results in hyperphosphorylation of Pex11p and peroxisome proliferation. This study provides the first evidence for control of peroxisome dynamics by phosphorylation-dependent regulation of a peroxin.
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Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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Jung S, Marelli M, Rachubinski RA, Goodlett DR, Aitchison JD. Dynamic changes in the subcellular distribution of Gpd1p in response to cell stress. J Biol Chem 2009; 285:6739-49. [PMID: 20026609 DOI: 10.1074/jbc.m109.058552] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gpd1p is a cytosolic NAD(+)-dependent glycerol 3-phosphate dehydrogenase that also localizes to peroxisomes and plays an essential role in the cellular response to osmotic stress and a role in redox balance. Here, we show that Gpd1p is directed to peroxisomes by virtue of an N-terminal type 2 peroxisomal targeting signal (PTS2) in a Pex7p-dependent manner. Significantly, localization of Gpd1p to peroxisomes is dependent on the metabolic status of cells and the phosphorylation of aminoacyl residues adjacent to the targeting signal. Exposure of cells to osmotic stress induces changes in the subcellular distribution of Gpd1p to the cytosol and nucleus. This behavior is similar to Pnc1p, which is coordinately expressed with Gpd1p, and under conditions of cell stress changes its subcellular distribution from peroxisomes to the nucleus where it mediates chromatin silencing. Although peroxisomes are necessary for the beta-oxidation of fatty acids in yeast, the localization of Gpd1p to peroxisomes is not. Rather, shifts in the distribution of Gpd1p to different cellular compartments in response to changing cellular status suggests a role for Gpd1p in the spatial regulation of redox potential, a process critical to cell survival, especially under the complex stress conditions expected to occur in the wild.
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Affiliation(s)
- Sunhee Jung
- Institute for Systems Biology, Seattle, Washington 98103, USA
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Chang J, Mast FD, Fagarasanu A, Rachubinski DA, Eitzen GA, Dacks JB, Rachubinski RA. Pex3 peroxisome biogenesis proteins function in peroxisome inheritance as class V myosin receptors. ACTA ACUST UNITED AC 2009; 187:233-46. [PMID: 19822674 PMCID: PMC2768826 DOI: 10.1083/jcb.200902117] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pex3 links peroxisome formation and inheritance. By binding to class V myosin, biogenesis protein Pex3 also directs the organelles into daughter cells. In Saccharomyces cerevisiae, peroxisomal inheritance from mother cell to bud is conducted by the class V myosin motor, Myo2p. However, homologues of S. cerevisiae Myo2p peroxisomal receptor, Inp2p, are not readily identifiable outside the Saccharomycetaceae family. Here, we demonstrate an unexpected role for Pex3 proteins in peroxisome inheritance. Both Pex3p and Pex3Bp are peroxisomal integral membrane proteins that function as peroxisomal receptors for class V myosin through direct interaction with the myosin globular tail. In cells lacking Pex3Bp, peroxisomes are preferentially retained by the mother cell, whereas most peroxisomes gather and are transferred en masse to the bud in cells overexpressing Pex3Bp or Pex3p. Our results reveal an unprecedented role for members of the Pex3 protein family in peroxisome motility and inheritance in addition to their well-established role in peroxisome biogenesis at the endoplasmic reticulum. Our results point to a temporal link between peroxisome formation and inheritance and delineate a general mechanism of peroxisome inheritance in eukaryotic cells.
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Affiliation(s)
- Jinlan Chang
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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Fagarasanu A, Mast FD, Knoblach B, Jin Y, Brunner MJ, Logan MR, Glover JNM, Eitzen GA, Aitchison JD, Weisman LS, Rachubinski RA. Myosin-driven peroxisome partitioning in S. cerevisiae. ACTA ACUST UNITED AC 2009; 186:541-54. [PMID: 19687257 PMCID: PMC2733749 DOI: 10.1083/jcb.200904050] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In Saccharomyces cerevisiae, the class V myosin motor Myo2p propels the movement of most organelles. We recently identified Inp2p as the peroxisome-specific receptor for Myo2p. In this study, we delineate the region of Myo2p devoted to binding peroxisomes. Using mutants of Myo2p specifically impaired in peroxisome binding, we dissect cell cycle–dependent and peroxisome partitioning–dependent mechanisms of Inp2p regulation. We find that although total Inp2p levels oscillate with the cell cycle, Inp2p levels on individual peroxisomes are controlled by peroxisome inheritance, as Inp2p aberrantly accumulates and decorates all peroxisomes in mother cells when peroxisome partitioning is abolished. We also find that Inp2p is a phosphoprotein whose level of phosphorylation is coupled to the cell cycle irrespective of peroxisome positioning in the cell. Our findings demonstrate that both organelle positioning and cell cycle progression control the levels of organelle-specific receptors for molecular motors to ultimately achieve an equidistribution of compartments between mother and daughter cells.
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Affiliation(s)
- Andrei Fagarasanu
- Department of Cell Biology and 2 Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G2H7, Canada
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Abstract
Recent studies have provided evidence that peroxisomes constitute a multicompartmental endomembrane system. The system begins to form with the targeting of certain peroxisomal membrane proteins to the ER and their exit from the ER via preperoxisomal carriers. These carriers undergo a multistep maturation into metabolically active peroxisomes containing the entire complement of peroxisomal membrane and matrix proteins. At each step, the import of a subset of proteins and the uptake of certain membrane lipids result in the formation of a distinct, more mature compartment of the peroxisomal endomembrane system. Individual peroxisomal compartments proliferate by undergoing one or several rounds of division. Herein, we discuss various strategies that evolutionarily diverse organisms use to coordinate compartment formation, maturation, and division in the peroxisomal endomembrane system. We also critically evaluate the molecular and cellular mechanisms governing these processes, outline the most important unanswered questions, and suggest directions for future research.
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Neuspiel M, Schauss AC, Braschi E, Zunino R, Rippstein P, Rachubinski RA, Andrade-Navarro MA, McBride HM. Cargo-selected transport from the mitochondria to peroxisomes is mediated by vesicular carriers. Curr Biol 2008; 18:102-8. [PMID: 18207745 DOI: 10.1016/j.cub.2007.12.038] [Citation(s) in RCA: 415] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Revised: 11/29/2007] [Accepted: 12/07/2007] [Indexed: 11/26/2022]
Abstract
Mitochondria and peroxisomes share a number of common biochemical processes, including the beta oxidation of fatty acids and the scavenging of peroxides. Here, we identify a new outer-membrane mitochondria-anchored protein ligase (MAPL) containing a really interesting new gene (RING)-finger domain. Overexpression of MAPL leads to mitochondrial fragmentation, indicating a regulatory function controlling mitochondrial morphology. In addition, confocal- and electron-microscopy studies of MAPL-YFP led to the observation that MAPL is also incorporated within unique, DRP1-independent, 70-100 nm diameter mitochondria-derived vesicles (MDVs). Importantly, vesicles containing MAPL exclude another outer-membrane marker, TOM20, and vesicles containing TOM20 exclude MAPL, indicating that MDVs selectively incorporate their cargo. We further demonstrate that MAPL-containing vesicles fuse with a subset of peroxisomes, marking the first evidence for a direct relationship between these two functionally related organelles. In contrast, a distinct vesicle population labeled with TOM20 does not fuse with peroxisomes, indicating that the incorporation of specific cargo is a primary determinant of MDV fate. These data are the first to identify MAPL, describe and characterize MDVs, and define a new intracellular transport route between mitochondria and peroxisomes.
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Affiliation(s)
- Margaret Neuspiel
- Lipoproteins and Atherosclerosis Group, University of Ottawa Heart Institute, 40 Ruskin St., Ottawa, Ontario K1Y 4W7, Canada
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Saleem RA, Knoblach B, Mast FD, Smith JJ, Boyle J, Dobson CM, Long-O'Donnell R, Rachubinski RA, Aitchison JD. Genome-wide analysis of signaling networks regulating fatty acid-induced gene expression and organelle biogenesis. ACTA ACUST UNITED AC 2008; 181:281-92. [PMID: 18426976 PMCID: PMC2315675 DOI: 10.1083/jcb.200710009] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Reversible phosphorylation is the most common posttranslational modification used in the regulation of cellular processes. This study of phosphatases and kinases required for peroxisome biogenesis is the first genome-wide analysis of phosphorylation events controlling organelle biogenesis. We evaluate signaling molecule deletion strains of the yeast Saccharomyces cerevisiae for presence of a green fluorescent protein chimera of peroxisomal thiolase, formation of peroxisomes, and peroxisome functionality. We find that distinct signaling networks involving glucose-mediated gene repression, derepression, oleate-mediated induction, and peroxisome formation promote stages of the biogenesis pathway. Additionally, separate classes of signaling proteins are responsible for the regulation of peroxisome number and size. These signaling networks specify the requirements of early and late events of peroxisome biogenesis. Among the numerous signaling proteins involved, Pho85p is exceptional, with functional involvements in both gene expression and peroxisome formation. Our study represents the first global study of signaling networks regulating the biogenesis of an organelle.
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Yan M, Rachubinski DA, Joshi S, Rachubinski RA, Subramani S. Dysferlin domain-containing proteins, Pex30p and Pex31p, localized to two compartments, control the number and size of oleate-induced peroxisomes in Pichia pastoris. Mol Biol Cell 2008; 19:885-98. [PMID: 18094040 PMCID: PMC2262989 DOI: 10.1091/mbc.e07-10-1042] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Revised: 11/26/2007] [Accepted: 12/11/2007] [Indexed: 11/11/2022] Open
Abstract
Yarrowia lipolytica Pex23p and Saccharomyces cerevisiae Pex30p, Pex31p, and Pex32p comprise a family of dysferlin domain-containing peroxins. We show that the deletion of their Pichia pastoris homologues, PEX30 and PEX31, does not affect the function or division of methanol-induced peroxisomes but results in fewer and enlarged, functional, oleate-induced peroxisomes. Synthesis of Pex30p is constitutive, whereas that of Pex31p is oleate-induced but at a much lower level relative to Pex30p. Pex30p interacts with Pex31p and is required for its stability. At steady state, both Pex30p and Pex31p exhibit a dual localization to the endoplasmic reticulum (ER) and peroxisomes. However, Pex30p is localized mostly to the ER, whereas Pex31p is predominantly on peroxisomes. Consistent with ER-to-peroxisome trafficking of these proteins, Pex30p accumulates on peroxisomes upon overexpression of Pex31p. Additionally, Pex31p colocalizes with Pex30p at the ER in pex19Delta cells and can be chased from the ER to peroxisomes in a Pex19p-dependent manner. The dysferlin domains of Pex30p and Pex31p, which are dispensable for their interaction, stability, and subcellular localization, are essential for normal peroxisome number and size. The growth environment-specific role of these peroxins, their dual localization, and the function of their dysferlin domains provide novel insights into peroxisome morphogenesis.
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Affiliation(s)
- Mingda Yan
- *Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322; and
| | | | - Saurabh Joshi
- *Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322; and
| | | | - Suresh Subramani
- *Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322; and
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Abstract
Eukaryotic cells divide their metabolic labor between functionally distinct, membrane-enveloped organelles, each precisely tailored for a specific set of biochemical reactions. Peroxisomes are ubiquitous, endoplasmic reticulum-derived organelles that perform requisite biochemical functions intimately connected to lipid metabolism. Upon cell division, cells have to strictly control peroxisome division and inheritance to maintain an appropriate number of peroxisomes in each cell. Peroxisome division follows a specific sequence of events that include peroxisome elongation, membrane constriction, and peroxisome fission. Pex11 proteins mediate the elongation step of peroxisome division, whereas dynamin-related proteins execute the final fission. The mechanisms responsible for peroxisome membrane constriction are poorly understood. Molecular players involved in peroxisome inheritance are just beginning to be elucidated. Inp1p and Inp2p are two recently identified peroxisomal proteins that perform antagonistic functions in regulating peroxisome inheritance in budding yeast. Inp1p promotes the retention of peroxisomes in mother cells and buds by attaching peroxisomes to as-yet-unidentified cortical structures. Inp2p is implicated in the motility of peroxisomes by linking them to the Myo2p motor, which then propels their movement along actin cables. The functions of Inp1p and Inp2p are cell cycle regulated and coordinated to ensure a fair distribution of peroxisomes at cytokinesis.
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Affiliation(s)
- Andrei Fagarasanu
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada.
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Chang J, Fagarasanu A, Rachubinski RA. Peroxisomal peripheral membrane protein YlInp1p is required for peroxisome inheritance and influences the dimorphic transition in the yeast Yarrowia lipolytica. Eukaryot Cell 2007; 6:1528-37. [PMID: 17644654 PMCID: PMC2043367 DOI: 10.1128/ec.00185-07] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Eukaryotic cells have evolved molecular mechanisms to ensure the faithful inheritance of organelles by daughter cells in order to maintain the benefits afforded by the compartmentalization of biochemical functions. Little is known about the inheritance of peroxisomes, organelles of lipid metabolism. We have analyzed peroxisome dynamics and inheritance in the dimorphic yeast Yarrowia lipolytica. Most peroxisomes are anchored at the periphery of cells of Y. lipolytica. In vivo video microscopy showed that at cell division, approximately half of the anchored peroxisomes in the mother cell are dislodged individually from their static positions and transported to the bud. Peroxisome motility is dependent on the actin cytoskeleton. YlInp1p is a peripheral peroxisomal membrane protein that affects the partitioning of peroxisomes between mother cell and bud in Y. lipolytica. In cells lacking YlInp1p, most peroxisomes were transferred to the bud, with only a few remaining in the mother cell, while in cells overexpressing YlInp1p, peroxisomes were preferentially retained in the mother cell, resulting in buds nearly devoid of peroxisomes. Our results are consistent with a role for YlInp1p in anchoring peroxisomes in cells. YlInp1p has a role in the dimorphic transition in Y. lipolytica, as cells lacking the YlINP1 gene more readily convert from the yeast to the mycelial form in oleic acid-containing medium, the metabolism of which requires peroxisomal activity, than does the wild-type strain. This study reports the first analysis of organelle inheritance in a true dimorphic yeast and identifies the first protein required for peroxisome inheritance in Y. lipolytica.
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Affiliation(s)
- Jinlan Chang
- Department of Cell Biology, University of Alberta, MSB 5-14, Edmonton, Alberta T6G 2H7, Canada
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