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Verhoeven N, Oshima Y, Cartier E, Neutzner A, Boyman L, Karbowski M. Outer mitochondrial membrane E3 Ub ligase MARCH5 controls mitochondrial steps in peroxisome biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555756. [PMID: 37693581 PMCID: PMC10491203 DOI: 10.1101/2023.08.31.555756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Peroxisome de novo biogenesis requires yet unidentified mitochondrial proteins. We report that the outer mitochondrial membrane (OMM)-associated E3 Ub ligase MARCH5 is vital for generating mitochondria-derived pre-peroxisomes. MARCH5 knockout results in accumulation of immature peroxisomes and lower expression of various peroxisomal proteins. Upon fatty acid-induced peroxisomal biogenesis, MARCH5 redistributes to newly formed peroxisomes; the peroxisomal biogenesis under these conditions is inhibited in MARCH5 knockout cells. MARCH5 activity-deficient mutants are stalled on peroxisomes and induce accumulation of peroxisomes containing high levels of the OMM protein Tom20 (mitochondria-derived pre-peroxisomes). Furthermore, depletion of peroxisome biogenesis factor Pex14 leads to the formation of MARCH5- and Tom20-positive peroxisomes, while no peroxisomes are detected in Pex14/MARCH5 dko cells. Reexpression of WT, but not MARCH5 mutants, restores Tom20-positive pre-peroxisomes in Pex14/MARCH5 dko cells. Thus, MARCH5 acts upstream of Pex14 in mitochondrial steps of peroxisome biogenesis. Our data validate the hybrid, mitochondria-dependent model of peroxisome biogenesis and reveal that MARCH5 is an essential mitochondrial protein in this process. Summary The authors found that mitochondrial E3 Ub ligase MARCH5 controls the formation of mitochondria-derived pre-peroxisomes. The data support the hybrid, mitochondria-dependent model of peroxisome biogenesis and reveal that MARCH5 is an essential mitochondrial protein in this process.
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Mast FD, Rachubinski RA, Aitchison JD. Peroxisome prognostications: Exploring the birth, life, and death of an organelle. J Cell Biol 2020; 219:133827. [PMID: 32211898 PMCID: PMC7054992 DOI: 10.1083/jcb.201912100] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 02/07/2023] Open
Abstract
Peroxisomes play a central role in human health and have biochemical properties that promote their use in many biotechnology settings. With a primary role in lipid metabolism, peroxisomes share a niche with lipid droplets within the endomembrane-secretory system. Notably, factors in the ER required for the biogenesis of peroxisomes also impact the formation of lipid droplets. The dynamic interface between peroxisomes and lipid droplets, and also between these organelles and the ER and mitochondria, controls their metabolic flux and their dynamics. Here, we review our understanding of peroxisome biogenesis to propose and reframe models for understanding how peroxisomes are formed in cells. To more fully understand the roles of peroxisomes and to take advantage of their many properties that may prove useful in novel therapeutics or biotechnology applications, we recast mechanisms controlling peroxisome biogenesis in a framework that integrates inference from these models with experimental data.
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Affiliation(s)
- Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA
| | | | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA.,Department of Pediatrics, University of Washington, Seattle, WA
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3
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Wróblewska JP, van der Klei IJ. Peroxisome Maintenance Depends on De Novo Peroxisome Formation in Yeast Mutants Defective in Peroxisome Fission and Inheritance. Int J Mol Sci 2019; 20:ijms20164023. [PMID: 31426544 PMCID: PMC6719073 DOI: 10.3390/ijms20164023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/13/2019] [Accepted: 08/15/2019] [Indexed: 01/15/2023] Open
Abstract
There is an ongoing debate on how peroxisomes form: by growth and fission of pre-existing peroxisomes or de novo from another membrane. It has been proposed that, in wild type yeast cells, peroxisome fission and careful segregation of the organelles over mother cells and buds is essential for organelle maintenance. Using live cell imaging we observed that cells of the yeast Hansenula polymorpha, lacking the peroxisome fission protein Pex11, still show peroxisome fission and inheritance. Also, in cells of mutants without the peroxisome inheritance protein Inp2 peroxisome segregation can still occur. In contrast, peroxisome fission and inheritance were not observed in cells of a pex11 inp2 double deletion strain. In buds of cells of this double mutant, new organelles likely appear de novo. Growth of pex11 inp2 cells on methanol, a growth substrate that requires functional peroxisomes, is retarded relative to the wild type control. Based on these observations we conclude that in H. polymorpha de novo peroxisome formation is a rescue mechanism, which is less efficient than organelle fission and inheritance to maintain functional peroxisomes.
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Affiliation(s)
- Justyna P Wróblewska
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (BBA), University of Groningen, PO Box 11103, 9300 CC Groningen, The Netherlands
| | - Ida J van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (BBA), University of Groningen, PO Box 11103, 9300 CC Groningen, The Netherlands.
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A defect in the peroxisomal biogenesis in germ cells induces a spermatogenic arrest at the round spermatid stage in mice. Sci Rep 2019; 9:9553. [PMID: 31267012 PMCID: PMC6606614 DOI: 10.1038/s41598-019-45991-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 06/18/2019] [Indexed: 12/14/2022] Open
Abstract
Peroxisomes are involved in the degradation of very long-chain fatty acids (VLCFAs) by β-oxidation. Besides neurological defects, peroxisomal dysfunction can also lead to testicular abnormalities. However, underlying alterations in the testes due to a peroxisomal defect are not well characterized yet. To maintain all metabolic functions, peroxisomes require an import machinery for the transport of matrix proteins. One component of this translocation machinery is PEX13. Its inactivation leads to a peroxisomal biogenesis defect. We have established a germ cell-specific KO of Pex13 to study the function of peroxisomes during spermatogenesis in mice. Exon 2 of floxed Pex13 was specifically excised in germ cells prior to meiosis by using a transgenic mouse strain carrying a STRA8 inducible Cre recombinase. Germ cell differentiation was interrupted at the round spermatid stage in Pex13 KO mice with formation of multinucleated giant cells (MNCs) and loss of mature spermatids. Due to a different cellular content in the germinal epithelium of Pex13 KO testes compared to control, whole testes biopsies were used for the analyses. Thus, differences in lipid composition and gene expression are only shown for whole testicular tissue but cannot be limited to single cells. Gas chromatography revealed an increase of shorter fatty acids and a decrease of n-6 docosapentaenoic acid (C22:5n-6) and n-3 docosahexaenoic acid (C22:6n-3), the main components of sperm plasma membranes. Representative genes of the metabolite transport and peroxisomal β-oxidation were strongly down-regulated. In addition, structural components of the blood-testis barrier (BTB) were altered. To conclude, defects in the peroxisomal compartment interfere with normal spermatogenesis.
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Ganguli G, Mukherjee U, Sonawane A. Peroxisomes and Oxidative Stress: Their Implications in the Modulation of Cellular Immunity During Mycobacterial Infection. Front Microbiol 2019; 10:1121. [PMID: 31258517 PMCID: PMC6587667 DOI: 10.3389/fmicb.2019.01121] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 05/03/2019] [Indexed: 12/12/2022] Open
Abstract
Host redox dependent physiological responses play crucial roles in the determination of mycobacterial infection process. Mtb explores oxygen rich lung microenvironments to initiate infection process, however, later on the bacilli adapt to oxygen depleted conditions and become non-replicative and unresponsive toward anti-TB drugs to enter in the latency stage. Mtb is equipped with various sensory mechanisms and a battery of pro- and anti-oxidant enzymes to protect themselves from the host oxidative stress mechanisms. After host cell invasion, mycobacteria induces the expression of NADPH oxidase 2 (NOX2) to generate superoxide radicals (O 2 - ), which are then converted to more toxic hydrogen peroxide (H2O2) by superoxide dismutase (SOD) and subsequently reduced to water by catalase. However, the metabolic cascades and their key regulators associated with cellular redox homeostasis are poorly understood. Phagocytosed mycobacteria en route through different subcellular organelles, where the local environment generated during infection determines the outcome of disease. For a long time, mitochondria were considered as the key player in the redox regulation, however, accumulating evidences report vital role for peroxisomes in the maintenance of cellular redox equilibrium in eukaryotic cells. Deletion of peroxisome-associated peroxin genes impaired detoxification of reactive oxygen species and peroxisome turnover post-infection, thereby leading to altered synthesis of transcription factors, various cell-signaling cascades in favor of the bacilli. This review focuses on how mycobacteria would utilize host peroxisomes to alter redox balance and metabolic regulatory mechanisms to support infection process. Here, we discuss implications of peroxisome biogenesis in the modulation of host responses against mycobacterial infection.
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Affiliation(s)
- Geetanjali Ganguli
- School of Biotechnology, KIIT (deemed to be University), Bhubaneswar, India
| | - Utsav Mukherjee
- School of Biotechnology, KIIT (deemed to be University), Bhubaneswar, India
| | - Avinash Sonawane
- School of Biotechnology, KIIT (deemed to be University), Bhubaneswar, India
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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Luo M, Zhuang X. Review: Selective degradation of peroxisome by autophagy in plants: Mechanisms, functions, and perspectives. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:485-491. [PMID: 30080638 DOI: 10.1016/j.plantsci.2018.06.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/28/2018] [Accepted: 06/29/2018] [Indexed: 06/08/2023]
Abstract
Peroxisome, a single-membrane organelle conserved in eukaryotic, is responsible for a series of oxidative reactions with its specific enzymatic components. A counterbalance between peroxisome biogenesis and degradation is crucial for the homeostasis of peroxisomes. One such degradation mechanism, termed pexophagy, is a type of selective autophagic process to deliver the excess/damaged peroxisomes into the vacuole. In plants, pexophagy is involved in the remodeling of seedlings and quality control of peroxisomes. Here, we describe the recent advance in plant pexophagy, with a focus to discuss the key regulators in plants in comparison with those in yeast and mammals, as well as future directions for pexophagy studies in plants.
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Affiliation(s)
- Mengqian Luo
- Centre for Cell & Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Xiaohong Zhuang
- Centre for Cell & Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China.
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7
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Intracellular organelles in health and kidney disease. Nephrol Ther 2018; 15:9-21. [PMID: 29887266 DOI: 10.1016/j.nephro.2018.04.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 02/01/2023]
Abstract
Subcellular organelles consist of smaller substructures called supramolecular assemblies and these in turn consist of macromolecules. Various subcellular organelles have critical functions that consist of genetic disorders of organelle biogenesis and several metabolic disturbances that occur during non-genetic diseases e.g. infection, intoxication and drug treatments. Mitochondrial damage can cause renal dysfunction as ischemic acute renal injury, chronic kidney disease progression. Moreover, mitochondrial dysfunction is an early event in aldosterone-induced podocyte injury and cardiovascular disease due to oxidative stress in chronic kidney disease. Elevated production of reactive oxygen species could be able to activate NLRP3 inflammasome representing new deregulated biological machinery and a novel therapeutic target in hemodialysis patients. Peroxisomes are actively involved in apoptosis and inflammation, innate immunity, aging and in the pathogenesis of age related diseases, such as diabetes mellitus and cancer. Peroxisomal catalase causes alterations of mitochondrial membrane proteins and stimulates generation of mitochondrial reactive oxygen species. High concentrations of hydrogen peroxide exacerbate organelles and cellular aging. The importance of proper peroxisomal function for the biosynthesis of bile acids has been firmly established. Endoplasmic reticulum stress-induced pathological diseases in kidney cause glomerular injury and tubulointerstitial injury. Furthermore, there is a link between oxidative stress and inflammations in pathological states are associated with endoplasmic reticulum stress. Proteinuria and hyperglycemia in diabetic nephropathy may induce endoplasmic reticulum stress in tubular cells of the kidney. Due to the accumulation in the proximal tubule lysosomes, impaired function of these organelles may be an important mechanism leading to proximal tubular toxicity.
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Lauersen KJ, Willamme R, Coosemans N, Joris M, Kruse O, Remacle C. Peroxisomal microbodies are at the crossroads of acetate assimilation in the green microalga Chlamydomonas reinhardtii. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.03.026] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Fan J, Li X, Issop L, Culty M, Papadopoulos V. ACBD2/ECI2-Mediated Peroxisome-Mitochondria Interactions in Leydig Cell Steroid Biosynthesis. Mol Endocrinol 2016; 30:763-82. [PMID: 27167610 DOI: 10.1210/me.2016-1008] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Fatty acid metabolism and steroid biosynthesis are 2 major pathways shared by peroxisomes and mitochondria. Both organelles are in close apposition to the endoplasmic reticulum, with which they communicate via interorganelle membrane contact sites to promote cellular signaling and the exchange of ions and lipids. To date, no convincing evidence of the direct contact between peroxisomes and mitochondria was reported in mammalian cells. Hormone-induced, tightly controlled steroid hormone biosynthesis requires interorganelle interactions. Using immunofluorescent staining and live-cell imaging, we found that dibutyryl-cAMP treatment of MA-10 mouse tumor Leydig cells rapidly induces peroxisomes to approach mitochondria and form peroxisome-mitochondrial contact sites/fusion, revealed by the subcellular distribution of the endogenous acyl-coenzyme A-binding domain (ACBD)2/ECI2 isoform A generated by alternative splicing, and further validated using a proximity ligation assay. This event occurs likely via a peroxisome-like structure, which is mediated by peroxisomal and mitochondrial matrix protein import complexes: peroxisomal import receptor peroxisomal biogenesis factor 5 (PEX5), and the mitochondrial import receptor subunit translocase of outer mitochondrial membrane 20 homolog (yeast) protein. Similar results were obtained using the mLTC-1 mouse tumor Leydig cells. Ectopic expression of the ACBD2/ECI2 isoform A in MA-10 cells led to increased basal and hormone-stimulated steroid formation, indicating that ACBD2/ECI2-mediated peroxisomes-mitochondria interactions favor in the exchange of metabolites and/or macromolecules between these 2 organelles in support of steroid biosynthesis. Considering the widespread occurrence of the ACBD2/ECI2 protein, we propose that this protein might serve as a tool to assist in understanding the contact between peroxisomes and mitochondria.
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Affiliation(s)
- Jinjiang Fan
- The Research Institute of the McGill University Health Centre (J.F., X.L., L.I., M.C., V.P.) and Departments of Medicine (J.F., L.I., M.C., V.P.), Biochemistry (X.L., V.P.), and Pharmacology and Therapeutics (M.C., V.P.), McGill University, Montréal, Québec, Canada H4A 3J1
| | - Xinlu Li
- The Research Institute of the McGill University Health Centre (J.F., X.L., L.I., M.C., V.P.) and Departments of Medicine (J.F., L.I., M.C., V.P.), Biochemistry (X.L., V.P.), and Pharmacology and Therapeutics (M.C., V.P.), McGill University, Montréal, Québec, Canada H4A 3J1
| | - Leeyah Issop
- The Research Institute of the McGill University Health Centre (J.F., X.L., L.I., M.C., V.P.) and Departments of Medicine (J.F., L.I., M.C., V.P.), Biochemistry (X.L., V.P.), and Pharmacology and Therapeutics (M.C., V.P.), McGill University, Montréal, Québec, Canada H4A 3J1
| | - Martine Culty
- The Research Institute of the McGill University Health Centre (J.F., X.L., L.I., M.C., V.P.) and Departments of Medicine (J.F., L.I., M.C., V.P.), Biochemistry (X.L., V.P.), and Pharmacology and Therapeutics (M.C., V.P.), McGill University, Montréal, Québec, Canada H4A 3J1
| | - Vassilios Papadopoulos
- The Research Institute of the McGill University Health Centre (J.F., X.L., L.I., M.C., V.P.) and Departments of Medicine (J.F., L.I., M.C., V.P.), Biochemistry (X.L., V.P.), and Pharmacology and Therapeutics (M.C., V.P.), McGill University, Montréal, Québec, Canada H4A 3J1
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Rehan VK, Torday JS. The lung alveolar lipofibroblast: an evolutionary strategy against neonatal hyperoxic lung injury. Antioxid Redox Signal 2014; 21:1893-904. [PMID: 24386954 PMCID: PMC4202930 DOI: 10.1089/ars.2013.5793] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 01/05/2014] [Indexed: 01/28/2023]
Abstract
SIGNIFICANCE Oxygen, the main mode of support for premature infants with immature lungs, can cause toxicity by producing reactive oxygen species (ROS) that disrupt homeostasis; yet, these same molecules were entrained to promote vertebrate lung phylogeny. By providing a deeper understanding of this paradox, we propose physiologically rational strategies to prevent chronic lung disease (CLD) of prematurity. RECENT ADVANCES To prevent neonatal hyperoxic lung damage biologically, we have exploited the alveolar defense mechanism(s) that evolutionarily evolved to combat increased atmospheric oxygen during the vertebrate water to land transition. CRITICAL ISSUES Over the course of vertebrate lung evolution, ROS promoted the formation of lipofibroblasts, specialized adepithelial cells, which protect the alveoli against oxidant injury; peroxisome proliferator-activated receptor gamma (PPARγ), the master switch for lipofibroblast differentiation, prevents such oxidant lung injury, both by directly promoting mesodermal differentiation and its antioxidant defenses, and indirectly by stimulating the developmental epithelial-mesenchymal paracrine interactions that have physiologically determined lung surfactant production in accord with the lung's phylogenetic adaptation to atmospheric oxygen, preventing Respiratory Distress Syndrome at birth. FUTURE DIRECTIONS The molecular strategy (PPARγ agonists) to prevent CLD of prematurity, proposed by us, although seems to be robust, effective, and safe under experimental conditions, it awaits detailed pharmacokinetic and pharmacodynamic studies for its safe and effective clinical translation to human infants. Antioxid. Redox Signal. 21, 1893-1904. "I have procured air [oxygen]…between five and six times as good as the best common air that I have ever met with." -Joseph Priestley, 1775.
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Affiliation(s)
- Virender K Rehan
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center , Torrance, California
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Reunov AV. Plant peroxisomes: The role in metabolism of reactive oxygen species and the processes they mediate. ACTA ACUST UNITED AC 2014. [DOI: 10.1134/s2079086414040082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Rochon D, Singh B, Reade R, Theilmann J, Ghoshal K, Alam SB, Maghodia A. The p33 auxiliary replicase protein of Cucumber necrosis virus targets peroxisomes and infection induces de novo peroxisome formation from the endoplasmic reticulum. Virology 2014; 452-453:133-42. [PMID: 24606690 DOI: 10.1016/j.virol.2013.12.035] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 12/23/2013] [Accepted: 12/24/2013] [Indexed: 11/17/2022]
Abstract
Tombusviruses replicate on pre-existing organelles such as peroxisomes or mitochondria, the membranes of which become extensively reorganized into multivesicular bodies (MVBs) during the infection process. Cucumber necrosis virus (CNV) has previously been shown to replicate in association with peroxisomes in yeast. We show that CNV induces MVBs from peroxisomes in infected plants and that GFP-tagged p33 auxiliary replicase protein colocalizes with YFP(SKL), a peroxisomal marker. Most remarkably, the ER of CNV infected Nicotiana benthamiana 16C plants undergoes a dramatic reorganization producing numerous new peroxisome-like structures that associate with CNV p33, thus likely serving as a new site for viral RNA replication. We also show that plants agroinfiltrated with p33 develop CNV-like necrotic symptoms which are associated with increased levels of peroxide. Since peroxisomes are a site for peroxide catabolism, and peroxide is known to induce plant defense responses, we suggest that dysfunctional peroxisomes contribute to CNV induced necrosis.
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Affiliation(s)
- D'Ann Rochon
- Agriculture and Agri-Food Canada Pacific Agri-Food Research Centre, 4200 Hwy 97, Summerland, BC, Canada V0H 1Z0; University of British Columbia Faculty of Land and Food Systems Vancouver, BC, Canada V6T 1Z4.
| | - Bhavana Singh
- University of British Columbia Faculty of Land and Food Systems Vancouver, BC, Canada V6T 1Z4
| | - Ron Reade
- Agriculture and Agri-Food Canada Pacific Agri-Food Research Centre, 4200 Hwy 97, Summerland, BC, Canada V0H 1Z0
| | - Jane Theilmann
- Agriculture and Agri-Food Canada Pacific Agri-Food Research Centre, 4200 Hwy 97, Summerland, BC, Canada V0H 1Z0
| | - Kankana Ghoshal
- University of British Columbia Faculty of Land and Food Systems Vancouver, BC, Canada V6T 1Z4
| | - Syed Benazir Alam
- University of British Columbia Faculty of Land and Food Systems Vancouver, BC, Canada V6T 1Z4
| | - Ajay Maghodia
- Agriculture and Agri-Food Canada Pacific Agri-Food Research Centre, 4200 Hwy 97, Summerland, BC, Canada V0H 1Z0; University of British Columbia Faculty of Land and Food Systems Vancouver, BC, Canada V6T 1Z4
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Contreras MA, Alzate O, Singh AK, Singh I. PPARα activation induces N(ε)-Lys-acetylation of rat liver peroxisomal multifunctional enzyme type 1. Lipids 2013; 49:119-31. [PMID: 24092543 DOI: 10.1007/s11745-013-3843-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/09/2013] [Indexed: 11/28/2022]
Abstract
Peroxisomes are ubiquitous subcellular organelles that participate in metabolic and disease processes, with few of its proteins undergoing posttranslational modifications. As the role of lysine-acetylation has expanded into the cellular intermediary metabolism, we used a combination of differential centrifugation, organelle isolation by linear density gradient centrifugation, western blot analysis, and peptide fingerprinting and amino acid sequencing by mass spectrometry to investigate protein acetylation in control and ciprofibrate-treated rat liver peroxisomes. Organelle protein samples isolated by density gradient centrifugation from PPARα-agonist treated rat liver screened with an anti-N(ε)-acetyl lysine antibody revealed a single protein band of 75 kDa. Immunoprecipitation with this antibody resulted in the precipitation of a protein from the protein pool of ciprofibrate-induced peroxisomes, but not from the protein pool of non-induced peroxisomes. Peptide mass fingerprinting analysis identified the protein as the peroxisomal multifunctional enzyme type 1. In addition, mass spectrometry-based amino acid sequencing resulted in the identification of unique peptides containing 4 acetylated-Lys residues (K¹⁵⁵, K¹⁷³, K¹⁹⁰, and K⁵⁸³). This is the first report that demonstrates posttranslational acetylation of a peroxisomal enzyme in PPARα-dependent proliferation of peroxisomes in rat liver.
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Affiliation(s)
- Miguel A Contreras
- Department of Pediatrics, The Darby Children's Research Institute, Medical University of South Carolina, Charleston, SC, 29425, USA,
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Kim PK, Mullen RT. PEX16: a multifaceted regulator of peroxisome biogenesis. Front Physiol 2013; 4:241. [PMID: 24027535 PMCID: PMC3759792 DOI: 10.3389/fphys.2013.00241] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 08/14/2013] [Indexed: 11/16/2022] Open
Abstract
Peroxisomes are formed by two distinct pathways: the growth and fission of mature peroxisomes and de novo synthesis at the endoplasmic reticulum (ER). While many of the molecular mechanisms underlying these two pathways remain to be elucidated, it is generally accepted that their relative contribution to peroxisome formation may vary depending on the species, cell type and/or physiological status of the organism. One pertinent example of the apparent differences in the regulation of peroxisome biogenesis among evolutionarily diverse species is the involvement of the peroxin PEX16. In Yarrowia lipolytica, for instance, PEX16 is an intraperoxisomal peripheral membrane protein that participates in peroxisomal fission. By contrast, Human PEX16 is an integral membrane protein that is thought to function at the ER during the early stages of de novo peroxisome formation and also recruits peroxisomal membrane proteins directly to mature peroxisomes. Similarly, PEX16 in the plant Arabidopsis thaliana is speculated to be a PMP receptor at the ER and peroxisomes, and is also required for the formation of other ER-derived organelles, such as oil and protein bodies. Here we briefly review the current knowledge of Y. lipolytica, human and A. thaliana PEX16 in the context of our overall understanding of peroxisome biogenesis and the role of the ER in this process in these three divergent species.
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Affiliation(s)
- Peter K Kim
- Cell Biology Program, Department of Biochemistry, Hospital for Sick Children, University of Toronto Toronto, ON, Canada ; Department of Biochemistry, University of Toronto Toronto, ON, Canada
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Barton K, Mathur N, Mathur J. Simultaneous live-imaging of peroxisomes and the ER in plant cells suggests contiguity but no luminal continuity between the two organelles. Front Physiol 2013; 4:196. [PMID: 23898304 PMCID: PMC3721060 DOI: 10.3389/fphys.2013.00196] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/08/2013] [Indexed: 11/13/2022] Open
Abstract
Transmission electron micrographs of peroxisomes in diverse organisms, including plants, suggest their close association and even luminal connectivity with the endoplasmic reticulum (ER). After several decades of debate de novo peroxisome biogenesis from the ER is strongly favored in yeasts and mammals. Unfortunately many of the proteins whose transit through the ER constitutes a major evidence for peroxisome biogenesis from the ER do not exhibit a similar localization in plants. Consequently, at best the ER acts as a membrane source for peroxisome in plants. However, in addition to their de novo biogenesis from the ER an increase in peroxisome numbers also occurs through fission of existing peroxisomes. In recent years live-imaging has been used to visualize peroxisomes and the ER but the precise spatio-temporal relationship between the two organelles has not been well-explored. Here we present our assessment of the peroxisome-ER relationship through imaging of living Arabidopsis thaliana plants simultaneously expressing different color combinations of fluorescent proteins targeted to both organelles. Our observations on double transgenic wild type and a drp3a/apm1 mutant Arabidopsis plants suggest strong correlations between the dynamic behavior of peroxisomes and the neighboring ER. Although peroxisomes and ER are closely aligned there appears to be no luminal continuity between the two. Similarly, differentially colored elongated peroxisomes of a drp3a mutant expressing a photoconvertible peroxisomal matrix protein are unable to fuse and share luminal protein despite considerable intermingling. Substantiation of our observations is suggested through 3D iso-surface rendering of image stacks, which shows closed ended peroxisomes enmeshed among ER tubules possibly through membrane contact sites (MCS). Our observations support the idea that increase in peroxisome numbers in a plant cell occurs mainly through the fission of existing peroxisomes in an ER aided manner.
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Affiliation(s)
- Kiah Barton
- Laboratory of Plant Development and Interactions, Department of Molecular and Cellular Biology, University of Guelph Guelph, ON, Canada
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Weis BL, Schleiff E, Zerges W. Protein targeting to subcellular organelles via MRNA localization. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:260-73. [PMID: 23457718 DOI: 10.1016/j.bbamcr.2012.04.004] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cells have complex membranous organelles for the compartmentalization and the regulation of most intracellular processes. Organelle biogenesis and maintenance requires newly synthesized proteins, each of which needs to go from the ribosome translating its mRNA to the correct membrane for insertion or transclocation to an a organellar subcompartment. Decades of research have revealed how proteins are targeted to the correct organelle and translocated across one or more organelle membranes ro the compartment where they function. The paradigm examples involve interactions between a peptide sequence in the protein, localization factors, and various membrane embedded translocation machineries. Membrane translocation is either cotranslational or posttranslational depending on the protein and target organelle. Meanwhile research in embryos, neurons and yeast revealed an alternative targeting mechanism in which the mRNA is localized and only then translated to synthesize the protein in the correct location. In these cases, the targeting information is coded by the cis-acting sequences in the mRNA ("Zipcodes") that interact with localization factors and, in many cases, are transported by the molecular motors on the cytoskeletal filaments. Recently, evidence has been found for this "mRNA based" mechanism in organelle protein targeting to endoplasmic reticulum, mitochondria, and the photosynthetic membranes within chloroplasts. Here we review known and potential roles of mRNA localization in protein targeting to and within organelles. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
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Affiliation(s)
- Benjamin L Weis
- Goether University, Cluster of Excellence Macromolecular Complexes, Institute for Molecular Biosciences, Max-von-Laue Str. 9, D-60438 Frankfort, Germany
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Abstract
Inborn errors of metabolism may impact on muscle and peripheral nerve. Abnormalities involve mitochondria and other subcellular organelles such as peroxisomes and lysosomes related to the turnover and recycling of cellular compartments. Treatable causes are β-oxidation defects producing progressive neuropathy; pyruvate dehydrogenase deficiency, porphyria, or vitamin B12 deficiency causing recurrent episodes of neuropathy or acute motor deficit mimicking Guillain-Barré syndrome. On the other hand, lysosomal (mucopolysaccharidosis, Gaucher and Fabry diseases), mitochondriopathic (mitochondrial or nuclear mutations or mDNA depletion), peroxisomal (adrenomyeloneuropathy, Refsum disease, sterol carrier protein-2 deficiency, cerebrotendinous xanthomatosis, α-methylacyl racemase deficiency) diseases are multisystemic disorders involving also the heart, liver, brain, retina, and kidney. Pathophysiology of most metabolic myopathies is related to the impairment of energy production or to abnormal production of reactive oxygen species (ROS). Main symptoms are exercise intolerance with myalgias, cramps and recurrent myoglobinuria or limb weakness associated with elevation of serum creatine kinase. Carnitine palmitoyl transferase deficiency, followed by acid maltase deficiency, and lipin deficiency, are the most common cause of isolated rhabdomyolysis. Metabolic myopathies are frequently associated to extra-neuromuscular disorders particularly involving the heart, liver, brain, retina, skin, and kidney.
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Affiliation(s)
- Adele D'Amico
- Molecular Medicine and Unit of Neuromuscular and Neurodegenerative Diseases, IRCCS-Children's Hospital Bambino Gesù, Rome, Italy
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18
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Dietrich MO, Horvath TL. Limitations in anti-obesity drug development: the critical role of hunger-promoting neurons. Nat Rev Drug Discov 2012; 11:675-91. [DOI: 10.1038/nrd3739] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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From networks of protein interactions to networks of functional dependencies. BMC SYSTEMS BIOLOGY 2012; 6:44. [PMID: 22607727 PMCID: PMC3434018 DOI: 10.1186/1752-0509-6-44] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 05/20/2012] [Indexed: 11/23/2022]
Abstract
Background As protein-protein interactions connect proteins that participate in either the same or different functions, networks of interacting and functionally annotated proteins can be converted into process graphs of inter-dependent function nodes (each node corresponding to interacting proteins with the same functional annotation). However, as proteins have multiple annotations, the process graph is non-redundant, if only proteins participating directly in a given function are included in the related function node. Results Reasoning that topological features (e.g., clusters of highly inter-connected proteins) might help approaching structured and non-redundant understanding of molecular function, an algorithm was developed that prioritizes inclusion of proteins into the function nodes that best overlap protein clusters. Specifically, the algorithm identifies function nodes (and their mutual relations), based on the topological analysis of a protein interaction network, which can be related to various biological domains, such as cellular components (e.g., peroxisome and cellular bud) or biological processes (e.g., cell budding) of the model organism S. cerevisiae. Conclusions The method we have described allows converting a protein interaction network into a non-redundant process graph of inter-dependent function nodes. The examples we have described show that the resulting graph allows researchers to formulate testable hypotheses about dependencies among functions and the underlying mechanisms.
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Kanzawa N, Shimozawa N, Wanders RJA, Ikeda K, Murakami Y, Waterham HR, Mukai S, Fujita M, Maeda Y, Taguchi R, Fujiki Y, Kinoshita T. Defective lipid remodeling of GPI anchors in peroxisomal disorders, Zellweger syndrome, and rhizomelic chondrodysplasia punctata. J Lipid Res 2012; 53:653-63. [PMID: 22253471 DOI: 10.1194/jlr.m021204] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Many cell surface proteins in mammalian cells are anchored to the plasma membrane via glycosylphosphatidylinositol (GPI). The predominant form of mammalian GPI contains 1-alkyl-2-acyl phosphatidylinositol (PI), which is generated by lipid remodeling from diacyl PI. The conversion of diacyl PI to 1-alkyl-2-acyl PI occurs in the ER at the third intermediate in the GPI biosynthetic pathway. This lipid remodeling requires the alkyl-phospholipid biosynthetic pathway in peroxisome. Indeed, cells defective in dihydroxyacetone phosphate acyltransferase (DHAP-AT) or alkyl-DHAP synthase express only the diacyl form of GPI-anchored proteins. A defect in the alkyl-phospholipid biosynthetic pathway causes a peroxisomal disorder, rhizomelic chondrodysplasia punctata (RCDP), and defective biogenesis of peroxisomes causes Zellweger syndrome, both of which are lethal genetic diseases with multiple clinical phenotypes such as psychomotor defects, mental retardation, and skeletal abnormalities. Here, we report that GPI lipid remodeling is defective in cells from patients with Zellweger syndrome having mutations in the peroxisomal biogenesis factors PEX5, PEX16, and PEX19 and in cells from patients with RCDP types 1, 2, and 3 caused by mutations in PEX7, DHAP-AT, and alkyl-DHAP synthase, respectively. Absence of the 1-alkyl-2-acyl form of GPI-anchored proteins might account for some of the complex phenotypes of these two major peroxisomal disorders.
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Affiliation(s)
- Noriyuki Kanzawa
- Department of Immunoregulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
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21
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Borgne FL, Demarquoy J. Interaction between peroxisomes and mitochondria in fatty acid metabolism. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ojmip.2012.21005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Aung K, Hu J. The Arabidopsis tail-anchored protein PEROXISOMAL AND MITOCHONDRIAL DIVISION FACTOR1 is involved in the morphogenesis and proliferation of peroxisomes and mitochondria. THE PLANT CELL 2011; 23:4446-61. [PMID: 22147290 PMCID: PMC3269876 DOI: 10.1105/tpc.111.090142] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 10/20/2011] [Accepted: 11/18/2011] [Indexed: 05/19/2023]
Abstract
Peroxisomes and mitochondria are multifunctional eukaryotic organelles that are not only interconnected metabolically but also share proteins in division. Two evolutionarily conserved division factors, dynamin-related protein (DRP) and its organelle anchor FISSION1 (FIS1), mediate the fission of both peroxisomes and mitochondria. Here, we identified and characterized a plant-specific protein shared by these two types of organelles. The Arabidopsis thaliana PEROXISOMAL and MITOCHONDRIAL DIVISION FACTOR1 (PMD1) is a coiled-coil protein tethered to the membranes of peroxisomes and mitochondria by its C terminus. Null mutants of PMD1 contain enlarged peroxisomes and elongated mitochondria, and plants overexpressing PMD1 have an increased number of these organelles that are smaller in size and often aggregated. PMD1 lacks physical interaction with the known division proteins DRP3 and FIS1; it is also not required for DRP3's organelle targeting. Affinity purifications pulled down PMD1's homolog, PMD2, which exclusively targets to mitochondria and plays a specific role in mitochondrial morphogenesis. PMD1 and PMD2 can form homo- and heterocomplexes. Organelle targeting signals reside in the C termini of these proteins. Our results suggest that PMD1 facilitates peroxisomal and mitochondrial proliferation in a FIS1/DRP3-independent manner and that the homologous proteins PMD1 and PMD2 perform nonredundant functions in organelle morphogenesis.
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Affiliation(s)
- Kyaw Aung
- Michigan State University–Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Jianping Hu
- Michigan State University–Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
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Nakayama M, Sato H, Okuda T, Fujisawa N, Kono N, Arai H, Suzuki E, Umeda M, Ishikawa HO, Matsuno K. Drosophila carrying pex3 or pex16 mutations are models of Zellweger syndrome that reflect its symptoms associated with the absence of peroxisomes. PLoS One 2011; 6:e22984. [PMID: 21826223 PMCID: PMC3149631 DOI: 10.1371/journal.pone.0022984] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 07/10/2011] [Indexed: 11/19/2022] Open
Abstract
The peroxisome biogenesis disorders (PBDs) are currently difficult-to-treat multiple-organ dysfunction disorders that result from the defective biogenesis of peroxisomes. Genes encoding Peroxins, which are required for peroxisome biogenesis or functions, are known causative genes of PBDs. The human peroxin genes PEX3 or PEX16 are required for peroxisomal membrane protein targeting, and their mutations cause Zellweger syndrome, a class of PBDs. Lack of understanding about the pathogenesis of Zellweger syndrome has hindered the development of effective treatments. Here, we developed potential Drosophila models for Zellweger syndrome, in which the Drosophila pex3 or pex16 gene was disrupted. As found in Zellweger syndrome patients, peroxisomes were not observed in the homozygous Drosophila pex3 mutant, which was larval lethal. However, the pex16 homozygote lacking its maternal contribution was viable and still maintained a small number of peroxisome-like granules, even though PEX16 is essential for the biosynthesis of peroxisomes in humans. These results suggest that the requirements for pex3 and pex16 in peroxisome biosynthesis in Drosophila are different, and the role of PEX16 orthologs may have diverged between mammals and Drosophila. The phenotypes of our Zellweger syndrome model flies, such as larval lethality in pex3, and reduced size, shortened longevity, locomotion defects, and abnormal lipid metabolisms in pex16, were reminiscent of symptoms of this disorder, although the Drosophila pex16 mutant does not recapitulate the infant death of Zellweger syndrome. Furthermore, pex16 mutants showed male-specific sterility that resulted from the arrest of spermatocyte maturation. pex16 expressed in somatic cyst cells but not germline cells had an essential role in the maturation of male germline cells, suggesting that peroxisome-dependent signals in somatic cyst cells could contribute to the progression of male germ-cell maturation. These potential Drosophila models for Zellweger syndrome should contribute to our understanding of its pathology.
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Affiliation(s)
- Minoru Nakayama
- Genome and Drug Research Center, Tokyo University of Science, Noda, Chiba, Japan
- Department of Biological Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
- Research Institute for Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Hiroyasu Sato
- Department of Biological Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Takayuki Okuda
- Department of Biological Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Nao Fujisawa
- Department of Biological Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Nozomu Kono
- Graduate School of Pharmaceutical Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Hiroyuki Arai
- Graduate School of Pharmaceutical Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Emiko Suzuki
- Structural Biology Center, National Institute of Genetics, and Department of Genetics, The Graduate University for Advanced Studies, Mishima, Shizuoka, Japan
| | - Masato Umeda
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Hiroyuki O. Ishikawa
- Genome and Drug Research Center, Tokyo University of Science, Noda, Chiba, Japan
| | - Kenji Matsuno
- Genome and Drug Research Center, Tokyo University of Science, Noda, Chiba, Japan
- Department of Biological Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
- Research Institute for Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
- * E-mail:
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Cell-free sorting of peroxisomal membrane proteins from the endoplasmic reticulum. Proc Natl Acad Sci U S A 2011; 108:9113-8. [PMID: 21576455 DOI: 10.1073/pnas.1018749108] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Several yeast and mammalian peroxisomal membrane proteins (PMPs) are delivered to peroxisomes via the endoplasmic reticulum (ER). Fluorescence microscopy showed a focused assembly of PMPs in a specialized domain of the ER, referred to as the preperoxisomal ER. It is proposed that preperoxisomal vesicles containing PMPs bud from this domain to either fuse with preexisting peroxisomes or to mature into functional peroxisomes by uptake of peroxisomal membrane and matrix proteins. However, such vesicular entities are not identified nor are the biochemical requirements for the budding process known. We developed an in vitro cell-free ER-budding assay using Pichia pastoris and followed two endogenous PMPs, Pex11p and Pex3p during their ER exit. Both the PMPs were copackaged in the ER-budded vesicles that float on a Nycodenz gradient. PMP budding from the ER was dependent on ATP, temperature, cytosol, and Pex19p and generated preperoxisomal vesicles with an incomplete complement of PMPs. Surprisingly, Pex11p budding was independent of Pex3p; however, the budded vesicles were devoid of most of the PMPs otherwise present in the wild-type vesicles and might represent peroxisomal remnants. Our findings provide a biochemical platform to uncover the mechanism of PMP budding from the ER.
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25
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Molecular mechanisms of organelle inheritance: lessons from peroxisomes in yeast. Nat Rev Mol Cell Biol 2010; 11:644-54. [PMID: 20717147 DOI: 10.1038/nrm2960] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Preserving a functional set of cytoplasmic organelles in a eukaryotic cell requires a process of accurate organelle inheritance at cell division. Studies of peroxisome inheritance in yeast have revealed that polarized transport of a subset of peroxisomes to the emergent daughter cell is balanced by retention mechanisms operating in both mother cell and bud to achieve an equitable distribution of peroxisomes between them. It is becoming apparent that some common mechanistic principles apply to the inheritance of all organelles, but at the same time, inheritance factors specific for each organelle type allow the cell to differentially and specifically control the inheritance of its different organelle populations.
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Ishizaki H, Spitzer M, Wildenhain J, Anastasaki C, Zeng Z, Dolma S, Shaw M, Madsen E, Gitlin J, Marais R, Tyers M, Patton EE. Combined zebrafish-yeast chemical-genetic screens reveal gene-copper-nutrition interactions that modulate melanocyte pigmentation. Dis Model Mech 2010; 3:639-51. [PMID: 20713646 DOI: 10.1242/dmm.005769] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Hypopigmentation is a feature of copper deficiency in humans, as caused by mutation of the copper (Cu(2+)) transporter ATP7A in Menkes disease, or an inability to absorb copper after gastric surgery. However, many causes of copper deficiency are unknown, and genetic polymorphisms might underlie sensitivity to suboptimal environmental copper conditions. Here, we combined phenotypic screens in zebrafish for compounds that affect copper metabolism with yeast chemical-genetic profiles to identify pathways that are sensitive to copper depletion. Yeast chemical-genetic interactions revealed that defects in intracellular trafficking pathways cause sensitivity to low-copper conditions; partial knockdown of the analogous Ap3s1 and Ap1s1 trafficking components in zebrafish sensitized developing melanocytes to hypopigmentation in low-copper environmental conditions. Because trafficking pathways are essential for copper loading into cuproproteins, our results suggest that hypomorphic alleles of trafficking components might underlie sensitivity to reduced-copper nutrient conditions. In addition, we used zebrafish-yeast screening to identify a novel target pathway in copper metabolism for the small-molecule MEK kinase inhibitor U0126. The zebrafish-yeast screening method combines the power of zebrafish as a disease model with facile genome-scale identification of chemical-genetic interactions in yeast to enable the discovery and dissection of complex multigenic interactions in disease-gene networks.
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Affiliation(s)
- Hironori Ishizaki
- Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit and The University of Edinburgh, Western General Hospital, Edinburgh, UK
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Coca M, San Segundo B. AtCPK1 calcium-dependent protein kinase mediates pathogen resistance in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 63:526-40. [PMID: 20497373 DOI: 10.1111/j.1365-313x.2010.04255.x] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In mammals, lipid bodies play a key role during pathological and infectious diseases. However, our knowledge on the function of plant lipid bodies, apart from their role as the major site of lipid storage in seed tissues, remains limited. Here, we provide evidence that a calcium-dependent protein kinase (CPK) mediates pathogen resistance in Arabidopsis. AtCPK1 expression is rapidly induced by fungal elicitors. Loss-of-function mutants of AtCPK1 exhibit higher susceptibility to pathogen infection compared to wild-type plants. Conversely, over-expression of AtCPK1 leads to accumulation of salicylic acid (SA) and constitutive expression of SA-regulated defence and disease resistance genes, which, in turn, results in broad-spectrum protection against pathogen infection. Expression studies in mutants affected in SA-mediated defence responses revealed an interlocked feedback loop governing AtCPK1 expression and components of the SA-dependent signalling pathway. Moreover, we demonstrate the dual localization of AtCPK1 in lipid bodies and peroxisomes. Overall, our findings identify AtCPK1 as a component of the innate immune system of Arabidopsis plants.
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Affiliation(s)
- María Coca
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB, Jordi Girona 18, 08034 Barcelona, Spain
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28
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Zhang X, Hu J. The Arabidopsis chloroplast division protein DYNAMIN-RELATED PROTEIN5B also mediates peroxisome division. THE PLANT CELL 2010; 22:431-42. [PMID: 20179140 PMCID: PMC2845408 DOI: 10.1105/tpc.109.071324] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2009] [Revised: 01/26/2010] [Accepted: 02/03/2010] [Indexed: 05/17/2023]
Abstract
Peroxisomes are highly dynamic organelles involved in various metabolic pathways. The division of peroxisomes is regulated by factors such as the PEROXIN11 (PEX11) proteins that promote peroxisome elongation and the dynamin-related proteins (DRPs) and FISSION1 (FIS1) proteins that function together to mediate organelle fission. In Arabidopsis thaliana, DRP3A/DRP3B and FIS1A (BIGYIN)/FIS1B are two pairs of homologous proteins known to function in both peroxisomal and mitochondrial division. Here, we report that DRP5B, a DRP distantly related to the DRP3s and originally identified as a chloroplast division protein, also contributes to peroxisome division. DRP5B localizes to both peroxisomes and chloroplasts. Mutations in the DRP5B gene lead to peroxisome division defects and compromised peroxisome functions. Using coimmunoprecipitation and bimolecular fluorescence complementation assays, we further demonstrate that DRP5B can interact or form a complex with itself and with DRP3A, DRP3B, FIS1A, and most of the Arabidopsis PEX11 isoforms. Our data suggest that, in contrast with DRP3A and DRP3B, whose orthologs exist across plant, fungal, and animal kingdoms, DRP5B is a plant/algal invention to facilitate the division of their organelles (i.e., chloroplasts and peroxisomes). In addition, our results support the notion that proteins involved in the early (elongation) and late (fission) stages of peroxisome division may act cooperatively.
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Affiliation(s)
- Xinchun Zhang
- Michigan State University–Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Jianping Hu
- Michigan State University–Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
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29
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Baluska F. Cell-cell channels, viruses, and evolution: via infection, parasitism, and symbiosis toward higher levels of biological complexity. Ann N Y Acad Sci 2009; 1178:106-19. [PMID: 19845631 DOI: 10.1111/j.1749-6632.2009.04995.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Between prokaryotic cells and eukaryotic cells there is dramatic difference in complexity which represents a problem for the current version of the cell theory, as well as for the current version of evolution theory. In the past few decades, the serial endosymbiotic theory of Lynn Margulis has been confirmed. This results in a radical departure from our understanding of living systems: the eukaryotic cell represents de facto"cells-within-cell." Higher order "cells-within-cell" situations are obvious at the eukaryotic cell level in the form of secondary and tertiary endosymbiosis, or in the male and female gametophytes of higher plants. The next challenge of the current version of the cell theory is represented by the fact that the multicellular fungi and plants are, in fact, supracellular assemblies as their cells are not physically separated from each other. Moreover, there are also examples of alliances and mergings between multicellular organisms. Infection, especially the viral one, but also bacterial and fungal infections, followed by symbiosis, is proposed to act as the major force that drives the biological evolution toward higher complexity.
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30
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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] [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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Toro AA, Araya CA, Córdova GJ, Arredondo CA, Cárdenas HG, Moreno RE, Venegas A, Koenig CS, Cancino J, Gonzalez A, Santos MJ. Pex3p-dependent peroxisomal biogenesis initiates in the endoplasmic reticulum of human fibroblasts. J Cell Biochem 2009; 107:1083-96. [PMID: 19479899 DOI: 10.1002/jcb.22210] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The mechanisms of peroxisomal biogenesis remain incompletely understood, specially regarding the role of the endoplasmic reticulum (ER) in human cells, where genetic disorders of peroxisome biogenesis lead to Zellweger syndrome (ZS). The Pex3p peroxisomal membrane protein (PMP) required for early steps of peroxisome biogenesis has been detected in the ER in yeast but not in mammalian cells. Here, we show that Pex3p-GFP expressed in a new ZS cell line (MR), which lacks peroxisomes due to a mutation in the PEX3 gene, localizes first in the ER and subsequently in newly formed peroxisomes. Pex3p bearing an artificial N-glycosylation site shows an electrophoretic shift indicative of ER targeting while en route to preformed peroxisomes in normal fibroblast. A signal peptide that forces its entry into the ER does not eliminate its capability to drive peroxisome biogenesis in ZS cells. Thus, Pex3p is able to drive peroxisome biogenesis from the ER and its ER pathway is not privative of ZS cells. Cross-expression experiments of Pex3p in GM623 cells lacking Pex16p or Pex16p in MR cells lacking Pex3p, showed evidence that Pex3p requires Pex16p for ER location but is dispensable for the ER location of Pex16p. These results indicate that Pex3p follows the ER-to-peroxisomal route in mammalian cells and provides new clues to understand its function.
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Affiliation(s)
- Andrés A Toro
- Departamento de Biología Celular y Molecular, Centro de Regulación Celular y Patología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, and MIFAB, Chile
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Kamigaki A, Kondo M, Mano S, Hayashi M, Nishimura M. Suppression of peroxisome biogenesis factor 10 reduces cuticular wax accumulation by disrupting the ER network in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2009; 50:2034-46. [PMID: 19892830 DOI: 10.1093/pcp/pcp152] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Peroxisome biogenesis factor 10 (PEX10) is a component of the peroxisomal matrix protein import machinery. To analyze the physiological function of PEX10, we used transgenic AtPEX10i Arabidopsis plants that had suppressed expression of the PEX10 gene due to RNA interference. AtPEX10i plants had patches of paleness on leaves, and abnormal floral organs that were typical of cuticular wax-deficient mutants. Quantitative analysis of cuticular wax revealed that the amount of wax in AtPEX10i plants was indeed lower than that in control plants. This result was confirmed by toluidine blue staining and scanning electron microscopic analysis of AtPEX10i. The CER1, CER4, WAX2 and SHN1 genes are known to be responsible for wax biosynthesis in Arabidopsis. Of these, CER1, CER4 and WAX2 were found to be localized on the endoplasmic reticulum (ER). In AtPEX10i plants, the expression of these genes was down-regulated, and CER1, CER4 and WAX2 were mislocalized to the cytosol. We also found that AtPEX10i plants had defects in ER morphology. Based on these results, we propose that PEX10 is essential for the maintenance of ER morphology and for the expression of CER1, CER4, WAX2 and SHN1 genes, which contribute to the biosynthesis of cuticular wax.
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Affiliation(s)
- Akane Kamigaki
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, 444-8585, Japan
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Abstract
The ER (endoplasmic reticulum) in higher plants forms a pleomorphic web of membrane tubules and small cisternae that pervade the cytoplasm, but in particular form a polygonal network at the cortex of the cell which may be anchored to the plasma membrane. The network is associated with the actin cytoskeleton and demonstrates extensive mobility, which is most likely to be dependent on myosin motors. The ER is characterized by a number of domains which may be associated with specific functions such as protein storage, or with direct interaction with other organelles such as the Golgi apparatus, peroxisomes and plastids. In the present review we discuss the nature of the network, the role of shape-forming molecules such as the recently described reticulon family of proteins and the function of some of the major domains within the ER network.
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Abstract
With every cell division, peroxisomes duplicate and are segregated between progeny cells. Here, we discuss the different modes of peroxisome multiplication and the machinery that is involved in each case. Peroxisomes have been considered by many to be peripheral to mainstream cell biology. However, this is changing in response to the recent finding that peroxisomes obtain membrane constituents from the endoplasmic reticulum, making them the latest branch of the endomembrane system to be identified. Furthermore, the observations that peroxisome and mitochondrial biogenesis can occur in a coordinated manner, and that these organelles share factors for their multiplication, demonstrate previously unanticipated aspects of cellular organisation.
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Affiliation(s)
- Ewald H Hettema
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
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Kaur N, Reumann S, Hu J. Peroxisome biogenesis and function. THE ARABIDOPSIS BOOK 2009; 7:e0123. [PMID: 22303249 PMCID: PMC3243405 DOI: 10.1199/tab.0123] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Peroxisomes are small and single membrane-delimited organelles that execute numerous metabolic reactions and have pivotal roles in plant growth and development. In recent years, forward and reverse genetic studies along with biochemical and cell biological analyses in Arabidopsis have enabled researchers to identify many peroxisome proteins and elucidate their functions. This review focuses on the advances in our understanding of peroxisome biogenesis and metabolism, and further explores the contribution of large-scale analysis, such as in sillco predictions and proteomics, in augmenting our knowledge of peroxisome function In Arabidopsis.
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Affiliation(s)
| | - Sigrun Reumann
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, N-4036 Stavanger, Norway
| | - Jianping Hu
- MSU-DOE Plant Research Laboratory and
- Plant Biology Department, Michigan State University, East Lansing, MI 48824
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36
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Abstract
Peroxisomes play an important role in lipid metabolic pathways and are implicated in many human disorders. Their biogenesis has been studied over the last two decades using many uni and multi-cellular model systems and many aspects of the mechanisms and proteins involved in peroxisome biogenesis are conserved from yeast to humans. In this manuscript we review the recent progress made in our understanding of the mechanisms by which matrix and membrane proteins are sorted to and assembled into peroxisomes.
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Affiliation(s)
- Changle Ma
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA
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Anthonio EA, Brees C, Baumgart-Vogt E, Hongu T, Huybrechts SJ, Van Dijck P, Mannaerts GP, Kanaho Y, Van Veldhoven PP, Fransen M. Small G proteins in peroxisome biogenesis: the potential involvement of ADP-ribosylation factor 6. BMC Cell Biol 2009; 10:58. [PMID: 19686593 PMCID: PMC3224584 DOI: 10.1186/1471-2121-10-58] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 08/17/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Peroxisomes execute diverse and vital functions in virtually every eukaryote. New peroxisomes form by budding from pre-existing organelles or de novo by vesiculation of the ER. It has been suggested that ADP-ribosylation factors and COPI coatomer complexes are involved in these processes. RESULTS Here we show that all viable Saccharomyces cerevisiae strains deficient in one of the small GTPases which have an important role in the regulation of vesicular transport contain functional peroxisomes, and that the number of these organelles in oleate-grown cells is significantly upregulated in the arf1 and arf3 null strains compared to the wild-type strain. In addition, we provide evidence that a portion of endogenous Arf6, the mammalian orthologue of yeast Arf3, is associated with the cytoplasmic face of rat liver peroxisomes. Despite this, ablation of Arf6 did neither influence the regulation of peroxisome abundance nor affect the localization of peroxisomal proteins in cultured fetal hepatocytes. However, co-overexpression of wild-type, GTP hydrolysis-defective or (dominant-negative) GTP binding-defective forms of Arf1 and Arf6 caused mislocalization of newly-synthesized peroxisomal proteins and resulted in an alteration of peroxisome morphology. CONCLUSION These observations suggest that Arf6 is a key player in mammalian peroxisome biogenesis. In addition, they also lend strong support to and extend the concept that specific Arf isoform pairs may act in tandem to regulate exclusive trafficking pathways.
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Affiliation(s)
- Erin A Anthonio
- Department of Molecular Cell Biology, Catholic University of Leuven, Leuven, Belgium.
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Huybrechts SJ, Van Veldhoven PP, Brees C, Mannaerts GP, Los GV, Fransen M. Peroxisome dynamics in cultured mammalian cells. Traffic 2009; 10:1722-33. [PMID: 19719477 DOI: 10.1111/j.1600-0854.2009.00970.x] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Despite the identification and characterization of various proteins that are essential for peroxisome biogenesis, the origin and the turnover of peroxisomes are still unresolved critical issues. In this study, we used the HaloTag technology as a new approach to examine peroxisome dynamics in cultured mammalian cells. This technology is based on the formation of a covalent bond between the HaloTag protein--a mutated bacterial dehalogenase which is fused to the protein of interest--and a synthetic haloalkane ligand that contains a fluorophore or affinity tag. By using cell-permeable ligands of distinct fluorescence, it is possible to image distinct pools of newly synthesized proteins, generated from a single genetic HaloTag-containing construct, at different wavelengths. Here, we show that peroxisomes display an age-related heterogeneity with respect to their capacity to incorporate newly synthesized proteins. We also demonstrate that these organelles do not exchange their protein content. In addition, we present evidence that the matrix protein content of pre-existing peroxisomes is not evenly distributed over new organelles. Finally, we show that peroxisomes in cultured mammalian cells, under basal growth conditions, have a half-life of approximately 2 days and are mainly degraded by an autophagy-related mechanism. The implications of these findings are discussed.
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Affiliation(s)
- Sofie J Huybrechts
- Katholieke Universiteit Leuven, Faculteit Geneeskunde, Departement Moleculaire Celbiologie, LIPIT, Campus Gasthuisberg (O&N 1), Leuven, Belgium
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Mathur J. Rapid peroxisomal responses to ROS suggest an alternative mechanistic model for post-biogenesis peroxisomal life cycle in plants. PLANT SIGNALING & BEHAVIOR 2009; 4:787-9. [PMID: 19820326 PMCID: PMC2801401 DOI: 10.4161/psb.4.8.9232] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 06/08/2009] [Indexed: 05/20/2023]
Abstract
Plants adapt to and survive in some of the harshest environments. Their success can be ascribed to an ability to maintain an optimal subcellular redox environment. Peroxisomes, ubiquitous ROS producing and scavenging organelles in eukaryotes play an important role in cellular homeostasis. Recently the formation of thin membrane extensions called peroxules has provided further evidence for peroxisomal role in rapidly sensing and responding to alterations in subcellular ROS. Within a cell the transient extension and retraction of peroxules is asynchronous but takes place within seconds. Peroxules follow tracks defined by tubules of the endoplasmic reticulum and their formation does not appear to involve an elaborate transcriptional-translational machinery. Rather the rapidity of peroxisomal responses suggests ROS instigated membrane modifications aimed at local ROS scavenging or leading to peroxisome elongation prior to their fission for increasing peroxisome numbers within a cell. A model on post-biogenesis peroxisomal life-cycle taking cognizance of rapid peroxisomal responses is presented.
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Affiliation(s)
- Jaideep Mathur
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, CA.
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40
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Tartakoff AM, Tao T. Comparative and evolutionary aspects of macromolecular translocation across membranes. Int J Biochem Cell Biol 2009; 42:214-29. [PMID: 19643202 DOI: 10.1016/j.biocel.2009.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Revised: 07/21/2009] [Accepted: 07/21/2009] [Indexed: 01/10/2023]
Abstract
Membrane barriers preserve the integrity of organelles of eukaryotic cells, yet the genesis and ongoing functions of the same organelles requires that their limiting membranes allow import and export of selected macromolecules. Multiple distinct mechanisms are used for this purpose, only some of which have been traced to prokaryotes. Some can accommodate both monomeric and also large heterooligomeric cargoes. The best characterized of these is nucleocytoplasmic transport. This synthesis compares the unidirectional and bidirectional mechanisms of macromolecular transport of the endoplasmic reticulum, mitochondria, peroxisomes and the nucleus, calls attention to the powerful experimental approaches which have been used for their elucidation, discusses their regulation and evolutionary origins, and highlights relatively unexplored areas.
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Affiliation(s)
- Alan M Tartakoff
- Department of Pathology & Cell Biology Program, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA.
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41
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Sinclair AM, Trobacher CP, Mathur N, Greenwood JS, Mathur J. Peroxule extension over ER-defined paths constitutes a rapid subcellular response to hydroxyl stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 59:231-42. [PMID: 19292761 DOI: 10.1111/j.1365-313x.2009.03863.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plants survive against myriad environmental odds while remaining rooted to a single spot. The time scale over which plant cells can respond to environmental cues is seldom appreciated. Fluorescent protein-assisted live imaging of peroxisomes reveals that they respond within seconds of exposure to hydrogen peroxide and hydroxyl radicals by producing dynamic extensions called peroxules. Observations of the Arabidopsis flu mutant and treatments with xenobiotics eliciting singlet oxygen and superoxide reactive oxygen species suggest that the observed responses are specific for hydroxyl radicals. Prolonged exposure to hydroxyl radicals inhibits peroxule extension, and instead causes motile and spherical peroxisomes in a cell to become immotile and elongate several-fold. Expression of photo-convertible EosFP-PTS1 demonstrates that vermiform peroxisomes result from rapid stretching of individual peroxisomes, while the subsequent 'beads-on-a-string' morphology results from differential protein distribution within an elongated tubule. Over time, the beads in elongated peroxisomes also extend peroxules randomly before undergoing asynchronous, asymmetrical fission. Peroxule extension does not appear to involve cytoskeletal elements directly, but is closely aligned with and reflects the dynamics of ER tubules. Peroxisomal responses reveal a rapidly invoked subcellular machinery that is involved in recognition of hydroxyl stress thresholds, and its possible remediation locally through extension of peroxules or globally by increasing peroxisome numbers. A matrix protein retro-flow mechanism that supports peroxisome-ER connectivity in plant cells is suggested.
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Affiliation(s)
- Alison M Sinclair
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
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42
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Aung K, Hu J. The Arabidopsis peroxisome division mutant pdd2 is defective in the DYNAMIN-RELATED PROTEIN3A (DRP3A) gene. PLANT SIGNALING & BEHAVIOR 2009; 57:146-59. [PMID: 19816122 DOI: 10.1111/j.1365-313x.2008.03677.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In plants, the division of peroxisomes is mediated by several classes of proteins, including PEROXIN11 (PEX11), FISSION1 (FIS1) and DYNAMIN-RELATED PROTEIN3 (DRP3). DRP3A and DRP3B are two homologous dynamin-related proteins playing overlapping roles in the division of both peroxisomes and mitochondria, with DRP3A performing a stronger function than DRP3B in peroxisomal fission. Here, we report the identification and characterization of the peroxisome division defective 2 (pdd2) mutant, which was later proven to be another drp3A allele. The pdd2 mutant generates a truncated DRP3A protein and exhibits pale green and retarded growth phenotypes. Intriguingly, this mutant displays much stronger peroxisome division deficiency in root cells than in leaf mesophyll cells. Our data suggest that the partial GTPase effector domain retained in pdd2 may have contributed to the distinct mutant phenotype of this mutant.
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Affiliation(s)
- Kyaw Aung
- Department of Energy Plant Research Laboratory and Plant Biology Department, Michigan State University, East Lansing, MI, USA
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43
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Fujimoto M, Arimura SI, Mano S, Kondo M, Saito C, Ueda T, Nakazono M, Nakano A, Nishimura M, Tsutsumi N. Arabidopsis dynamin-related proteins DRP3A and DRP3B are functionally redundant in mitochondrial fission, but have distinct roles in peroxisomal fission. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 58:388-400. [PMID: 19144001 DOI: 10.1111/j.1365-313x.2009.03786.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Two similar Arabidopsis dynamin-related proteins, DRP3A and DRP3B, are thought to be key factors in both mitochondrial and peroxisomal fission. However, the functional and genetic relationships between DRP3A and DRP3B have not been fully investigated. In a yeast two-hybrid assay, DRP3A and DRP3B interacted with themselves and with each other. DRP3A and DRP3B localized to mitochondria and peroxisomes, and co-localized with each other in leaf epidermal cells. In two T-DNA insertion mutants, drp3a and drp3b, the mitochondria are a little longer and fewer in number than those in the wild-type cells. In the double mutant, drp3a/drp3b, mitochondria are connected to each other, resulting in massive elongation. Overexpression of either DRP3A or DRP3B in drp3a/drp3b restored the particle shape of mitochondria, suggesting that DRP3A and DRP3B are functionally redundant in mitochondrial fission. In the case of peroxisomal fission, DRP3A and DRP3B appear to have different functions: peroxisomes in drp3a were larger and fewer in number than those in the wild type, whereas peroxisomes in drp3b were as large and as numerous as those in the wild type, and peroxisomes in drp3a/drp3b were as large and as numerous as those in drp3a. Although overexpression of DRP3A in drp3a/drp3b restored the shape and number of peroxisomes, overexpression of DRP3B did not restore the phenotypes, and often caused elongation instead. These results suggest that DRP3B and DRP3A have redundant molecular functions in mitochondrial fission, whereas DRP3B has a minor role in peroxisomal fission that is distinct from that of DRP3A.
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Affiliation(s)
- Masaru Fujimoto
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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44
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Phosphatidylethanolamine synthesized by three different pathways is supplied to peroxisomes of the yeast Saccharomyces cerevisiae. Biochim Biophys Acta Mol Cell Biol Lipids 2009; 1791:379-87. [DOI: 10.1016/j.bbalip.2009.01.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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45
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Titorenko VI, Rachubinski RA. Spatiotemporal dynamics of the ER-derived peroxisomal endomembrane system. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2009; 272:191-244. [PMID: 19121819 DOI: 10.1016/s1937-6448(08)01605-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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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46
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Biogenesis of peroxisomes and mitochondria: linked by division. Histochem Cell Biol 2009; 131:441-6. [PMID: 19219450 DOI: 10.1007/s00418-009-0561-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2009] [Indexed: 10/21/2022]
Abstract
Peroxisomes and mitochondria are metabolically linked organelles, which are crucial to human health and development. The search for components involved in their dynamics and maintenance led to the interesting finding that mitochondria and peroxisomes share components of their division machinery. Recently, it became clear that this is a common strategy used by mammals, fungi and plants. Furthermore, a closer interrelationship between peroxisomes and mitochondria has been proposed, which might have an impact on functionality and disease conditions. Here, we briefly highlight the major findings, views and open questions concerning peroxisomal formation, division, and interrelationship with mitochondria.
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47
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Smith JJ, Aitchison JD. Regulation of peroxisome dynamics. Curr Opin Cell Biol 2009; 21:119-26. [PMID: 19188056 PMCID: PMC2681484 DOI: 10.1016/j.ceb.2009.01.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 12/30/2008] [Accepted: 01/08/2009] [Indexed: 10/21/2022]
Abstract
Peroxisomes are single-membraned organelles ubiquitous to eukaryotic cells that house metabolic reactions that generate and destroy harmful oxidative intermediates. They are dynamic structures whose morphology, abundance, composition, and function depend on the cell type and environment. Perhaps due to the potentially damaging and protective metabolic roles of peroxisomes and their dynamic presence in the cell, peroxisome biogenesis is emerging as a process that involves complex underlying mechanisms of regulated formation and maintenance. There are roughly 30 known peroxins, proteins involved in peroxisome biogenesis, many of which have been conserved from yeast to mammals. This review focuses on the biogenesis of peroxisomes with an emphasis on the regulation of peroxisome formation and the import of peroxisomal matrix proteins in the model organism Saccharomyces cerevisiae.
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Affiliation(s)
- Jennifer J Smith
- Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA.
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48
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Zhang XC, Hu JP. FISSION1A and FISSION1B proteins mediate the fission of peroxisomes and mitochondria in Arabidopsis. MOLECULAR PLANT 2008; 1:1036-47. [PMID: 19825601 DOI: 10.1093/mp/ssn056] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Peroxisomes and mitochondria are metabolically diverse organelles that act in concert in a number of pathways in eukaryotes, including photorespiration and lipid mobilization in plants. The division machineries of these two types of organelles also share several components such as dynamin-related proteins (DRPs) and their organelle anchor, the FISSION1 (FIS1) protein. In Arabidopsis, members of the DRP3 and FIS1 small protein families, namely DRP3A, DRP3B, FIS1A, and FIS1B, are each dual-targeted to peroxisomes and mitochondria and are required for the division of both organelles; DRP3A and DRP3B are partially redundant in function. To further determine the contribution of FIS1A and FIS1B to the division of peroxisomes and mitochondria, we analyzed plants overexpressing FIS1A or FIS1B and mutants in which the functions of both proteins were disrupted. Domains in FIS1A and FIS1B required for peroxisomal targeting were also dissected. Our results demonstrate that FIS1A and FIS1B play rate-limiting and partially overlapping roles in promoting the fission of peroxisomes and mitochondria. Furthermore, although the C-terminus of FIS1 is both necessary and sufficient for targeting to peroxisomes, the role of the short C-terminal segment adjacent to the transmembrane domain may differ among diverse species in peroxisomal targeting.
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Affiliation(s)
- Xin-Chun Zhang
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
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49
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Pracharoenwattana I, Smith SM. When is a peroxisome not a peroxisome? TRENDS IN PLANT SCIENCE 2008; 13:522-5. [PMID: 18768343 DOI: 10.1016/j.tplants.2008.07.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2008] [Revised: 07/25/2008] [Accepted: 07/25/2008] [Indexed: 05/23/2023]
Abstract
It is time to drop the glyoxysome name. Recent functional genomics analysis together with cell biology studies emphasize the unifying features of peroxisomes rather than their differences. Plant peroxisomes contain 300 or more proteins, the functions of which are dominated by activities related to fatty acid oxidation (>70 enzymes). By comparison, relatively few proteins are committed to metabolism of reactive oxygen species ( approximately 20) and to photorespiration ( approximately 10). Analysis of triglyceride metabolism in Arabidopsis seedlings now indicates that only two enzymes (isocitrate lyase and malate synthase) potentially distinguish glyoxysomes from other peroxisomes. Future research is best served by focusing on the common features of peroxisomes to establish how these dynamic organelles contribute to energy metabolism, development and responses to environmental challenges.
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Affiliation(s)
- Itsara Pracharoenwattana
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre of Excellence for Plant Metabolomics, University of Western Australia, Crawley, Western Australia 6009, Australia
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50
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Bassham DC, Brandizzi F, Otegui MS, Sanderfoot AA. The secretory system of Arabidopsis. THE ARABIDOPSIS BOOK 2008; 6:e0116. [PMID: 22303241 PMCID: PMC3243370 DOI: 10.1199/tab.0116] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Over the past few years, a vast amount of research has illuminated the workings of the secretory system of eukaryotic cells. The bulk of this work has been focused on the yeast Saccharomyces cerevisiae, or on mammalian cells. At a superficial level, plants are typical eukaryotes with respect to the operation of the secretory system; however, important differences emerge in the function and appearance of endomembrane organelles. In particular, the plant secretory system has specialized in several ways to support the synthesis of many components of the complex cell wall, and specialized kinds of vacuole have taken on a protein storage role-a role that is intended to support the growing seedling, but has been co-opted to support human life in the seeds of many crop plants. In the past, most research on the plant secretory system has been guided by results in mammalian or fungal systems but recently plants have begun to stand on their own as models for understanding complex trafficking events within the eukaryotic endomembrane system.
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Affiliation(s)
- Diane C. Bassham
- Department of Genetics, Development and Cell Biology and Plant Sciences Institute, Iowa State University, 455 Bessey Hall, Ames, Iowa 50011
| | - Federica Brandizzi
- MSU-DOE Plant Research Laboratory, Michigan State University, S-238 Plant Biology, East Lansing, Michigan 48824
| | - Marisa S. Otegui
- Department of Botany, University of Wisconsin- Madison, 224 Birge Hall, 430 Lincoln Drive, Madison, Wisconsin 53706
| | - Anton A. Sanderfoot
- Department of Plant Biology, University of Minnesota-Twin Cities, 250 Bioscience Center, 1445 Gortner Ave, St. Paul, Minnesota 55108
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