651
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Murray MS, Holmes RP, Lowther WT. Active site and loop 4 movements within human glycolate oxidase: implications for substrate specificity and drug design. Biochemistry 2008; 47:2439-49. [PMID: 18215067 DOI: 10.1021/bi701710r] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human glycolate oxidase (GO) catalyzes the FMN-dependent oxidation of glycolate to glyoxylate and glyoxylate to oxalate, a key metabolite in kidney stone formation. We report herein the structures of recombinant GO complexed with sulfate, glyoxylate, and an inhibitor, 4-carboxy-5-dodecylsulfanyl-1,2,3-triazole (CDST), determined by X-ray crystallography. In contrast to most alpha-hydroxy acid oxidases including spinach glycolate oxidase, a loop region, known as loop 4, is completely visible when the GO active site contains a small ligand. The lack of electron density for this loop in the GO-CDST complex, which mimics a large substrate, suggests that a disordered to ordered transition may occur with the binding of substrates. The conformational flexibility of Trp110 appears to be responsible for enabling GO to react with alpha-hydroxy acids of various chain lengths. Moreover, the movement of Trp110 disrupts a hydrogen-bonding network between Trp110, Leu191, Tyr134, and Tyr208. This loss of interactions is the first indication that active site movements are directly linked to changes in the conformation of loop 4. The kinetic parameters for the oxidation of glycolate, glyoxylate, and 2-hydroxy octanoate indicate that the oxidation of glycolate to glyoxylate is the primary reaction catalyzed by GO, while the oxidation of glyoxylate to oxalate is most likely not relevant under normal conditions. However, drugs that exploit the unique structural features of GO may ultimately prove to be useful for decreasing glycolate and glyoxylate levels in primary hyperoxaluria type 1 patients who have the inability to convert peroxisomal glyoxylate to glycine.
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Affiliation(s)
- Michael S Murray
- Center for Structural Biology and Department of Biochemistry, Wake Forest University Health Sciences, Medical Center Boulevard, Winston-Salem, North Carolina 27157, USA
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652
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Thoms S, Debelyy MO, Nau K, Meyer HE, Erdmann R. Lpx1p is a peroxisomal lipase required for normal peroxisome morphology. FEBS J 2008; 275:504-14. [DOI: 10.1111/j.1742-4658.2007.06217.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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653
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Jourdain I, Sontam D, Johnson C, Dillies C, Hyams JS. Dynamin-dependent biogenesis, cell cycle regulation and mitochondrial association of peroxisomes in fission yeast. Traffic 2007; 9:353-65. [PMID: 18088324 DOI: 10.1111/j.1600-0854.2007.00685.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Peroxisomes were visualized for the first time in living fission yeast cells. In small, newly divided cells, the number of peroxisomes was low but increased in parallel with the increase in cell length/volume that accompanies cell cycle progression. In cells grown in oleic acid, both the size and the number of peroxisomes increased. The peroxisomal inventory of cells lacking the dynamin-related proteins Dnm1 or Vps1 was similar to that in wild type. By contrast, cells of the double mutant dnm1Delta vps1Delta contained either no peroxisomes at all or a small number of morphologically aberrant organelles. Peroxisomes exhibited either local Brownian movement or longer-range linear displacements, which continued in the absence of either microtubules or actin filaments. On the contrary, directed peroxisome motility appeared to occur in association with mitochondria and may be an indirect function of intrinsic mitochondrial dynamics. We conclude that peroxisomes are present in fission yeast and that Dnm1 and Vps1 act redundantly in peroxisome biogenesis, which is under cell cycle control. Peroxisome movement is independent of the cytoskeleton but is coupled to mitochondrial dynamics.
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Affiliation(s)
- Isabelle Jourdain
- Institute of Molecular Biosciences, Massey University, Private Bag 11222, Palmerston North, New Zealand.
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654
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Platta HW, Erdmann R. Peroxisomal dynamics. Trends Cell Biol 2007; 17:474-84. [PMID: 17913497 DOI: 10.1016/j.tcb.2007.06.009] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Revised: 06/08/2007] [Accepted: 06/12/2007] [Indexed: 11/20/2022]
Abstract
Peroxisomes are a dynamic compartment in almost all eukaryotic cells and have diverse metabolic roles in response to environmental changes and cellular demands. The accompanying changes in enzyme content or abundance of peroxisomes are accomplished by dynamically operating membrane- and matrix-protein transport machineries. This review discusses recent progress in understanding peroxisomal proliferation and maintenance, insertion of peroxisomal membrane proteins, compartmentalization of peroxisomal matrix proteins and selective degradation of peroxisomes via pexophagy.
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Affiliation(s)
- Harald W Platta
- Ruhr-Universität Bochum, Medizinische Fakultät, Institut für Physiologische Chemie, Abteilung für Systembiochemie, Universitätsstr. 150, D-44780 Bochum, Germany
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655
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Schrader M, Yoon Y. Mitochondria and peroxisomes: Are the ‘Big Brother’ and the ‘Little Sister’ closer than assumed? Bioessays 2007; 29:1105-14. [DOI: 10.1002/bies.20659] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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656
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de Sotomayor MA, Mingorance C, Rodriguez-Rodriguez R, Marhuenda E, Herrera MD. l-carnitine and its propionate: improvement of endothelial function in SHR through superoxide dismutase-dependent mechanisms. Free Radic Res 2007; 41:884-91. [PMID: 17654045 DOI: 10.1080/10715760701416467] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
To clarify the mechanism underlying the antioxidant properties of l-carnitine (LC) and propionyl-l-carnitine (PLC) on spontaneously hypertensive (SHR) and normotensive WKY, animals were treated with either PLC or LC (200 mg kg(- 1)). Aorta was dissected and contraction to (R)-( - )-phenylephrine (Phe) and relaxation to carbachol (CCh) were assessed in the presence or not of the NO synthase (NOS) inhibitor, l-NAME. [image omitted] production was evaluated by lucigenin-enhanced chemiluminescence and its participation on relaxation was observed after incubation with superoxide dismutase (SOD) plus catalase. Protein expressions of eNOS, Cu/Zn-SOD and Mn-SOD were studied by western blot. Both LC and PLC treatments improved endothelial function of SHR through increasing NO participation and decreasing [image omitted] probably involving higher Cu/Zn-SOD expression. PLC treatment augmented eNOS expression in SHR. Surprisingly, LC increased [image omitted] produced by aorta from WKY and thus diminished NO and damaged endothelial function. Conversely, PLC did not affect CCh-induced relaxation in WKY. These results demonstrate that LC and PLC prevent endothelial dysfunction in SHR through an antioxidant effect.
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657
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Noland RC, Woodlief TL, Whitfield BR, Manning SM, Evans JR, Dudek RW, Lust RM, Cortright RN. Peroxisomal-mitochondrial oxidation in a rodent model of obesity-associated insulin resistance. Am J Physiol Endocrinol Metab 2007; 293:E986-E1001. [PMID: 17638705 DOI: 10.1152/ajpendo.00399.2006] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peroxisomal oxidation yields metabolites that are more efficiently utilized by mitochondria. This is of potential clinical importance because reduced fatty acid oxidation is suspected to promote excess lipid accumulation in obesity-associated insulin resistance. Our purpose was to assess peroxisomal contributions to mitochondrial oxidation in mixed gastrocnemius (MG), liver, and left ventricle (LV) homogenates from lean and fatty (fa/fa) Zucker rats. Results indicate that complete mitochondrial oxidation (CO(2) production) using various lipid substrates was increased approximately twofold in MG, unaltered in LV, and diminished approximately 50% in liver of fa/fa rats. In isolated mitochondria, malonyl-CoA inhibited CO(2) production from palmitate 78%, whereas adding isolated peroxisomes reduced inhibition to 21%. These data demonstrate that peroxisomal products may enter mitochondria independently of CPT I, thus providing a route to maintain lipid disposal under conditions where malonyl-CoA levels are elevated, such as in insulin-resistant tissues. Peroxisomal metabolism of lignoceric acid in fa/fa rats was elevated in both liver and MG (LV unaltered), but peroxisomal product distribution varied. A threefold elevation in incomplete oxidation was solely responsible for increased hepatic peroxisomal oxidation (CO(2) unaltered). Alternatively, only CO(2) was detected in MG, indicating that peroxisomal products were exclusively partitioned to mitochondria for complete lipid disposal. These data suggest tissue-specific destinations for peroxisome-derived products and emphasize a potential role for peroxisomes in skeletal muscle lipid metabolism in the obese, insulin-resistant state.
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Affiliation(s)
- Robert C Noland
- Department of Physiology, East Carolina University, Greenville, NC 27858, USA
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658
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Nenicu A, Lüers GH, Kovacs W, David M, Zimmer A, Bergmann M, Baumgart-Vogt E. Peroxisomes in human and mouse testis: differential expression of peroxisomal proteins in germ cells and distinct somatic cell types of the testis. Biol Reprod 2007; 77:1060-72. [PMID: 17881773 DOI: 10.1095/biolreprod.107.061242] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
The vital importance of peroxisomal metabolism for regular function of the testis is stressed by the severe spermatogenesis defects induced by peroxisomal dysfunction. However, only sparse information is available on the role and enzyme composition of this organelle in distinct cell types of the testis. In the present study, we characterized the peroxisomal compartment in human and mouse testis in primary cultures of murine somatic cells (Sertoli, peritubular myoid, and Leydig cells) and in GFP-PTS1 transgenic mice with a variety of morphological and biochemical techniques. Formerly, peroxisomes were thought to be absent in late stages of spermatogenesis. However, our results obtained by detection of different peroxisomal marker proteins show the presence of these organelles in most cell types in the testis, except for mature spermatozoa. Furthermore, we demonstrate a strong heterogeneity of peroxisomal protein content in various cell types of the human and mouse testis and show marked differences in structure, abundance, and localization of these organelles in spermatids, depending on their maturation. Highest and selective enrichment of the peroxisomal lipid transporters (ABCD1 and ABCD3) as well as ACOX2, the key regulatory enzyme of the beta-oxidation pathway 2 for side chain oxidation of cholesterol, were found in Sertoli cells, whereas Leydig cells were enriched in catalase and ABCD2. Our results suggest a cell type-specific metabolic function of peroxisomes in the testis and point to an important role for peroxisomes in spermiogenesis and in the lipid metabolism of Sertoli cells.
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Affiliation(s)
- Anca Nenicu
- Institute for Anatomy and Cell Biology II, Justus Liebig University, 35385 Giessen, Germany
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659
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Wiese S, Gronemeyer T, Ofman R, Kunze M, Grou CP, Almeida JA, Eisenacher M, Stephan C, Hayen H, Schollenberger L, Korosec T, Waterham HR, Schliebs W, Erdmann R, Berger J, Meyer HE, Just W, Azevedo JE, Wanders RJA, Warscheid B. Proteomics characterization of mouse kidney peroxisomes by tandem mass spectrometry and protein correlation profiling. Mol Cell Proteomics 2007; 6:2045-57. [PMID: 17768142 DOI: 10.1074/mcp.m700169-mcp200] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The peroxisome represents a ubiquitous single membrane-bound key organelle that executes various metabolic pathways such as fatty acid degradation by alpha- and beta-oxidation, ether-phospholipid biosynthesis, metabolism of reactive oxygen species, and detoxification of glyoxylate in mammals. To fulfil this vast array of metabolic functions, peroxisomes accommodate approximately 50 different enzymes at least as identified until now. Interest in peroxisomes has been fueled by the discovery of a group of genetic diseases in humans, which are caused by either a defect in peroxisome biogenesis or the deficient activity of a distinct peroxisomal enzyme or transporter. Although this research has greatly improved our understanding of peroxisomes and their role in mammalian metabolism, deeper insight into biochemistry and functions of peroxisomes is required to expand our knowledge of this low abundance but vital organelle. In this work, we used classical subcellular fractionation in combination with MS-based proteomics methodologies to characterize the proteome of mouse kidney peroxisomes. We could identify virtually all known components involved in peroxisomal metabolism and biogenesis. Moreover through protein localization studies by using a quantitative MS screen combined with statistical analyses, we identified 15 new peroxisomal candidates. Of these, we further investigated five candidates by immunocytochemistry, which confirmed their localization in peroxisomes. As a result of this joint effort, we believe to have compiled the so far most comprehensive protein catalogue of mammalian peroxisomes.
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Affiliation(s)
- Sebastian Wiese
- Medizinisches Proteom-Center, Ruhr-Universitaet Bochum, Universitaetsstrasse 150, 44780 Bochum, Germany
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660
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Razeto A, Mattiroli F, Carpanelli E, Aliverti A, Pandini V, Coda A, Mattevi A. The crucial step in ether phospholipid biosynthesis: structural basis of a noncanonical reaction associated with a peroxisomal disorder. Structure 2007; 15:683-92. [PMID: 17562315 DOI: 10.1016/j.str.2007.04.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Revised: 04/13/2007] [Accepted: 04/13/2007] [Indexed: 01/17/2023]
Abstract
Ether phospholipids are essential constituents of eukaryotic cell membranes. Rhizomelic chondrodysplasia punctata type 3 is a severe peroxisomal disorder caused by inborn deficiency of alkyldihydroxyacetonephosphate synthase (ADPS). The enzyme carries out the most characteristic step in ether phospholipid biosynthesis: formation of the ether bond. The crystal structure of ADPS from Dictyostelium discoideum shows a fatty-alcohol molecule bound in a narrow hydrophobic tunnel, specific for aliphatic chains of 16 carbons. Access to the tunnel is controlled by a flexible loop and a gating helix at the protein-membrane interface. Structural and mutagenesis investigations identify a cluster of hydrophilic catalytic residues, including an essential tyrosine, possibly involved in substrate proton abstraction, and the arginine that is mutated in ADPS-deficient patients. We propose that ether bond formation might be orchestrated through a covalent imine intermediate with the flavin, accounting for the noncanonical employment of a flavin cofactor in a nonredox reaction.
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MESH Headings
- Alkyl and Aryl Transferases/chemistry
- Alkyl and Aryl Transferases/genetics
- Alkyl and Aryl Transferases/metabolism
- Amino Acid Sequence
- Amino Acid Substitution
- Animals
- Binding Sites
- Catalysis
- Chondrodysplasia Punctata, Rhizomelic/enzymology
- Chondrodysplasia Punctata, Rhizomelic/metabolism
- Chondrodysplasia Punctata, Rhizomelic/pathology
- Conserved Sequence
- Crystallography, X-Ray
- Dictyostelium/enzymology
- Dimerization
- Flavin-Adenine Dinucleotide/chemistry
- Flavin-Adenine Dinucleotide/metabolism
- Histidine/metabolism
- Humans
- Hydrogen Bonding
- Lipid Metabolism, Inborn Errors
- Models, Biological
- Models, Chemical
- Models, Molecular
- Molecular Sequence Data
- Molecular Structure
- Peroxisomal Disorders/enzymology
- Peroxisomal Disorders/genetics
- Phenylalanine/metabolism
- Phospholipid Ethers/chemistry
- Phospholipid Ethers/metabolism
- Protein Binding
- Protein Conformation
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Recombinant Proteins/chemistry
- Recombinant Proteins/metabolism
- Sequence Homology, Amino Acid
- Spectrum Analysis, Raman
- Substrate Specificity
- Tyrosine/metabolism
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Affiliation(s)
- Adelia Razeto
- Dipartimento di Genetica e Microbiologia, Università di Pavia, via Ferrata 1, 27100 Pavia, Italy
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661
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Abstract
The structural properties of alkyldihydroxyacetonephosphate synthase (ADPS) described by Razeto et al. (2007) in this issue of Structure provide new insights into how this peroxisomal flavoenzyme catalyzes a nonredox reaction in the conversion of an ester to an ether linkage in plasmologen biosynthesis.
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662
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Islinger M, Lüers GH, Li KW, Loos M, Völkl A. Rat Liver Peroxisomes after Fibrate Treatment. J Biol Chem 2007; 282:23055-69. [PMID: 17522052 DOI: 10.1074/jbc.m610910200] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Fibrates are known to induce peroxisome proliferation and the expression of peroxisomal beta-oxidation enzymes. To analyze fibrate-induced changes of complex metabolic networks, we have compared the proteome of rat liver peroxisomes from control and bezafibrate-treated rats. Highly purified peroxisomes were subfractionated, and the proteins of the matrix, peripheral, and integral membrane subfractions thus obtained were analyzed by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry after labeling of tryptic peptides with the iTRAQ reagent. By means of this quantitative technique, we were able to identify 134 individual proteins, covering most of the known peroxisomal proteome. Ten predicted new open reading frames were verified by cDNA cloning, and seven of them could be localized to peroxisomes by immunocytochemistry. Moreover, quantitative mass spectrometry substantiated the induction of most of the known peroxisome proliferator-activated receptor alpha-regulated peroxisomal proteins upon treatment with bezafibrate, documenting the suitability of the iTRAQ procedure in larger scale experiments. However, not all proteins reacted to a similar extent but exerted a fibrate-specific induction scheme showing the variability of peroxisome proliferator-activated receptoralpha-transmitted responses to specific ligands. In view of our data, rat hepatic peroxisomes are apparently not specialized to sequester very long chain fatty acids (C22-C26) but rather metabolize preferentially long chain fatty acids (C16-18).
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Affiliation(s)
- Markus Islinger
- Department of Anatomy and Cell Biology, Ruprecht-Karl University, 69120 Heidelberg, Germany.
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663
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664
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Jia Z, Moulson CL, Pei Z, Miner JH, Watkins PA. Fatty Acid Transport Protein 4 Is the Principal Very Long Chain Fatty Acyl-CoA Synthetase in Skin Fibroblasts. J Biol Chem 2007; 282:20573-83. [PMID: 17522045 DOI: 10.1074/jbc.m700568200] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fatty acid transport protein 4 (FATP4) is a fatty acyl-CoA synthetase that preferentially activates very long chain fatty acid substrates, such as C24:0, to their CoA derivatives. To gain better insight into the physiological functions of FATP4, we established dermal fibroblast cell lines from FATP4-deficient wrinkle-free mice and wild type (w.t.) mice. FATP4 -/- fibroblasts had no detectable FATP4 protein by Western blot. Compared with w.t. fibroblasts, cells lacking FATP4 had an 83% decrease in C24:0 activation. Peroxisomal degradation of C24:0 was reduced by 58%, and rates of C24:0 incorporation into major phospholipid species (54-64% decrease), triacylglycerol (64% decrease), and cholesterol esters (58% decrease) were significantly diminished. Because these lipid metabolic processes take place in different subcellular organelles, we used immunofluorescence and Western blotting of subcellular fractions to investigate the distribution of FATP4 protein and measured enzyme activity in fractions from w.t. and FATP4 -/- fibroblasts. FATP4 protein and acyl-CoA synthetase activity localized to multiple organelles, including mitochondria, peroxisomes, endoplasmic reticulum, and the mitochondria-associated membrane fraction. We conclude that in murine skin fibroblasts, FATP4 is the major enzyme producing very long chain fatty acid-CoA for lipid metabolic pathways. Although FATP4 deficiency primarily affected very long chain fatty acid metabolism, mutant fibroblasts also showed reduced uptake of a fluorescent long chain fatty acid and reduced levels of long chain polyunsaturated fatty acids. FATP4-deficient cells also contained abnormal neutral lipid droplets. These additional defects indicate that metabolic abnormalities in these cells are not limited to very long chain fatty acids.
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Affiliation(s)
- Zhenzhen Jia
- Kennedy Krieger Institute, Johns Hopkins University School of Medicine, 707 N. Broadway, Baltimore, MD 21205, USA
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665
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Oaxaca-Castillo D, Andreoletti P, Vluggens A, Yu S, van Veldhoven PP, Reddy JK, Cherkaoui-Malki M. Biochemical characterization of two functional human liver acyl-CoA oxidase isoforms 1a and 1b encoded by a single gene. Biochem Biophys Res Commun 2007; 360:314-9. [PMID: 17603022 PMCID: PMC2732019 DOI: 10.1016/j.bbrc.2007.06.059] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Accepted: 06/01/2007] [Indexed: 01/17/2023]
Abstract
Human acyl-CoA oxidase 1 (ACOX1) is a rate-limiting enzyme in peroxisomal fatty acids beta-oxidation and its deficiency is associated with a lethal, autosomal recessive disease, called pseudoneonatal-adrenoleukodystrophy. Two mRNA variants, transcribed from a single gene encode ACOX1a or ACOX1b isoforms, respectively. Recently, a mutation in a splice site has been reported [H. Rosewich, H.R. Waterham, R.J. Wanders, S. Ferdinandusse, M. Henneke, D. Hunneman, J. Gartner, Pitfall in metabolic screening in a patient with fatal peroxisomal beta-oxidation defect, Neuropediatrics 37 (2006) 95-98.], which results in the defective peroxisomal fatty acids beta-oxidation. Here, we show that these mRNA splice variants are expressed differentially in human liver. We investigated the biochemical role of the two human ACOX1 isoforms by heterologous expression of the catalytically active ACOX1a and ACOX1b enzymes in Escherichia coli. ACOX1a seems to be more labile and exhibits only 50% specific activity toward palmitoyl-CoA as compared to ACOX1b.
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Affiliation(s)
- David Oaxaca-Castillo
- INSERM, U866, Dijon, F-21000, France
- Université de Bourgogne, Faculté des Sciences Gabriel, Centre de Recherche-Biochimie Métabolique et Nutritionnelle (LBMN), Dijon, F-21000, France
- GDR CNRS 2583, Dijon, F-21000, France
| | - Pierre Andreoletti
- INSERM, U866, Dijon, F-21000, France
- Université de Bourgogne, Faculté des Sciences Gabriel, Centre de Recherche-Biochimie Métabolique et Nutritionnelle (LBMN), Dijon, F-21000, France
- GDR CNRS 2583, Dijon, F-21000, France
| | - Aurore Vluggens
- INSERM, U866, Dijon, F-21000, France
- Université de Bourgogne, Faculté des Sciences Gabriel, Centre de Recherche-Biochimie Métabolique et Nutritionnelle (LBMN), Dijon, F-21000, France
- GDR CNRS 2583, Dijon, F-21000, France
| | - Sangtao Yu
- The Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Paul P. van Veldhoven
- Departement Moleculaire Celbiologie, Afdeling Farmacologie, Faculteit Geneeskunde, Katholieke Universiteit Leuven, O & N1, Herestraat 49, Box 601, 3000, Leuven, Belgium
| | - Janardan K. Reddy
- The Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Mustapha Cherkaoui-Malki
- INSERM, U866, Dijon, F-21000, France
- Université de Bourgogne, Faculté des Sciences Gabriel, Centre de Recherche-Biochimie Métabolique et Nutritionnelle (LBMN), Dijon, F-21000, France
- GDR CNRS 2583, Dijon, F-21000, France
- Corresponding Author : Mustapha Cherkaoui Malki, Centre de Recherche INSERM, LBMN ; 6, Bd Gabriel, 21000 Dijon, France, Tel: 33 3 80 39 62 05, Fax: 33 3 80 39 62 50,
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666
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Abstract
In recent years, few fields in medicine have witnessed discoveries as momentous as those pertaining to the liver. Dramatic advances have been made, particularly in the areas of molecular biology and genetics. A joint EASL/AASLD Monothematic Conference was held on June 23rd-24th, 2006, in Modena, Italy, to bring the latest breakthroughs in different fields of genetics to hepatologists. This article reports the highlights of the conference and summarizes the main conclusions and implications for clinical and experimental hepatology.
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Affiliation(s)
- Antonello Pietrangelo
- Center for Hemochromatosis, University Hospital of Modena, Via del Pozza 71, 41100 Modena, Italy.
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667
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Razeto A, Mattiroli F, Bossi R, Coda A, Mattevi A. Identifying a recombinant alkyldihydroxyacetonephosphate synthase suited for crystallographic studies. Protein Expr Purif 2007; 55:343-51. [PMID: 17601746 DOI: 10.1016/j.pep.2007.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Revised: 05/04/2007] [Accepted: 05/08/2007] [Indexed: 11/20/2022]
Abstract
Alkyldihydroxyacetonephosphate is the building block for the biosynthesis of ether phospholipids, which are essential components of eukaryotic cell membranes and are involved in a variety of signaling processes. The metabolite is synthesized by alkyldihydroxyacetonephosphate synthase (ADPS), a peroxisomal flavoenzyme. Deficiency in ADPS activity causes rhizomelic chondrodysplasia punctata type 3, a very severe genetic disease. ADPS is unusual in that it uses a typical redox cofactor such as FAD to catalyze a non-redox reaction. With the goal of undertaking a structural investigation of the enzyme, we have characterized recombinant ADPS from different sources: Cavia porcellus, Drosophila melanogaster, Homo sapiens, Archaeoglobus fulgidus, and Dictyostelium discoideum. The protein from D. discoideum was found to be the best candidate for structural studies. We describe a protocol for expression and purification of large amounts of pure and stable enzyme in its holo (FAD-bound) form. A search of deletion mutants identified a protein variant that forms crystals diffracting up to 2A resolution.
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Affiliation(s)
- Adelia Razeto
- Dipartimento di Genetica e Microbiologia, Università di Pavia, via Ferrata 1, 27100 Pavia, Italy
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668
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Ashibe B, Hirai T, Higashi K, Sekimizu K, Motojima K. Dual subcellular localization in the endoplasmic reticulum and peroxisomes and a vital role in protecting against oxidative stress of fatty aldehyde dehydrogenase are achieved by alternative splicing. J Biol Chem 2007; 282:20763-73. [PMID: 17510064 DOI: 10.1074/jbc.m611853200] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fatty aldehyde dehydrogenase (FALDH, ALDH3A2) is thought to be involved in the degradation of phytanic acid, a saturated branched chain fatty acid derived from chlorophyll. However, the identity, subcellular distribution, and physiological roles of FALDH are unclear because several variants produced by alternative splicing are present in varying amounts at different subcellular locations. Subcellular fractionation experiments do not provide a clear-cut conclusion because of the incomplete separation of organelles. We established human cell lines heterologously expressing mouse FALDH from each cDNA without tagging under the control of an inducible promoter and detected the variant FALDH proteins using a mouse FALDH-specific antibody. One variant, FALDH-V, was exclusively detected in peroxisomal membranes. Human FALDH-V with an amino-terminal Myc sequence also localized to peroxisomes. The most dominant form, FALDH-N, and other variants examined, however, were distributed in the endoplasmic reticulum. A gas chromatography-mass spectrometry-based analysis of metabolites in FALDH-expressing cells incubated with phytol or phytanic acid showed that FALDH-V, not FALDH-N, is the key aldehyde dehydrogenase in the degradation pathway and that it protects peroxisomes from oxidative stress. In contrast, both FALDHs had a protective effect against oxidative stress induced by a model aldehyde for lipid peroxidation, dodecanal. These results suggest that FALDH variants are produced by alternative splicing and share an important role in protecting against oxidative stress in an organelle-specific manner.
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Affiliation(s)
- Bunichiro Ashibe
- Department of Biochemistry, Meiji Pharmaceutical University, Noshio 2-522-1, Kiyose, Tokyo 204-8588, Japan
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669
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Negishi K, Noiri E, Sugaya T, Li S, Megyesi J, Nagothu K, Portilla D. A role of liver fatty acid-binding protein in cisplatin-induced acute renal failure. Kidney Int 2007; 72:348-58. [PMID: 17495861 DOI: 10.1038/sj.ki.5002304] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Previous studies from our laboratory showed that increased fatty acid oxidation by the kidney is cytoprotective during cisplatin (CP)-mediated nephrotoxicity. In this study, we determined the effects of CP and fibrates on peroxisome proliferation and the expression of liver fatty acid-binding protein (L-FABP) in normal mice, and in mice transgenically overexpressing human L-FABP (h-L-FABP). Labeling of peroxisomes demonstrated reduced peroxisomal staining in the proximal tubule of CP-treated mice compared with control mice. There was increased peroxisomal labeling in the proximal tubules of both control and CP-treated mice when either was treated with fibrate; a known peroxisome proliferator-activated receptor-alpha ligand. L-FABP protein expression, not detected in control or CP-treated mice, was significantly increased in the proximal tubules of fibrate-treated mice of either group. In the transgenic mice, CP increased the shedding of h-L-FABP in the urine, which was decreased by fibrate as was the acute renal failure. A cytosolic pattern of h-L-FABP expression was found in the proximal tubules of untreated transgenic mice with a nuclear presence in CP-treated mice. Fibrate pretreatment restored the cytosolic expression pattern in CP-treated mice. Our study shows that fibrate may improve CP-induced acute renal failure due to both peroxisome proliferation and increased L-FABP in the cytosol of the proximal tubule.
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Affiliation(s)
- K Negishi
- Department of Nephrology and Endocrinology, University of Tokyo, Tokyo, Japan
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670
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Kim MC, Kim TH, Park JH, Moon BY, Lee CH, Cho SH. Expression of rice acyl-CoA oxidase isoenzymes in response to wounding. JOURNAL OF PLANT PHYSIOLOGY 2007; 164:665-8. [PMID: 17000027 DOI: 10.1016/j.jplph.2006.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2006] [Revised: 08/09/2006] [Accepted: 08/18/2006] [Indexed: 05/10/2023]
Abstract
To elucidate the role of acyl-CoA oxidase (ACX; EC 1.3.3.6) in plants, the expression patterns of rice ACXs in response to wounding were characterized. Three isogenes of ACX were identified in the rice genome. The deduced proteins of OsACX1, OsACX2 and OsACX3 consist of 669, 699 and 685 amino acid residues, respectively. The results from reverse transcriptase-PCR indicate that OsACX1 is expressed in leaves, stems, and roots, but was barely detectable in germinating seeds. OsACX2 was expressed predominantly in seeds. Only OsACX1 was upregulated by wounding, both locally and systemically. The expression of OsACX2 and OsACX3 remained unchanged. It is suggested that OsACX2 is involved in providing germinating seeds with sugar and energy, while OsACX1 plays a role in the synthesis of jasmonic acid in response to wounding.
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Affiliation(s)
- Moon Chul Kim
- Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea
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671
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Antonenkov VD, Ohlmeier S, Sormunen RT, Hiltunen JK. UK114, a YjgF/Yer057p/UK114 family protein highly conserved from bacteria to mammals, is localized in rat liver peroxisomes. Biochem Biophys Res Commun 2007; 357:252-7. [PMID: 17416349 DOI: 10.1016/j.bbrc.2007.03.136] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Accepted: 03/22/2007] [Indexed: 11/25/2022]
Abstract
Mammalian UK114 belongs to a highly conserved family of proteins with unknown functions. Although it is believed that UK114 is a cytosolic or mitochondrial protein there is no detailed study of its intracellular localization. Using analytical subcellular fractionation, electron microscopic colloidal gold technique, and two-dimensional gel electrophoresis of peroxisomal matrix proteins combined with mass spectrometric analysis we show here that a large portion of UK114 is present in rat liver peroxisomes. The peroxisomal UK114 is a soluble matrix protein and it is not inducible by the peroxisomal proliferator clofibrate. The data predict involvement of UK114 in peroxisomal metabolism.
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Affiliation(s)
- Vasily D Antonenkov
- Department of Biochemistry, Biocenter Oulu, University of Oulu, Linnanmaa, P.O. Box 3000, FIN-90014 Oulu, Finland.
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672
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Carvalho AF, Grou CP, Pinto MP, Alencastre IS, Costa-Rodrigues J, Fransen M, Sá-Miranda C, Azevedo JE. Functional characterization of two missense mutations in Pex5p - C11S and N526K. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2007; 1773:1141-8. [PMID: 17532062 DOI: 10.1016/j.bbamcr.2007.04.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2007] [Revised: 04/19/2007] [Accepted: 04/19/2007] [Indexed: 11/29/2022]
Abstract
Most newly synthesized peroxisomal proteins are targeted to the organelle by Pex5p, the peroxisomal cycling receptor. Pex5p interacts with these proteins in the cytosol, transports them to the peroxisomal docking/translocation machinery and promotes their translocation across the organelle membrane. Finally, Pex5p is recycled back to the cytosol in order to catalyse additional rounds of transportation. Although several properties of this protein sorting pathway have been recently uncovered, we are still far from comprehending many of its basic principles. Here, we describe the mechanistic implications of two single-amino acid substitutions in Pex5p. The first mutation characterized, Cys11Ser, blocks the recycling of Pex5p back into the cytosol at the step in which stage 2 Pex5p is converted into stage 3 Pex5p. The mutation Asn526Lys, previously described in a child with neonatal adrenoleukodystrophy and shown to abolish the PTS1-binding capacity of Pex5p, results in a Pex5p protein exhibiting import capacity. Protease assays suggest that the Asn526Lys mutation causes conformational alterations at the N-terminal half of Pex5p mimicking the ones induced by binding of a PTS1-containing peptide to the normal peroxin. The implications of these findings on the mechanism of protein translocation across the peroxisomal membrane are discussed.
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673
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Vucetic S, Xie H, Iakoucheva LM, Oldfield CJ, Dunker AK, Obradovic Z, Uversky VN. Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions. J Proteome Res 2007; 6:1899-916. [PMID: 17391015 PMCID: PMC2588346 DOI: 10.1021/pr060393m] [Citation(s) in RCA: 193] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biologically active proteins without stable ordered structure (i.e., intrinsically disordered proteins) are attracting increased attention. Functional repertoires of ordered and disordered proteins are very different, and the ability to differentiate whether a given function is associated with intrinsic disorder or with a well-folded protein is crucial for modern protein science. However, there is a large gap between the number of proteins experimentally confirmed to be disordered and their actual number in nature. As a result, studies of functional properties of confirmed disordered proteins, while helpful in revealing the functional diversity of protein disorder, provide only a limited view. To overcome this problem, a bioinformatics approach for comprehensive study of functional roles of protein disorder was proposed in the first paper of this series (Xie, H.; Vucetic, S.; Iakoucheva, L. M.; Oldfield, C. J.; Dunker, A. K.; Obradovic, Z.; Uversky, V. N. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J. Proteome Res. 2007, 5, 1882-1898). Applying this novel approach to Swiss-Prot sequences and functional keywords, we found over 238 and 302 keywords to be strongly positively or negatively correlated, respectively, with long intrinsically disordered regions. This paper describes approximately 90 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes, and coding sequence diversities possessing strong positive and negative correlation with long disordered regions.
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Affiliation(s)
- Slobodan Vucetic
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
| | - Hongbo Xie
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
| | - Lilia M. Iakoucheva
- Laboratory of Statistical Genetics, The Rockefeller University, New York, NY 10021
| | - Christopher J. Oldfield
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University, School of Medicine, Indianapolis, IN 46202
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University, School of Medicine, Indianapolis, IN 46202
| | - Zoran Obradovic
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
| | - Vladimir N. Uversky
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University, School of Medicine, Indianapolis, IN 46202
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- CORRESPONDING AUTHOR FOOTNOTE: Correspondence should be addressed to: Vladimir N. Uversky, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS#4021, Indianapolis, IN 46202, USA; Phone: 317-278-9194; Fax: 317-274-4686; E-mail:
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674
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Visser WF, van Roermund CWT, Ijlst L, Waterham HR, Wanders RJA. Demonstration of bile acid transport across the mammalian peroxisomal membrane. Biochem Biophys Res Commun 2007; 357:335-40. [PMID: 17416343 DOI: 10.1016/j.bbrc.2007.03.083] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Accepted: 03/06/2007] [Indexed: 10/23/2022]
Abstract
It is well established that peroxisomes play a crucial role in de novo bile acid biosynthesis. The primary bile acids resulting from peroxisomal beta-oxidation are conjugated to either glycine or taurine in the peroxisomal lumen by a bile acid aminotransferase (BAT). These conjugated bile acids are subsequently secreted into the bile. In this paper we show that the export of glycine- and taurine-conjugated bile acids from mammalian peroxisomes proceeds via specific transporter. The transport activity of this protein was detected by reconstitution of peroxisomal membrane proteins in liposomes and measuring the uptake of radiolabeled substrates into these proteoliposomes. The transporter was further characterized using this assay, which led to the identification of DIDS as an inhibitor of the peroxisomal bile-acid transporter, and allowed us to establish some kinetic parameters for the transport activity.
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Affiliation(s)
- Wouter F Visser
- University of Amsterdam, Academic Medical Centre, Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, F0-224, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands.
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675
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Maynard EL, Berg JM. Quantitative analysis of peroxisomal targeting signal type-1 binding to wild-type and pathogenic mutants of Pex5p supports an affinity threshold for peroxisomal protein targeting. J Mol Biol 2007; 368:1259-66. [PMID: 17399738 DOI: 10.1016/j.jmb.2007.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2006] [Accepted: 03/02/2007] [Indexed: 11/26/2022]
Abstract
Peroxisomal biogenesis disorders (PBDs) are caused by mutations in 12 distinct genes that encode the components of the peroxisome assembly machinery. Three mutations in the gene encoding Pex5p, the peroxisomal targeting signal type-1 (PTS1) receptor, have been reported, each associated with a disorder of the Zellweger spectrum of different severity. Here, we report studies of the affinities of mutated forms of Pex5p for a series of PTS1 peptides and conclude that PTS1-affinity reductions are correlated with disease severity and cell biological phenotype. A quantitative model has been developed that allows estimation of the dissociation constants for complexes with a wide range of PTS1 sequences bound to wild-type and mutant Pex5p. In the context of this model, the binding measurements suggest that no PTS1-containing proteins are targeted by Pex5p(N489K) and only a relatively small subset of PTS1-containing proteins with the highest affinity for Pex5p are targeted to peroxisomes by Pex5p(S563W). Furthermore, the results of the analysis are consistent with an approximate dissociation constant threshold near 500 nM required for efficient protein targeting to peroxisomes.
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Affiliation(s)
- Ernest L Maynard
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
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676
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Schumann U, Prestele J, O'Geen H, Brueggeman R, Wanner G, Gietl C. Requirement of the C3HC4 zinc RING finger of the Arabidopsis PEX10 for photorespiration and leaf peroxisome contact with chloroplasts. Proc Natl Acad Sci U S A 2007; 104:1069-74. [PMID: 17215364 PMCID: PMC1783365 DOI: 10.1073/pnas.0610402104] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Indexed: 11/18/2022] Open
Abstract
Plant peroxisomes perform multiple vital metabolic processes including lipid mobilization in oil-storing seeds, photorespiration, and hormone biosynthesis. Peroxisome biogenesis requires the function of peroxin (PEX) proteins, including PEX10, a C(3)HC(4) Zn RING finger peroxisomal membrane protein. Loss of function of PEX10 causes embryo lethality at the heart stage. We investigated the function of PEX10 with conditional sublethal mutants. Four T-DNA insertion lines expressing pex10 with a dysfunctional RING finger were created in an Arabidopsis WT background (DeltaZn plants). They could be normalized by growth in an atmosphere of high CO(2) partial pressure, indicating a defect in photorespiration. beta-Oxidation in mutant glyoxysomes was not affected. However, an abnormal accumulation of the photorespiratory metabolite glyoxylate, a lowered content of carotenoids and chlorophyll a and b, and a decreased quantum yield of photosystem II were detected under normal atmosphere, suggesting impaired leaf peroxisomes. Light and transmission electron microscopy demonstrated leaf peroxisomes of the DeltaZn plants to be more numerous, multilobed, clustered, and not appressed to the chloroplast envelope as in WT. We suggest that inactivation of the RING finger domain in PEX10 has eliminated protein interaction required for attachment of peroxisomes to chloroplasts and movement of metabolites between peroxisomes and chloroplasts.
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Affiliation(s)
- Uwe Schumann
- *Lehrstuhl für Botanik, Technische Universität München, Am Hochanger 4, D-85350 Freising, Germany
| | - Jakob Prestele
- *Lehrstuhl für Botanik, Technische Universität München, Am Hochanger 4, D-85350 Freising, Germany
| | | | - Robert Brueggeman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164; and
| | - Gerhard Wanner
- Lehrstuhl für Botanik, Ludwig-Maximilian-Universität, Menzinger Strasse 67, D-80638 München, Germany
| | - Christine Gietl
- *Lehrstuhl für Botanik, Technische Universität München, Am Hochanger 4, D-85350 Freising, Germany
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677
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Visser WF, van Roermund CWT, Ijlst L, Waterham HR, Wanders RJA. Metabolite transport across the peroxisomal membrane. Biochem J 2007; 401:365-75. [PMID: 17173541 PMCID: PMC1820816 DOI: 10.1042/bj20061352] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Accepted: 09/28/2006] [Indexed: 10/23/2022]
Abstract
In recent years, much progress has been made with respect to the unravelling of the functions of peroxisomes in metabolism, and it is now well established that peroxisomes are indispensable organelles, especially in higher eukaryotes. Peroxisomes catalyse a number of essential metabolic functions including fatty acid beta-oxidation, ether phospholipid biosynthesis, fatty acid alpha-oxidation and glyoxylate detoxification. The involvement of peroxisomes in these metabolic pathways necessitates the transport of metabolites in and out of peroxisomes. Recently, considerable progress has been made in the characterization of metabolite transport across the peroxisomal membrane. Peroxisomes posses several specialized transport systems to transport metabolites. This is exemplified by the identification of a specific transporter for adenine nucleotides and several half-ABC (ATP-binding cassette) transporters which may be present as hetero- and homo-dimers. The nature of the substrates handled by the different ABC transporters is less clear. In this review we will describe the current state of knowledge of the permeability properties of the peroxisomal membrane.
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Key Words
- fatty acid
- genetic disease
- metabolite
- peroxisome
- transport
- zellweger syndrome
- abc, atp-binding cassette
- cpt, carnitine palmitoyltransferase
- dhas, dihydroxyacetone synthetase
- dhca, dihydroxycholestanoic acid
- dnp, 2,4-dinitrophenol
- g3pdh, glycerol-3-phosphate dehydrogenase
- got, glutamate:aspartate aminotransferase
- lacs, long-chain acyl-coa synthetase
- mcf, mitochondrial carrier family
- mcfa, medium-chain fatty acid
- mct, monocarboxylate transporter
- mdh, malate dehydrogenase
- m-lp, mpv17-like protein
- pmp, peroxisomal membrane protein
- ros, reactive oxygen species
- scamc, short calcium-binding mitochondrial carrier
- thca, trihydroxycholestanoic acid
- xald, x-linked adrenoleukodystrophy
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Affiliation(s)
- Wouter F Visser
- University of Amsterdam, Academic Medical Centre, Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, F0-224, Meibergdreef 9, Amsterdam, 1105 AZ The Netherlands.
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678
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Antonenkov VD, Hiltunen JK. Peroxisomal membrane permeability and solute transfer. BIOCHIMICA ET BIOPHYSICA ACTA 2006; 1763:1697-706. [PMID: 17045662 DOI: 10.1016/j.bbamcr.2006.08.044] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Revised: 08/16/2006] [Accepted: 08/18/2006] [Indexed: 10/24/2022]
Abstract
The review is dedicated to recent progress in the study of peroxisomal membrane permeability to solutes which has been a matter of debate for more than 40 years. Apparently, the mammalian peroxisomal membrane is freely permeable to small solute molecules owing to the presence of pore-forming channels. However, the membrane forms a permeability barrier for 'bulky' solutes including cofactors (NAD/H, NADP/H, CoA, and acetyl/acyl-CoA esters) and ATP. Therefore, peroxisomes need specific protein transporters to transfer these compounds across the membrane. Recent electrophysiological studies have revealed channel-forming activities in the mammalian peroxisomal membrane. The possible involvement of the channels in the transfer of small metabolites and in the formation of peroxisomal shuttle systems is described.
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Affiliation(s)
- Vasily D Antonenkov
- Department of Biochemistry and Biocenter Oulu, University of Oulu, P.O. Box 3000, FIN-90014 Oulu, Finland.
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679
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Rottensteiner H, Theodoulou FL. The ins and outs of peroxisomes: Co-ordination of membrane transport and peroxisomal metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:1527-40. [PMID: 17010456 DOI: 10.1016/j.bbamcr.2006.08.012] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Revised: 08/15/2006] [Accepted: 08/18/2006] [Indexed: 11/28/2022]
Abstract
Peroxisomes perform a range of metabolic functions which require the movement of substrates, co-substrates, cofactors and metabolites across the peroxisomal membrane. In this review, we discuss the evidence for and against specific transport systems involved in peroxisomal metabolism and how these operate to co-ordinate biochemical reactions within the peroxisome with those in other compartments of the cell.
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Affiliation(s)
- Hanspeter Rottensteiner
- Medical Faculty of the Ruhr-University of Bochum, Department of Physiological Chemistry, Section of Systems Biochemistry, 44780 Bochum, Germany.
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680
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Wanders RJA, Visser WF, van Roermund CWT, Kemp S, Waterham HR. The peroxisomal ABC transporter family. Pflugers Arch 2006; 453:719-34. [PMID: 17039367 DOI: 10.1007/s00424-006-0142-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Accepted: 07/26/2006] [Indexed: 10/24/2022]
Abstract
This review describes the current state of knowledge about the ABCD family of peroxisomal half adenosine-triphosphate-binding cassette (ABC) transporters. ABCDs are predicted to be present in a variety of eukaryotic organisms, although at present, only ABCDs in the yeast Saccharomyces cerevisiae, the plant Arabidopsis thaliana, and different mammalian species have been identified and characterized to any significant extent. The functional role of none of these ABCDs has been established definitively and awaits successful reconstitution of ABCDs, either as homo- or heterodimers into liposomes, followed by transport studies. Data obtained in S. cerevisiae suggest that the two ABCDs, which have been identified in this organism, form a heterodimer, which actually transports acyl coenzyme A esters across the peroxisomal membrane. In mammals, four ABCDs have been identified, of which one [adrenoleukodystrophy protein (ALDP)] has been implicated in the transport of the coenzyme A esters of very-long-chain fatty acids. Mutations in the gene (ABCD1) encoding ALDP are the cause of a severe X-linked disease, called X-linked adrenoleukodystrophy. The availability of mutant mice in which Abcd1, Abcd2, or Abcd3 have been disrupted will help to resolve the true role of the peroxisomal half-ABC transporters.
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Affiliation(s)
- Ronald J A Wanders
- Department of Clinical Chemistry and Pediatrics, Emma Children's Hospital, Laboratory Genetic Metabolic Diseases, University of Amsterdam, Academic Medical Center, Amsterdam, The Netherlands.
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681
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Azevedo JE, Schliebs W. Pex14p, more than just a docking protein. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:1574-84. [PMID: 17046076 DOI: 10.1016/j.bbamcr.2006.09.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2006] [Revised: 08/29/2006] [Accepted: 09/04/2006] [Indexed: 01/01/2023]
Abstract
After binding newly synthesized peroxisomal matrix proteins in the cytosol, the second task of Pex5p, the peroxisomal cycling receptor, is to carry these proteins to the peroxisomal membrane. Defining the nature of the events that occur at this membrane system and which ultimately result in the translocation of the cargo proteins into the matrix of the organelle and in the recycling of Pex5p back to the cytosol, is one of the major goals of the research in this field. Presently, it is generally accepted that all these steps are promoted by a large protein complex embedded in the peroxisomal membrane. This docking/translocation machinery or importomer, as it is often called, comprises many different peroxins of which one of the best characterized is Pex14p. Here, we review data regarding this membrane peroxin with emphasis on the interactions that it establishes with Pex5p. The available evidence suggests that the key to understand how folded proteins are capable of passing an apparently impermeable membrane may largely reside in this pair of peroxins.
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Affiliation(s)
- Jorge E Azevedo
- Instituto de Biologia Molecular e Celular (IBMC) and Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Univ. do Porto, Portugal.
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682
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Ferdinandusse S, Houten SM. Peroxisomes and bile acid biosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:1427-40. [PMID: 17034878 DOI: 10.1016/j.bbamcr.2006.09.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Revised: 08/24/2006] [Accepted: 09/01/2006] [Indexed: 01/11/2023]
Abstract
Peroxisomes play an important role in the biosynthesis of bile acids because a peroxisomal beta-oxidation step is required for the formation of the mature C24-bile acids from C27-bile acid intermediates. In addition, de novo synthesized bile acids are conjugated within the peroxisome. In this review, we describe the current state of knowledge about all aspects of peroxisomal function in bile acid biosynthesis in health and disease. The peroxisomal enzymes involved in the synthesis of bile acids have been identified, and the metabolic and pathologic consequences of a deficiency of one of these enzymes are discussed, including the potential role of nuclear receptors therein.
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Affiliation(s)
- Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, F0-224 Academic Medical Center at the University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands.
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683
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Poirier Y, Antonenkov VD, Glumoff T, Hiltunen JK. Peroxisomal beta-oxidation--a metabolic pathway with multiple functions. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:1413-26. [PMID: 17028011 DOI: 10.1016/j.bbamcr.2006.08.034] [Citation(s) in RCA: 333] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Revised: 08/21/2006] [Accepted: 08/23/2006] [Indexed: 12/15/2022]
Abstract
Fatty acid degradation in most organisms occurs primarily via the beta-oxidation cycle. In mammals, beta-oxidation occurs in both mitochondria and peroxisomes, whereas plants and most fungi harbor the beta-oxidation cycle only in the peroxisomes. Although several of the enzymes participating in this pathway in both organelles are similar, some distinct physiological roles have been uncovered. Recent advances in the structural elucidation of numerous mammalian and yeast enzymes involved in beta-oxidation have shed light on the basis of the substrate specificity for several of them. Of particular interest is the structural organization and function of the type 1 and 2 multifunctional enzyme (MFE-1 and MFE-2), two enzymes evolutionarily distant yet catalyzing the same overall enzymatic reactions but via opposite stereochemistry. New data on the physiological roles of the various enzymes participating in beta-oxidation have been gathered through the analysis of knockout mutants in plants, yeast and animals, as well as by the use of polyhydroxyalkanoate synthesis from beta-oxidation intermediates as a tool to study carbon flux through the pathway. In plants, both forward and reverse genetics performed on the model plant Arabidopsis thaliana have revealed novel roles for beta-oxidation in the germination process that is independent of the generation of carbohydrates for growth, as well as in embryo and flower development, and the generation of the phytohormone indole-3-acetic acid and the signal molecule jasmonic acid.
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Affiliation(s)
- Yves Poirier
- Department of Plant Molecular Biology, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland
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684
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Baes M, Van Veldhoven PP. Generalised and conditional inactivation of Pex genes in mice. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:1785-93. [PMID: 17007945 DOI: 10.1016/j.bbamcr.2006.08.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Revised: 08/17/2006] [Accepted: 08/18/2006] [Indexed: 12/28/2022]
Abstract
During the past 10 years, several Pex genes have been knocked out in the mouse with the purpose to generate models to study the pathogenesis of peroxisome biogenesis disorders and/or to investigate the physiological importance of the Pex proteins. More recently, mice with selective inactivation of a Pex gene in particular cell types were created. The metabolic abnormalities in peroxisome deficient mice paralleled to a large extent those of Zellweger patients. Several but not all of the clinical and histological features reported in patients also occurred in peroxisome deficient mice as for example hypotonia, cortical and cerebellar malformations, endochondral ossification defects, hepatomegaly, liver fibrosis and ultrastructural abnormalities of mitochondria in hepatocytes. Although the molecular origins of the observed pathologies have not yet been resolved, several new insights on the importance of peroxisomes in different tissues have emerged.
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Affiliation(s)
- Myriam Baes
- Laboratory for Cell Metabolism, Campus Gasthuisberg Onderwijs en Navorsing II, bus 823 Herestraat 49 B-3000, Department of Pharmaceutical Sciences, Katholieke Universiteit Leuven, Leuven, Belgium.
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685
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Barreto L, Garcerá A, Jansson K, Sunnerhagen P, Herrero E. A peroxisomal glutathione transferase of Saccharomyces cerevisiae is functionally related to sulfur amino acid metabolism. EUKARYOTIC CELL 2006; 5:1748-59. [PMID: 16936141 PMCID: PMC1595348 DOI: 10.1128/ec.00216-06] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Saccharomyces cerevisiae cells contain three omega-class glutathione transferases with glutaredoxin activity (Gto1, Gto2, and Gto3), in addition to two glutathione transferases (Gtt1 and Gtt2) not classifiable into standard classes. Gto1 is located at the peroxisomes, where it is targeted through a PTS1-type sequence, whereas Gto2 and Gto3 are in the cytosol. Among the GTO genes, GTO2 shows the strongest induction of expression by agents such as diamide, 1-chloro-2,4-dinitrobenzene, tert-butyl hydroperoxide or cadmium, in a manner that is dependent on transcriptional factors Yap1 and/or Msn2/4. Diamide and 1-chloro-2,4-dinitrobenzene (causing depletion of reduced glutathione) also induce expression of GTO1 over basal levels. Phenotypic analyses with single and multiple mutants in the S. cerevisiae glutathione transferase genes show that, in the absence of Gto1 and the two Gtt proteins, cells display increased sensitivity to cadmium. A gto1-null mutant also shows growth defects on oleic acid-based medium, which is indicative of abnormal peroxisomal functions, and altered expression of genes related to sulfur amino acid metabolism. As a consequence, growth of the gto1 mutant is delayed in growth medium without lysine, serine, or threonine, and the mutant cells have low levels of reduced glutathione. The role of Gto1 at the S. cerevisiae peroxisomes could be related to the redox regulation of the Str3 cystathionine beta-lyase protein. This protein is also located at the peroxisomes in S. cerevisiae, where it is involved in transulfuration of cysteine into homocysteine, and requires a conserved cysteine residue for its biological activity.
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Affiliation(s)
- Lina Barreto
- Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, Universitat de Lleida, Montserrat Roig 2, 25008 Lleida, Spain
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686
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Abstract
Eight distinct inherited disorders have been linked to different enzyme defects in the isoprenoid/cholesterol biosynthetic pathway following the finding of abnormally increased levels of intermediate metabolites in patients and confirmed by the demonstration of disease-causing mutations in genes encoding the implicated enzymes. Patients afflicted with these disorders are characterized by multiple morphogenic and congenital anomalies including internal organ, skeletal and/or skin abnormalities underlining an important role for cholesterol in human embryogenesis and development. The etiology of the underlying pathophysiology may involve multiple affected processes due to lowered cholesterol and/or the elevated, teratogenic levels of the intermediate sterol precursors.
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Affiliation(s)
- Hans R Waterham
- Laboratory Genetic Metabolic Diseases, F0-224, Department of Pediatrics/Emma Children's Hospital, Academic Medical Center, University of Amsterdam, P.O. Box 22700, 1100 DE Amsterdam, The Netherlands.
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687
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Abstract
Peroxisomes are ubiquitous subcellular organelles, which are highly dynamic and display large plasticity in response to cellular and environmental conditions. Novel proteins and pathways that mediate and control peroxisome formation, growth, and division continue to be discovered, and the cellular machineries that act together to regulate peroxisome number and size are under active investigation. Here, advances in the field of peroxisomal dynamics and proliferation in mammals and yeast are reviewed. The authors address the signals, conditions, and proteins that affect, regulate, and control the number and size of this essential organelle, especially the components involved in the division of peroxisomes. Special emphasis is on the function of dynamin-related proteins (DRPs), on Fis1, a putative adaptor for DRPs, on the role of the Pex11 family of peroxisomal membrane proteins, and the cytoskeleton.
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Affiliation(s)
- Michael Schrader
- Department of Cell Biology and Cell Pathology, University of Marburg, 35037 Marburg, Germany
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