1
|
Enkler L, Szentgyörgyi V, Pennauer M, Prescianotto-Baschong C, Riezman I, Wiesyk A, Avraham RE, Spiess M, Zalckvar E, Kucharczyk R, Riezman H, Spang A. Arf1 coordinates fatty acid metabolism and mitochondrial homeostasis. Nat Cell Biol 2023; 25:1157-1172. [PMID: 37400497 PMCID: PMC10415182 DOI: 10.1038/s41556-023-01180-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/05/2023] [Indexed: 07/05/2023]
Abstract
Lipid mobilization through fatty acid β-oxidation is a central process essential for energy production during nutrient shortage. In yeast, this catabolic process starts in the peroxisome from where β-oxidation products enter mitochondria and fuel the tricarboxylic acid cycle. Little is known about the physical and metabolic cooperation between these organelles. Here we found that expression of fatty acid transporters and of the rate-limiting enzyme involved in β-oxidation is decreased in cells expressing a hyperactive mutant of the small GTPase Arf1, leading to an accumulation of fatty acids in lipid droplets. Consequently, mitochondria became fragmented and ATP synthesis decreased. Genetic and pharmacological depletion of fatty acids phenocopied the arf1 mutant mitochondrial phenotype. Although β-oxidation occurs in both mitochondria and peroxisomes in mammals, Arf1's role in fatty acid metabolism is conserved. Together, our results indicate that Arf1 integrates metabolism into energy production by regulating fatty acid storage and utilization, and presumably organelle contact sites.
Collapse
Affiliation(s)
| | | | | | | | - Isabelle Riezman
- Department of Biochemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Aneta Wiesyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Reut Ester Avraham
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | | | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Howard Riezman
- Department of Biochemistry, NCCR Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Anne Spang
- Biozentrum, University of Basel, Basel, Switzerland.
| |
Collapse
|
2
|
Bittner E, Stehlik T, Freitag J. Sharing the wealth: The versatility of proteins targeted to peroxisomes and other organelles. Front Cell Dev Biol 2022; 10:934331. [PMID: 36225313 PMCID: PMC9549241 DOI: 10.3389/fcell.2022.934331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Peroxisomes are eukaryotic organelles with critical functions in cellular energy and lipid metabolism. Depending on the organism, cell type, and developmental stage, they are involved in numerous other metabolic and regulatory pathways. Many peroxisomal functions require factors also relevant to other cellular compartments. Here, we review proteins shared by peroxisomes and at least one different site within the cell. We discuss the mechanisms to achieve dual targeting, their regulation, and functional consequences. Characterization of dual targeting is fundamental to understand how peroxisomes are integrated into the metabolic and regulatory circuits of eukaryotic cells.
Collapse
|
3
|
Umnajkitikorn K, Sade N, Rubio Wilhelmi MDM, Gilbert ME, Blumwald E. Silencing of OsCV (chloroplast vesiculation) maintained photorespiration and N assimilation in rice plants grown under elevated CO 2. PLANT, CELL & ENVIRONMENT 2020; 43:920-933. [PMID: 31953871 DOI: 10.1111/pce.13723] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 12/19/2019] [Accepted: 01/13/2020] [Indexed: 05/15/2023]
Abstract
High CO2 concentrations stimulate net photosynthesis by increasing CO2 substrate availability for Rubisco, simultaneously suppressing photorespiration. Previously, we reported that silencing the chloroplast vesiculation (cv) gene in rice increased source fitness, through the maintenance of chloroplast stability and the expression of photorespiration-associated genes. Because high atmospheric CO2 conditions diminished photorespiration, we tested whether CV silencing might be a viable strategy to improve the effects of high CO2 on grain yield and N assimilation in rice. Under elevated CO2 , OsCV expression was induced, and OsCV was targeted to peroxisomes where it facilitated the removal of OsPEX11-1 from the peroxisome and delivered it to the vacuole for degradation. This process correlated well with the reduction in the number of peroxisomes, the decreased catalase activity and the increased H2 O2 content in wild-type plants under elevated CO2 . At elevated CO2 , CV-silenced rice plants maintained peroxisome proliferation and photorespiration and displayed higher N assimilation than wild-type plants. This was supported by higher activity of enzymes involved in NO3- and NH4+ assimilation and higher total and seed protein contents. Co-immunoprecipitation of OsCV-interacting proteins suggested that, similar to its role in chloroplast protein turnover, OsCV acted as a scaffold, binding peroxisomal proteins.
Collapse
Affiliation(s)
- Kamolchanok Umnajkitikorn
- Department of Plant Sciences, University of California, Davis, CA
- School of Crop Production Technology, Institute of Agricultural Technology, Nakhon Ratchasima, Thailand
| | - Nir Sade
- Department of Molecular Biology & Ecology of Plants, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | | | | | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, CA
| |
Collapse
|
4
|
Kunze M. The type-2 peroxisomal targeting signal. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1867:118609. [PMID: 31751594 DOI: 10.1016/j.bbamcr.2019.118609] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/08/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022]
Abstract
The type-2 peroxisomal targeting signal (PTS2) is one of two peptide motifs destining soluble proteins for peroxisomes. This signal acts as amphiphilic α-helix exposing the side chains of all conserved residues to the same side. PTS2 motifs are recognized by a bipartite protein complex consisting of the receptor PEX7 and a co-receptor. Cargo-loaded receptor complexes are translocated across the peroxisomal membrane by a transient pore and inside peroxisomes, cargo proteins are released and processed in many, but not all species. The components of the bipartite receptor are re-exported into the cytosol by a ubiquitin-mediated and ATP-driven export mechanism. Structurally, PTS2 motifs resemble other N-terminal targeting signals, whereas the functional relation to the second peroxisomal targeting signal (PTS1) is unclear. Although only a few PTS2-carrying proteins are known in humans, subjects lacking a functional import mechanism for these proteins suffer from the severe inherited disease rhizomelic chondrodysplasia punctata.
Collapse
Affiliation(s)
- Markus Kunze
- Medical University of Vienna, Center for Brain Research, Department of Pathobiology of the Nervous System, Spitalgasse 4, 1090 Vienna, Austria.
| |
Collapse
|
5
|
Exner T, Romero-Brey I, Yifrach E, Rivera-Monroy J, Schrul B, Zouboulis CC, Stremmel W, Honsho M, Bartenschlager R, Zalckvar E, Poppelreuther M, Füllekrug J. An alternative membrane topology permits lipid droplet localization of peroxisomal fatty acyl-CoA reductase 1. J Cell Sci 2019; 132:jcs.223016. [PMID: 30745342 DOI: 10.1242/jcs.223016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 02/01/2019] [Indexed: 01/02/2023] Open
Abstract
Fatty acyl-CoA reductase 1 (Far1) is a ubiquitously expressed peroxisomal membrane protein that generates the fatty alcohols required for the biosynthesis of ether lipids. Lipid droplet localization of exogenously expressed and endogenous human Far1 was observed by fluorescence microscopy under conditions of increased triglyceride synthesis in tissue culture cells. This unexpected finding was supported further by correlative light electron microscopy and subcellular fractionation. Selective permeabilization, protease sensitivity and N-glycosylation tagging suggested that Far1 is able to assume two different membrane topologies, differing in the orientation of the short hydrophilic C-terminus towards the lumen or the cytosol, respectively. Two closely spaced hydrophobic domains are contained within the C-terminal region. When analyzed separately, the second domain was sufficient for the localization of a fluorescent reporter to lipid droplets. Targeting of Far1 to lipid droplets was not impaired in either Pex19 or ASNA1 (also known as TRC40) CRISPR/Cas9 knockout cells. In conclusion, our data suggest that Far1 is a novel member of the rather exclusive group of dual topology membrane proteins. At the same time, Far1 shows lipid metabolism-dependent differential subcellular localizations to peroxisomes and lipid droplets.
Collapse
Affiliation(s)
- Tarik Exner
- Molecular Cell Biology Laboratory Internal Medicine IV, University of Heidelberg, 69120 Heidelberg, Germany
| | - Inés Romero-Brey
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Eden Yifrach
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Jhon Rivera-Monroy
- Department of Molecular Biology, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Bianca Schrul
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Saarland University, 66421 Homburg/Saar, Germany
| | - Christos C Zouboulis
- Departments of Dermatology, Venereology, Allergology and Immunology, Dessau Medical Center, Brandenburg Medical School Theodor Fontane, 06847 Dessau, Germany
| | - Wolfgang Stremmel
- Molecular Cell Biology Laboratory Internal Medicine IV, University of Heidelberg, 69120 Heidelberg, Germany
| | - Masanori Honsho
- Medical Institute of Bioregulation, Kyushu University, 812-8582 Fukuoka, Japan
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Margarete Poppelreuther
- Molecular Cell Biology Laboratory Internal Medicine IV, University of Heidelberg, 69120 Heidelberg, Germany
| | - Joachim Füllekrug
- Molecular Cell Biology Laboratory Internal Medicine IV, University of Heidelberg, 69120 Heidelberg, Germany
| |
Collapse
|
6
|
Yofe I, Soliman K, Chuartzman SG, Morgan B, Weill U, Yifrach E, Dick TP, Cooper SJ, Ejsing CS, Schuldiner M, Zalckvar E, Thoms S. Pex35 is a regulator of peroxisome abundance. J Cell Sci 2017; 130:791-804. [PMID: 28049721 DOI: 10.1242/jcs.187914] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 11/24/2016] [Indexed: 12/12/2022] Open
Abstract
Peroxisomes are cellular organelles with vital functions in lipid, amino acid and redox metabolism. The cellular formation and dynamics of peroxisomes are governed by PEX genes; however, the regulation of peroxisome abundance is still poorly understood. Here, we use a high-content microscopy screen in Saccharomyces cerevisiae to identify new regulators of peroxisome size and abundance. Our screen led to the identification of a previously uncharacterized gene, which we term PEX35, which affects peroxisome abundance. PEX35 encodes a peroxisomal membrane protein, a remote homolog to several curvature-generating human proteins. We systematically characterized the genetic and physical interactome as well as the metabolome of mutants in PEX35, and we found that Pex35 functionally interacts with the vesicle-budding-inducer Arf1. Our results highlight the functional interaction between peroxisomes and the secretory pathway.
Collapse
Affiliation(s)
- Ido Yofe
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Kareem Soliman
- Department of Child and Adolescent Health, University Medical Center, Göttingen 37075, Germany
| | - Silvia G Chuartzman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Bruce Morgan
- Department of Cellular Biochemistry, University of Kaiserslautern, Kaiserslautern 67653, Germany.,Division of Redox Regulation, ZMBH-DKFZ Alliance, German Cancer Research Center (DKFZ), Heidelberg 69121, Germany
| | - Uri Weill
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eden Yifrach
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tobias P Dick
- Division of Redox Regulation, ZMBH-DKFZ Alliance, German Cancer Research Center (DKFZ), Heidelberg 69121, Germany
| | - Sara J Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense 5230, Denmark
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sven Thoms
- Department of Child and Adolescent Health, University Medical Center, Göttingen 37075, Germany
| |
Collapse
|
7
|
Mast FD, Jamakhandi A, Saleem RA, Dilworth DJ, Rogers RS, Rachubinski RA, Aitchison JD. Peroxins Pex30 and Pex29 Dynamically Associate with Reticulons to Regulate Peroxisome Biogenesis from the Endoplasmic Reticulum. J Biol Chem 2016; 291:15408-27. [PMID: 27129769 DOI: 10.1074/jbc.m116.728154] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 12/11/2022] Open
Abstract
Peroxisome proliferation occurs by at least two routes, division of existing peroxisomes and de novo biogenesis from the endoplasmic reticulum (ER). The proteins and molecular mechanisms governing peroxisome emergence from the ER are poorly characterized. In this study, we report that two integral membrane peroxins (proteins required for peroxisome biogenesis) in Saccharomyces cerevisiae, Pex29 and Pex30, reside in distinct regions of the ER and associate with Rtn1 and Yop1, reticulon family members that contribute to ER morphology, to govern peroxisome emergence from the ER. In vivo and in vitro analyses reveal that peroxisome proliferation is therefore not restricted to the peroxisome but begins at the level of the ER.
Collapse
Affiliation(s)
- Fred D Mast
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - Arvind Jamakhandi
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - Ramsey A Saleem
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - David J Dilworth
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - Richard S Rogers
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| | - Richard A Rachubinski
- the Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - John D Aitchison
- From the Center for Infectious Disease Research and Institute for Systems Biology, Seattle, Washington 98109 and
| |
Collapse
|
8
|
Small GTPases in peroxisome dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:1006-13. [PMID: 26775587 DOI: 10.1016/j.bbamcr.2016.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 01/05/2016] [Accepted: 01/07/2016] [Indexed: 12/12/2022]
Abstract
In this review article, we summarize current knowledge on peroxisome biogenesis/functions and the role that small GTPases may play in these processes. Precise intracellular distribution of cell organelles requires their regulated association to microtubules and the actin cytoskeleton. In this respect, RhoGDP/RhoGTP favor binding of peroxisomes to microtubules and actin filaments. In its GTP-bound form, RhoA activates a regulatory cascade involving Rho kinaseII and non-muscle myosinIIA. Such interactions frequently depend on phosphoinositides (PIs) of which PI4P, PI(4,5)P2, and PI(3,5)P2 were found to be present in the peroxisomal membrane. PIs are pivotal determinants of intracellular signaling and known to regulate a wide range of cellular functions. In many of these functions, small GTPases are implicated. The small GTPase ADP-ribosylation factor 1 (Arf1), for example, is known to stimulate synthesis of PI4P and PI(4,5)P2 on the Golgi to regulate protein and lipid sorting. In vitro binding assays localized Arf1 and the COPI complex to peroxisomes. In light of the recent discussion of pre-peroxisomal vesicle generation at the ER, peroxisomal Arf1-COPI vesicles may serve retrograde transport of ER-resident components. A mass spectrometric screen localized various Rab proteins to peroxisomes. Overexpression of these proteins in combination with laser-scanning fluorescence microscopy co-localized Rab6, Rab8, Rab10, Rab14, and Rab18 with peroxisomal structures. By analogy to the role these proteins play in other organelle dynamics, we may envisage what the function of these proteins may be in relation to the peroxisomal compartment.
Collapse
|
9
|
Mindthoff S, Grunau S, Steinfort LL, Girzalsky W, Hiltunen JK, Erdmann R, Antonenkov VD. Peroxisomal Pex11 is a pore-forming protein homologous to TRPM channels. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:271-83. [PMID: 26597702 DOI: 10.1016/j.bbamcr.2015.11.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/16/2015] [Accepted: 11/16/2015] [Indexed: 01/16/2023]
Abstract
More than 30 proteins (Pex proteins) are known to participate in the biogenesis of peroxisomes-ubiquitous oxidative organelles involved in lipid and ROS metabolism. The Pex11 family of homologous proteins is responsible for division and proliferation of peroxisomes. We show that yeast Pex11 is a pore-forming protein sharing sequence similarity with TRPM cation-selective channels. The Pex11 channel with a conductance of Λ=4.1 nS in 1.0M KCl is moderately cation-selective (PK(+)/PCl(-)=1.85) and resistant to voltage-dependent closing. The estimated size of the channel's pore (r~0.6 nm) supports the notion that Pex11 conducts solutes with molecular mass below 300-400 Da. We localized the channel's selectivity determining sequence. Overexpression of Pex11 resulted in acceleration of fatty acids β-oxidation in intact cells but not in the corresponding lysates. The β-oxidation was affected in cells by expression of the Pex11 protein carrying point mutations in the selectivity determining sequence. These data suggest that the Pex11-dependent transmembrane traffic of metabolites may be a rate-limiting step in the β-oxidation of fatty acids. This conclusion was corroborated by analysis of the rate of β-oxidation in yeast strains expressing Pex11 with mutations mimicking constitutively phosphorylated (S165D, S167D) or unphosphorylated (S165A, S167A) protein. The results suggest that phosphorylation of Pex11 is a mechanism that can control the peroxisomal β-oxidation rate. Our results disclose an unexpected function of Pex11 as a non-selective channel responsible for transfer of metabolites across peroxisomal membrane. The data indicate that peroxins may be involved in peroxisomal metabolic processes in addition to their role in peroxisome biogenesis.
Collapse
Affiliation(s)
- Sabrina Mindthoff
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Ruhr-Universität, Bochum, Germany
| | - Silke Grunau
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Laura L Steinfort
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Ruhr-Universität, Bochum, Germany
| | - Wolfgang Girzalsky
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Ruhr-Universität, Bochum, Germany
| | - J Kalervo Hiltunen
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Ralf Erdmann
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Ruhr-Universität, Bochum, Germany.
| | - Vasily D Antonenkov
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland.
| |
Collapse
|
10
|
Liu Y, Guo Y, Song N, Fan Y, Li K, Teng X, Guo Q, Ding Z. Proteomic pattern changes associated with obesity-induced asthenozoospermia. Andrology 2014; 3:247-59. [PMID: 25293813 DOI: 10.1111/andr.289] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 08/04/2014] [Accepted: 09/08/2014] [Indexed: 02/06/2023]
Abstract
Obesity, an increasingly frequent societal disease can also be accompanied by declines in spermatozoa quality and male subfecundity. To determine if there are obesity-associated proteomic changes potentially affecting sperm quality and motility, differential proteomic analysis was performed on spermatozoa from both obesity-associated asthenozoospermia and clinically healthy individuals, using a label-free quantitative LC-MS/MS approach. We resolved 1975 proteins in the human sperm proteome, amongst which, 105 proteins were less abundant, whereas 22 other proteins increased in obesity-associated asthenozoospermia. Functional category analyses indicated that the differentially expressed proteins are mainly related to cytoskeletal regulation, vesicle biogenesis, metabolism, and protein degradation involved in spermiogenesis and sperm motility. Furthermore, declines in endoplasmic reticulum protein 57 (ERp57) and actin-binding-related protein T2 (ACTRT2) expression were verified by immunofluorescence, Western blot, and flow cytometry analyses. It is evident that ERp57 is localized in the acrosome region, neck and principal piece of human spermatozoa, whereas ACTRT2 is localized in the post-acrosomal region and middle piece. Thus, these differences in protein expression in asthenozoospermia may contribute to the underlying sperm quality defects afflicting these individuals. Notably, declines in ERp57 and ACTRT2 expression in obesity-associated asthenozoospermia may play critical roles in reducing sperm motility.
Collapse
Affiliation(s)
- Y Liu
- Department of Human Anatomy, Histology and Embryology, Shanghai Key Laboratory for Reproductive Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Agrawal G, Subramani S. Emerging role of the endoplasmic reticulum in peroxisome biogenesis. Front Physiol 2013; 4:286. [PMID: 24115935 PMCID: PMC3792350 DOI: 10.3389/fphys.2013.00286] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 09/20/2013] [Indexed: 01/27/2023] Open
Abstract
During the past few years, we have witnessed a paradigm shift in our long-standing concept of peroxisome biogenesis. Recent biochemical and morphological studies have revealed a primary role of the endoplasmic reticulum (ER) in the de novo formation of peroxisomes, thus challenging the prevalent model invoking growth and division of pre-existing peroxisomes. Importantly, a novel sorting process has been recently defined at the ER that segregates and assembles specific sets of peroxisomal membrane proteins (PMPs) into distinct pre-peroxisomal vesicular carriers (ppVs) that later undergo heterotypic fusion to form mature peroxisomes. Consequently, the emerging model has redefined the function of many peroxins (most notably Pex3, Pex19, and Pex25) and assigned them novel roles in vesicular budding and subsequent peroxisome assembly. These advances establish a novel intracellular membrane trafficking route between the ER and peroxisomes, but the components remain elusive. This review will provide a historical perspective and focus on recent developments in the emerging role of the ER in peroxisome biogenesis.
Collapse
Affiliation(s)
- Gaurav Agrawal
- Section of Molecular Biology, Division of Biological Sciences, University of CaliforniaSan Diego, La Jolla, CA, USA
| | | |
Collapse
|
12
|
David C, Koch J, Oeljeklaus S, Laernsack A, Melchior S, Wiese S, Schummer A, Erdmann R, Warscheid B, Brocard C. A combined approach of quantitative interaction proteomics and live-cell imaging reveals a regulatory role for endoplasmic reticulum (ER) reticulon homology proteins in peroxisome biogenesis. Mol Cell Proteomics 2013; 12:2408-25. [PMID: 23689284 DOI: 10.1074/mcp.m112.017830] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Peroxisome biogenesis initiates at the endoplasmic reticulum (ER) and maturation allows for the formation of metabolically active organelles. Yet, peroxisomes can also multiply by growth and division. Several proteins, called peroxins, are known to participate in these processes but little is known about their organization to orchestrate peroxisome proliferation. Here, we demonstrate that regulation of peroxisome proliferation relies on the integrity of the tubular ER network. Using a dual track SILAC-based quantitative interaction proteomics approach, we established a comprehensive network of stable as well as transient interactions of the peroxin Pex30p, an integral membrane protein. Through association with merely ER resident proteins, in particular with proteins containing a reticulon homology domain, and with other peroxins, Pex30p designates peroxisome contact sites at ER subdomains. We show that Pex30p traffics through the ER and segregates in punctae to which peroxisomes specifically append, and we ascertain its transient interaction with all subunits of the COPI coatomer complex suggesting the involvement of a vesicle-mediated transport. We establish that the membrane protein Pex30p facilitates the connection of peroxisomes to the ER. Taken together, our data indicate that Pex30p-containing protein complexes act as focal points from which peroxisomes can form and that the tubular ER architecture organized by the reticulon homology proteins Rtn1p, Rtn2p and Yop1p controls this process.
Collapse
Affiliation(s)
- Christine David
- University of Vienna, Max F. Perutz Laboratories, Center of Molecular Biology, Department of Biochemistry and Cell Biology, Dr. Bohr-Gasse 9, A-1030, Vienna, Austria
| | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Dimitrov L, Lam SK, Schekman R. The role of the endoplasmic reticulum in peroxisome biogenesis. Cold Spring Harb Perspect Biol 2013; 5:a013243. [PMID: 23637287 DOI: 10.1101/cshperspect.a013243] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Peroxisomes are essential cellular organelles involved in lipid metabolism. Patients affected by severe peroxisome biogenesis disorders rarely survive their first year. Genetic screens in several model organisms have identified more than 30 PEX genes that are required for the formation of functional peroxisomes. Despite significant work on the PEX genes, the biogenic origin of peroxisomes remains controversial. For at least two decades, the prevailing model postulated that peroxisomes propagate by growth and fission of preexisting peroxisomes. In this review, we focus on the recent evidence supporting a new, semiautonomous model of peroxisomal biogenesis. According to this model, peroxisomal membrane proteins (PMPs) traffic from the endoplasmic reticulum (ER) to the peroxisome by a vesicular budding, targeting, and fusion process while peroxisomal matrix proteins are imported into the organelle by an autonomous, posttranslational mechanism. We highlight the contradictory conclusions reached to answer the question of how PMPs are inserted into the ER. We then review what we know and what still remains to be elucidated about the mechanism of PMP exit from the ER and the contribution of preperoxisomal vesicles to mature peroxisomes. Finally, we discuss discrepancies in our understanding of de novo peroxisome biogenesis in wild-type cells. We anticipate that resolving these key issues will lead to a more complete picture of peroxisome biogenesis.
Collapse
Affiliation(s)
- Lazar Dimitrov
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | | | | |
Collapse
|
14
|
Gronemeyer T, Wiese S, Grinhagens S, Schollenberger L, Satyagraha A, Huber LA, Meyer HE, Warscheid B, Just WW. Localization of Rab proteins to peroxisomes: a proteomics and immunofluorescence study. FEBS Lett 2013; 587:328-38. [PMID: 23333653 DOI: 10.1016/j.febslet.2012.12.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 12/19/2012] [Accepted: 12/19/2012] [Indexed: 11/18/2022]
Abstract
A proteomics screen was initiated to identify Rab proteins regulating transport to and away from peroxisomes. Mass spectrometry-based protein correlation profiling of rat liver organelles and immunofluorescence analysis of the peroxisome candidate Rab proteins revealed Rab6, Rab10, Rab14 and Rab18 to associate with the peroxisomal membrane. While Rab14 localized to peroxisomes predominantly in its dominant-active form, other Rab proteins associated with peroxisomes in both their GTP- and GDP-bound state. In summary, our data suggest that Rab6, Rab10, Rab14 and Rab18 associate with the peroxisomal compartment and similar as previously shown for Rab8, Rab18 in its GDP-bound state favors peroxisome proliferation.
Collapse
Affiliation(s)
- Thomas Gronemeyer
- Department of Molecular Genetics and Cell Biology, Ulm University, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Fission and proliferation of peroxisomes. Biochim Biophys Acta Mol Basis Dis 2011; 1822:1343-57. [PMID: 22240198 DOI: 10.1016/j.bbadis.2011.12.014] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 12/22/2011] [Accepted: 12/23/2011] [Indexed: 01/12/2023]
Abstract
Peroxisomes are remarkably dynamic, multifunctional organelles, which react to physiological changes in their cellular environment and adopt their morphology, number, enzyme content and metabolic functions accordingly. At the organelle level, the key molecular machinery controlling peroxisomal membrane elongation and remodeling as well as membrane fission is becoming increasingly established and defined. Key players in peroxisome division are conserved in animals, plants and fungi, and key fission components are shared with mitochondria. However, the physiological stimuli and corresponding signal transduction pathways regulating and modulating peroxisome maintenance and proliferation are, despite a few exceptions, largely unexplored. There is emerging evidence that peroxisomal dynamics and proper regulation of peroxisome number and morphology are crucial for the physiology of the cell, as well as for the pathology of the organism. Here, we discuss several key aspects of peroxisomal fission and proliferation and highlight their association with certain diseases. We address signaling and transcriptional events resulting in peroxisome proliferation, and focus on novel findings concerning the key division components and their interplay. Finally, we present an updated model of peroxisomal growth and division. This article is part of a Special Issue entitled: Metabolic Functions and Biogenesis of Peroxisomes in Health and Disease.
Collapse
|
16
|
Kunze M, Neuberger G, Maurer-Stroh S, Ma J, Eck T, Braverman N, Schmid JA, Eisenhaber F, Berger J. Structural requirements for interaction of peroxisomal targeting signal 2 and its receptor PEX7. J Biol Chem 2011; 286:45048-62. [PMID: 22057399 DOI: 10.1074/jbc.m111.301853] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The import of a subset of peroxisomal matrix proteins is mediated by the peroxisomal targeting signal 2 (PTS2). The results of our sequence and physical property analysis of known PTS2 signals and of a mutational study of the least characterized amino acids of a canonical PTS2 motif indicate that PTS2 forms an amphipathic helix accumulating all conserved residues on one side. Three-dimensional structural modeling of the PTS2 receptor PEX7 reveals a groove with an evolutionarily conserved charge distribution complementary to PTS2 signals. Mammalian two-hybrid assays and cross-complementation of a mutation in PTS2 by a compensatory mutation in PEX7 confirm the interaction site. An unstructured linker region separates the PTS2 signal from the core protein. This additional information on PTS2 signals was used to generate a PTS2 prediction algorithm that enabled us to identify novel PTS2 signals within human proteins and to describe KChIP4 as a novel peroxisomal protein.
Collapse
Affiliation(s)
- Markus Kunze
- Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
| | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Koch J, Brocard C. Membrane elongation factors in organelle maintenance: the case of peroxisome proliferation. Biomol Concepts 2011; 2:353-364. [PMID: 21984887 DOI: 10.1515/bmc.2011.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Separation of metabolic pathways in organelles is critical for eukaryotic life. Accordingly, the number, morphology and function of organelles have to be maintained through processes linked with membrane remodeling events. Despite their acknowledged significance and intense study many questions remain about the molecular mechanisms by which organellar membranes proliferate. Here, using the example of peroxisome proliferation, we give an overview of how proteins elongate membranes. Subsequent membrane fission is achieved by dynamin-related proteins shared with mitochondria. We discuss basic criteria that membranes have to fulfill for these fission factors to complete the scission. Because peroxisome elongation is always associated with unequal distribution of matrix and membrane proteins, we propose peroxisomal division to be non-stochastic and asymmetric. We further show that these organelles need not be functional to carry on membrane elongation and present the most recent findings concerning members of the Pex11 protein family as membrane elongation factors. These factors, beside known proteins such as BAR-domain proteins, represent another family of proteins containing an amphipathic α-helix with membrane bending activity.
Collapse
Affiliation(s)
- Johannes Koch
- Department of Biochemistry and Cell Biology, University of Vienna, Max F. Perutz Laboratories, Center of Molecular Biology, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | | |
Collapse
|
18
|
Coley AF, Dodson HC, Morris MT, Morris JC. Glycolysis in the african trypanosome: targeting enzymes and their subcellular compartments for therapeutic development. Mol Biol Int 2011; 2011:123702. [PMID: 22091393 PMCID: PMC3195984 DOI: 10.4061/2011/123702] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 02/16/2011] [Indexed: 12/16/2022] Open
Abstract
Subspecies of the African trypanosome, Trypanosoma brucei, which cause human African trypanosomiasis, are transmitted by the tsetse fly, with transmission-essential lifecycle stages occurring in both the insect vector and human host. During infection of the human host, the parasite is limited to using glycolysis of host sugar for ATP production. This dependence on glucose breakdown presents a series of targets for potential therapeutic development, many of which have been explored and validated as therapeutic targets experimentally. These include enzymes directly involved in glucose metabolism (e.g., the trypanosome hexokinases), as well as cellular components required for development and maintenance of the essential subcellular compartments that house the major part of the pathway, the glycosomes.
Collapse
Affiliation(s)
- April F Coley
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | | | | | | |
Collapse
|
19
|
Mast FD, Fagarasanu A, Knoblach B, Rachubinski RA. Peroxisome biogenesis: something old, something new, something borrowed. Physiology (Bethesda) 2011; 25:347-56. [PMID: 21186279 DOI: 10.1152/physiol.00025.2010] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic cells are characterized by their varied complement of organelles. One set of membrane-bound, usually spherical compartments are commonly grouped together under the term peroxisomes. Peroxisomes function in regulating the synthesis and availability of many diverse lipids by harnessing the power of oxidative reactions and contribute to a number of metabolic processes essential for cellular differentiation and organismal development.
Collapse
Affiliation(s)
- Fred D Mast
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | | | | | | |
Collapse
|
20
|
Schollenberger L, Gronemeyer T, Huber CM, Lay D, Wiese S, Meyer HE, Warscheid B, Saffrich R, Peränen J, Gorgas K, Just WW. RhoA regulates peroxisome association to microtubules and the actin cytoskeleton. PLoS One 2010; 5:e13886. [PMID: 21079737 PMCID: PMC2975642 DOI: 10.1371/journal.pone.0013886] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 10/18/2010] [Indexed: 11/24/2022] Open
Abstract
The current view of peroxisome inheritance provides for the formation of new peroxisomes by both budding from the endoplasmic reticulum and autonomous division. Here we investigate peroxisome-cytoskeleton interactions and show by proteomics, biochemical and immunofluorescence analyses that actin, non-muscle myosin IIA (NMM IIA), RhoA, Rho kinase II (ROCKII) and Rab8 associate with peroxisomes. Our data provide evidence that (i) RhoA in its inactive state, maintained for example by C. botulinum toxin exoenzyme C3, dissociates from peroxisomes enabling microtubule-based peroxisomal movements and (ii) dominant-active RhoA targets to peroxisomes, uncouples the organelles from microtubules and favors Rho kinase recruitment to peroxisomes. We suggest that ROCKII activates NMM IIA mediating local peroxisomal constrictions. Although our understanding of peroxisome-cytoskeleton interactions is still incomplete, a picture is emerging demonstrating alternate RhoA-dependent association of peroxisomes to the microtubular and actin cytoskeleton. Whereas association of peroxisomes to microtubules clearly serves bidirectional, long-range saltatory movements, peroxisome-acto-myosin interactions may support biogenetic functions balancing peroxisome size, shape, number, and clustering.
Collapse
Affiliation(s)
- Lukas Schollenberger
- Heidelberg Center of Biochemistry, University of Heidelberg, Heidelberg, Germany
| | - Thomas Gronemeyer
- Medical Proteom-Center, University of Bochum, Bochum, Germany
- Department for Molecular Genetics and Cell Biology, University of Ulm, Ulm, Germany
| | - Christoph M. Huber
- Heidelberg Center of Biochemistry, University of Heidelberg, Heidelberg, Germany
| | - Dorothee Lay
- Heidelberg Center of Biochemistry, University of Heidelberg, Heidelberg, Germany
| | - Sebastian Wiese
- Medical Proteom-Center, University of Bochum, Bochum, Germany
| | - Helmut E. Meyer
- Medical Proteom-Center, University of Bochum, Bochum, Germany
| | | | - Rainer Saffrich
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Johan Peränen
- Institute of Biotechnology, University of Helsinki, Finland
| | - Karin Gorgas
- Department of Anatomy and Medical Cell Biology, University of Heidelberg, Heidelberg, Germany
| | - Wilhelm W. Just
- Heidelberg Center of Biochemistry, University of Heidelberg, Heidelberg, Germany
- * E-mail:
| |
Collapse
|
21
|
Koch J, Pranjic K, Huber A, Ellinger A, Hartig A, Kragler F, Brocard C. PEX11 family members are membrane elongation factors that coordinate peroxisome proliferation and maintenance. J Cell Sci 2010; 123:3389-400. [PMID: 20826455 DOI: 10.1242/jcs.064907] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Dynamic changes of membrane structure are intrinsic to organelle morphogenesis and homeostasis. Ectopic expression of proteins of the PEX11 family from yeast, plant or human lead to the formation of juxtaposed elongated peroxisomes (JEPs),which is evocative of an evolutionary conserved function of these proteins in membrane tubulation. Microscopic examinations reveal that JEPs are composed of independent elongated peroxisomes with heterogeneous distribution of matrix proteins. We established the homo- and heterodimerization properties of the human PEX11 proteins and their interaction with the fission factor hFis1, which is known to recruit the GTPase DRP1 to the peroxisomal membrane. We show that excess of hFis1 but not of DRP1 is sufficient to fragment JEPs into normal round-shaped organelles, and illustrate the requirement of microtubules for JEP formation. Our results demonstrate that PEX11-induced JEPs represent intermediates in the process of peroxisome membrane proliferation and that hFis1 is the limiting factor for progression. Hence, we propose a model for a conserved role of PEX11 proteins in peroxisome maintenance through peroxisome polarization, membrane elongation and segregation.
Collapse
Affiliation(s)
- Johannes Koch
- Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Department of Biochemistry and Cell Biology, Dr Bohr-Gasse 9, 1030, Vienna, Austria
| | | | | | | | | | | | | |
Collapse
|
22
|
Molecular Basis of Peroxisome Division and Proliferation in Plants. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2010; 279:79-99. [DOI: 10.1016/s1937-6448(10)79003-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
|
23
|
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: 19] [Impact Index Per Article: 1.3] [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.
Collapse
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
| |
Collapse
|
24
|
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.
Collapse
Affiliation(s)
- Erin A Anthonio
- Department of Molecular Cell Biology, Catholic University of Leuven, Leuven, Belgium.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Endoplasmic reticulum-associated secretory proteins Sec20p, Sec39p, and Dsl1p are involved in peroxisome biogenesis. EUKARYOTIC CELL 2009; 8:830-43. [PMID: 19346454 DOI: 10.1128/ec.00024-09] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Two pathways have been identified for peroxisome formation: (i) growth and division and (ii) de novo synthesis. Recent experiments determined that peroxisomes originate at the endoplasmic reticulum (ER). Although many proteins have been implicated in the peroxisome biogenic program, no proteins in the eukaryotic secretory pathway have been identified as having roles in peroxisome formation. Using the yeast Saccharomyces cerevisiae regulatable Tet promoter Hughes clone collection, we found that repression of the ER-associated secretory proteins Sec20p and Sec39p resulted in mislocalization of the peroxisomal matrix protein chimera Pot1p-green fluorescent protein (GFP) to the cytosol. Likewise, the peroxisomal membrane protein chimera Pex3p-GFP localized to tubular-vesicular structures in cells suppressed for Sec20p, Sec39p, and Dsl1p, which form a complex at the ER. Loss of Sec39p attenuated formation of Pex3p-derived peroxisomal structures following galactose induction of Pex3p-GFP expression from the GAL1 promoter. Expression of Sec20p, Sec39p, and Dsl1p was moderately increased in yeast grown under conditions that proliferate peroxisomes, and Sec20p, Sec39p, and Dsl1p were found to cofractionate with peroxisomes and colocalize with Pex3p-monomeric red fluorescent protein under these conditions. Our results show that SEC20, SEC39, and DSL1 are essential secretory genes involved in the early stages of peroxisome assembly, and this work is the first to identify and characterize an ER-associated secretory machinery involved in peroxisome biogenesis.
Collapse
|
26
|
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.
Collapse
|
27
|
Ay N, Clauss K, Barth O, Humbeck K. Identification and characterization of novel senescence-associated genes from barley (Hordeum vulgare) primary leaves. PLANT BIOLOGY (STUTTGART, GERMANY) 2008; 10 Suppl 1:121-35. [PMID: 18721317 DOI: 10.1111/j.1438-8677.2008.00092.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Leaf senescence is the final developmental stage of a leaf. The progression of barley primary leaf senescence was followed by measuring the senescence-specific decrease in chlorophyll content and photosystem II efficiency. In order to isolate novel factors involved in leaf senescence, a differential display approach with mRNA populations from young and senescing primary barley leaves was applied. In this approach, 90 senescence up-regulated cDNAs were identified. Nine of these clones were, after sequence analyses, further characterized. The senescence-associated expression was confirmed by Northern analyses or quantitative RealTime-PCR. In addition, involvement of the phytohormones ethylene and abscisic acid in regulation of these nine novel senescence-induced cDNA fragments was investigated. Two cDNA clones showed homologies to genes with a putative regulatory function. Two clones possessed high homologies to barley retroelements, and five clones may be involved in degradation or transport processes. One of these genes was further analysed. It encodes an ADP ribosylation factor 1-like protein (HvARF1) and includes sequence motifs representing a myristoylation site and four typical and well conserved ARF-like protein domains. The localization of the protein was investigated by confocal laser scanning microscopy of onion epidermal cells after particle bombardment with chimeric HvARF1-GFP constructs. Possible physiological roles of these nine novel SAGs during barley leaf senescence are discussed.
Collapse
Affiliation(s)
- N Ay
- Institute of Plant Physiology, Martin-Luther University Halle-Wittenberg, Weinbergweg 10, Halle, Germany
| | | | | | | |
Collapse
|
28
|
Abstract
More than half a century of research on peroxisomes has revealed unique features of this ubiquitous subcellular organelle, which have often been in disagreement with existing dogmas in cell biology. About 50 peroxisomal enzymes have so far been identified, which contribute to several crucial metabolic processes such as β-oxidation of fatty acids, biosynthesis of ether phospholipids and metabolism of reactive oxygen species, and render peroxisomes indispensable for human health and development. It became obvious that peroxisomes are highly dynamic organelles that rapidly assemble, multiply and degrade in response to metabolic needs. However, many aspects of peroxisome biology are still mysterious. This review addresses recent exciting discoveries on the biogenesis, formation and degradation of peroxisomes, on peroxisomal dynamics and division, as well as on the interaction and cross talk of peroxisomes with other subcellular compartments. Furthermore, recent advances on the role of peroxisomes in medicine and in the identification of novel peroxisomal proteins are discussed.
Collapse
Affiliation(s)
- Michael Schrader
- Centre for Cell Biology and Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal.
| | | |
Collapse
|
29
|
Nayidu NK, Wang L, Xie W, Zhang C, Fan C, Lian X, Zhang Q, Xiong L. Comprehensive sequence and expression profile analysis of PEX11 gene family in rice. Gene 2008; 412:59-70. [PMID: 18291602 DOI: 10.1016/j.gene.2008.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Revised: 01/08/2008] [Accepted: 01/08/2008] [Indexed: 10/22/2022]
Abstract
PEX11 gene family has been shown to be involved in peroxisome biogenesis but very little is known about this gene family in rice. Here we show that five putative PEX11 genes (OsPEX11-1-5) present in rice genome and each contain three conserved motifs. The PEX11 sequences from rice and other species can be classified into three major groups. Among the five rice PEX11 genes, OsPEX11-2 and -3 are most likely duplicated. Expression profile and RT-PCR analysis suggested that the members of PEX11 family in rice had differential expression patterns: OsPEX11-1 and OsPEX11-4 had higher expression levels in leaf tissues than in the other tissues, OsPEX11-2 was detected only in germinated seeds, OsPEX11-3 was expressed predominantly in endosperm and germinated seeds, and OsPEX11-5 was expressed in all the tissues investigated. We also observed that the rice PEX11 genes had differential expression patterns under different abiotic stresses. OsPEX11-1 and OsPEX11-4 were induced by abscisic acid (ABA), hydrogen peroxide (H2O2), salt and low nitrogen stress conditions. OsPEX11-3 was responsive to ABA and H2O2 treatments, and OsPEX11-5 was responsive to ABA, H2O2, and salt treatments. However, OsPEX11-2 had no response to any of the stresses. Our results suggest that the rice PEX11 genes have diversification not only in sequences but also in expression patterns under normal and various stress conditions.
Collapse
Affiliation(s)
- Naghabushana K Nayidu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Orth T, Reumann S, Zhang X, Fan J, Wenzel D, Quan S, Hu J. The PEROXIN11 protein family controls peroxisome proliferation in Arabidopsis. THE PLANT CELL 2007; 19:333-50. [PMID: 17220199 PMCID: PMC1820951 DOI: 10.1105/tpc.106.045831] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2006] [Revised: 11/24/2006] [Accepted: 12/05/2006] [Indexed: 05/13/2023]
Abstract
PEROXIN11 (PEX11) is a peroxisomal membrane protein in fungi and mammals and was proposed to play a major role in peroxisome proliferation. To begin understanding how peroxisomes proliferate in plants and how changes in peroxisome abundance affect plant development, we characterized the extended Arabidopsis thaliana PEX11 protein family, consisting of the three phylogenetically distinct subfamilies PEX11a, PEX11b, and PEX11c to PEX11e. All five Arabidopsis PEX11 proteins target to peroxisomes, as demonstrated for endogenous and cyan fluorescent protein fusion proteins by fluorescence microscopy and immunobiochemical analysis using highly purified leaf peroxisomes. PEX11a and PEX11c to PEX11e behave as integral proteins of the peroxisome membrane. Overexpression of At PEX11 genes in Arabidopsis induced peroxisome proliferation, whereas reduction in gene expression decreased peroxisome abundance. PEX11c and PEX11e, but not PEX11a, PEX11b, and PEX11d, complemented to significant degrees the growth phenotype of the Saccharomyces cerevisiae pex11 null mutant on oleic acid. Heterologous expression of PEX11e in the yeast mutant increased the number and reduced the size of the peroxisomes. We conclude that all five Arabidopsis PEX11 proteins promote peroxisome proliferation and that individual family members play specific roles in distinct peroxisomal subtypes and environmental conditions and possibly in different steps of peroxisome proliferation.
Collapse
Affiliation(s)
- Travis Orth
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | | | | | | | | | | | | |
Collapse
|
31
|
Price HP, Stark M, Smith DF. Trypanosoma brucei ARF1 plays a central role in endocytosis and golgi-lysosome trafficking. Mol Biol Cell 2006; 18:864-73. [PMID: 17182848 PMCID: PMC1805098 DOI: 10.1091/mbc.e06-08-0736] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The ADP ribosylation factor (Arf)1 orthologue in the divergent eukaryote Trypanosoma brucei (Tb) shares characteristics with both Arf1 and Arf6 and has a vital role in intracellular protein trafficking. TbARF1 is Golgi localized in trypanosomes but associates with the plasma membrane when expressed in human cells. Depletion of TbARF1 by RNA interference causes a major decrease in endocytosis, which correlates with Rab5 dissociation from early endosomes. Although the Golgi remains intact, parasites display enlarged flagellar pockets and intracellular flagella. An increase in active GTP-bound TbARF1 in bloodstream parasites is rapidly lethal, correlating with a defect in Golgi-to-lysosome transport. We conclude that the essential Golgi-localizing T. brucei ARF1 has a primary role in the maintenance of both post-Golgi transport and endocytosis and that it is significantly divergent from other characterized ARFs.
Collapse
Affiliation(s)
| | - Meg Stark
- Technology Facility, Department of Biology, University of York, Heslington, York YO10 5YW, United Kingdom
| | | |
Collapse
|
32
|
Lay D, Gorgas K, Just WW. Peroxisome biogenesis: Where Arf and coatomer might be involved. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:1678-87. [PMID: 17023067 DOI: 10.1016/j.bbamcr.2006.08.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Revised: 08/12/2006] [Accepted: 08/23/2006] [Indexed: 11/24/2022]
Abstract
The present review summarizes recent observations on binding of Arf and COPI coat to isolated rat liver peroxisomes. The general structural and functional features of both Arf and coatomer were considered along with the requirements and dependencies of peroxisomal Arf and coatomer recruitment. Studies on the expression of mammalian Pex11 proteins, mainly Pex11alpha and Pex11beta, intimately related to the process of peroxisome proliferation, revealed a sequence of individual steps including organelle elongation/tubulation, formation of membrane and matrix protein patches segregating distinct proteins from each other, development of membrane constrictions and final membrane fission. Based on the similarities of the processes leading to cargo selection and concentration on Golgi membranes on the one hand and to the formation of peroxisomal protein patches on the other hand, an implication of Arf and COPI in distinct processes of peroxisomal proliferation is hypothesized. Alternatively, peroxisomal Arf/COPI might facilitate the formation of COPI-coated peroxisomal vesicles functioning in cargo transport and retrieval from peroxisomes to the ER. Recent observations suggesting transport of Pex3 and Pex19 during early steps of peroxisome biogenesis from the ER to peroxisomes inevitably propose such a retrieval mechanism, provided the ER to peroxisome pathway is based on transporting vesicles.
Collapse
Affiliation(s)
- Dorothee Lay
- Biochemie-Zentrum der Universität Heidelberg (BZH), Im Neuenheimer Feld 328D-69120 Heidelberg, Germany
| | | | | |
Collapse
|
33
|
Jeynov B, Lay D, Schmidt F, Tahirovic S, Just WW. Phosphoinositide synthesis and degradation in isolated rat liver peroxisomes. FEBS Lett 2006; 580:5917-24. [PMID: 17045591 DOI: 10.1016/j.febslet.2006.09.058] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 09/18/2006] [Accepted: 09/19/2006] [Indexed: 11/30/2022]
Abstract
Analyzing peroxisomal phosphoinositide (PId(#)) synthesis in highly purified rat liver peroxisomes we found synthesis of phosphatidylinositol 4-phosphate (PtdIns4P), PtdIns(4,5)P(2) and PtdIns(3,5)P(2). PtdIns3P was hardly detected in vitro, however, was observed in vivo after [(32)P]-phosphate labeling of primary rat hepatocytes. In comparison with other subcellular organelles peroxisomes revealed a unique PId pattern suggesting peroxisomal specificity of the observed synthesis. Use of phosphatase inhibitors enhanced the amount of PtdIns4P. The results obtained provide evidence that isolated rat liver peroxisomes synthesize PIds and suggest the association of PId 4-kinase and PId 5-kinase and PId 4-phosphatase activities with the peroxisomal membrane.
Collapse
Affiliation(s)
- Boyan Jeynov
- Biochemie-Zentrum der Universität Heidelberg (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | | | | | | | | |
Collapse
|
34
|
Titorenko VI, Mullen RT. Peroxisome biogenesis: the peroxisomal endomembrane system and the role of the ER. ACTA ACUST UNITED AC 2006; 174:11-7. [PMID: 16801391 PMCID: PMC2064154 DOI: 10.1083/jcb.200604036] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peroxisomes have long been viewed as semiautonomous, static, and homogenous organelles that exist outside the secretory and endocytic pathways of vesicular flow. However, growing evidence supports the view that peroxisomes actually constitute a dynamic endomembrane system that originates from the endoplasmic reticulum. This review highlights the various strategies used by evolutionarily diverse organisms for coordinating the flow of membrane-enclosed carriers through the peroxisomal endomembrane system and critically evaluates the dynamics and molecular mechanisms of this multistep process.
Collapse
|
35
|
Tanaka A, Kobayashi S, Fujiki Y. Peroxisome division is impaired in a CHO cell mutant with an inactivating point-mutation in dynamin-like protein 1 gene. Exp Cell Res 2006; 312:1671-84. [PMID: 16529741 DOI: 10.1016/j.yexcr.2006.01.028] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2005] [Revised: 01/30/2006] [Accepted: 01/30/2006] [Indexed: 11/17/2022]
Abstract
We earlier isolated a Chinese hamster ovary cell line ZP121 showing morphologically abnormal, tubular peroxisomes, and apparent dysmorphogenesis of mitochondria. Here, we identified an inactivating point-mutation in dynamin-like protein 1 gene, DLP1, responsible for the phenotype of ZP121. One allele of DLP1 possessed a point missense mutation resulting in G363D in the middle region of 699-amino-acid long DLP1, termed DLP1G363D, while the other allele was normal. DLP1G363D was apparently expressed at a higher level than DLP1. Abnormal morphogenesis of peroxisomes as well as mitochondria was restored when wild-type DLP1 was transfected. The GTPase activity of DLP1G363D was barely detectable, indicating that the G363D mutation severely affected the GTPase activity. Moreover, a higher level of DLP1G363D expression in CHO-K1 cells reproduced the ZP121-type phenotype, hence indicating its dominant-negative activity to the wild-type DLP1, most likely by forming a heteromeric tetramer. The G363D mutation also gave rise to a temperature-sensitive phenotype showing normal morphogenesis of peroxisomes and mitochondria at 40 degrees C. Microtubule organization was most likely involved in the elongation of peroxisomes. Furthermore, ZP121 was lowered in the level of phospholipids, plasmalogens, and phosphatidylethanolamine and was less sensitive to oxidative stresses. Thus, ZP121 is the first dlp1 mutant in mammalian cells.
Collapse
Affiliation(s)
- Atsushi Tanaka
- Department of Biology, Faculty of Sciences, Kyushu University Graduate School, Fukuoka 812-8581, Japan
| | | | | |
Collapse
|
36
|
Schrader M. Shared components of mitochondrial and peroxisomal division. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:531-41. [PMID: 16487606 DOI: 10.1016/j.bbamcr.2006.01.004] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Revised: 01/11/2006] [Accepted: 01/13/2006] [Indexed: 12/15/2022]
Abstract
Mitochondria and peroxisomes are ubiquitous subcellular organelles, which are highly dynamic and display large plasticity. Recent studies have led to the surprising finding that both organelles share components of their division machinery, namely the dynamin-related protein DLP1/Drp1 and hFis1, which recruits DLP1/Drp1 to the organelle membranes. This review addresses the current state of knowledge concerning the dynamics and fission of peroxisomes, especially in relation to mitochondrial morphology and division in mammalian cells.
Collapse
Affiliation(s)
- Michael Schrader
- Department of Cell Biology and Cell Pathology, University of Marburg, Robert-Koch Str. 6, 35037 Marburg, Germany.
| |
Collapse
|
37
|
Lingard MJ, Trelease RN. Five Arabidopsis peroxin 11 homologs individually promote peroxisome elongation, duplication or aggregation. J Cell Sci 2006; 119:1961-72. [PMID: 16636080 DOI: 10.1242/jcs.02904] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Pex11 homologs and dynamin-related proteins uniquely regulate peroxisome division (cell-cycle-dependent duplication) and proliferation (cell-cycle-independent multiplication). Arabidopsis plants possess five Pex11 homologs designated in this study as AtPex11a, -b, -c, -d and -e. Transcripts for four isoforms were found in Arabidopsis plant parts and in cells in suspension culture; by contrast, AtPex11a transcripts were found only in developing siliques. Within 2.5 hours after biolistic bombardments, myc-tagged or GFP-tagged AtPex11 a, -b, -c, -d and -e individually sorted from the cytosol directly to peroxisomes; none trafficked indirectly through the endoplasmic reticulum. Both termini of myc-tagged AtPex11 b, -c, -d and -e faced the cytosol, whereas the N- and C-termini of myc-AtPex11a faced the cytosol and matrix, respectively. In AtPex11a- or AtPex11e-transformed cells, peroxisomes doubled in number. Those peroxisomes bearing myc-AtPex11a, but not myc-AtPex11e, elongated prior to duplication. In cells transformed with AtPex11c or AtPex11d, peroxisomes elongated without subsequent fission. In AtPex11b-transformed cells, peroxisomes were aggregated and rounded. A C-terminal dilysine motif, present in AtPex11c, -d and -e, was not necessary for AtPex11d-induced peroxisome elongation. However, deletion of the motif from myc-AtPex11e led to peroxisome elongation and fission, indicating that the motif in this isoform promotes fission without elongation. In summary, all five overexpressed AtPex11 isoforms sort directly to peroxisomal membranes where they individually promote duplication (AtPex11a, -e), aggregation (AtPex11b), or elongation without fission (AtPex11c, -d).
Collapse
Affiliation(s)
- Matthew J Lingard
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85287-4501, USA
| | | |
Collapse
|
38
|
Shimizu M, Yamashita D, Yamaguchi T, Hirose F, Osumi T. Aspects of the regulatory mechanisms of PPAR functions: analysis of a bidirectional response element and regulation by sumoylation. Mol Cell Biochem 2006; 286:33-42. [PMID: 16534556 DOI: 10.1007/s11010-005-9052-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Accepted: 12/01/2004] [Indexed: 11/29/2022]
Abstract
Peroxisome proliferator-activated receptors (PPARs) constitute a subfamily of nuclear receptor superfamily. A wide variety of compounds including hypolipidemic agents, antidiabetic drugs, and long-chain fatty acids are the potential ligands of PPARs. To approach the regulatory mechanisms of PPARs, we studied on two subjects in this work. First, we identified a functional PPAR-binding site in the spacer region between the PEX11alpha and perilipin genes, which are arranged in tandem on the mouse genome. By gene reporter assays and in vivo as well as in vitro binding assays, we show that these genes are regulated tissue-selectively through this common binding site: The PEX11alpha gene is activated by PPARalpha in the liver, whereas the perilipin gene by PPARgamma in the adipose tissue. As the second subject, we found that PPARgamma2 is conjugated with small ubiquitin-related modifier (SUMO) at a specific lysine residue in the amino-terminal region. By site-directed mutagenesis combined with gene reporter assays and sumoylation analyses, we show that sumoylation represses the ligand-independent transactivating function carried by this region, and hence negatively regulates the whole transactivating competence of PPARgamma2. In addition, phosphorylation at a specific site in the amino-terminal region represses the transactivation by PPARgamma2 possibly through enhancing sumoylation.
Collapse
Affiliation(s)
- Makoto Shimizu
- Graduate School of Life Science, Himeji Institute of Technology, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
| | | | | | | | | |
Collapse
|
39
|
|
40
|
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.
Collapse
Affiliation(s)
- Michael Schrader
- Department of Cell Biology and Cell Pathology, University of Marburg, 35037 Marburg, Germany
| | | |
Collapse
|
41
|
McCartney AW, Greenwood JS, Fabian MR, White KA, Mullen RT. Localization of the tomato bushy stunt virus replication protein p33 reveals a peroxisome-to-endoplasmic reticulum sorting pathway. THE PLANT CELL 2005; 17:3513-31. [PMID: 16284309 PMCID: PMC1315385 DOI: 10.1105/tpc.105.036350] [Citation(s) in RCA: 211] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Revised: 09/26/2005] [Accepted: 10/12/2005] [Indexed: 05/05/2023]
Abstract
Tomato bushy stunt virus (TBSV), a positive-strand RNA virus, causes extensive inward vesiculations of the peroxisomal boundary membrane and formation of peroxisomal multivesicular bodies (pMVBs). Although pMVBs are known to contain protein components of the viral membrane-bound RNA replication complex, the mechanisms of protein targeting to peroxisomal membranes and participation in pMVB biogenesis are not well understood. We show that the TBSV 33-kD replication protein (p33), expressed on its own, targets initially from the cytosol to peroxisomes, causing their progressive aggregation and eventually the formation of peroxisomal ghosts. These altered peroxisomes are distinct from pMVBs; they lack internal vesicles and are surrounded by novel cytosolic vesicles that contain p33 and appear to be derived from evaginations of the peroxisomal boundary membrane. Concomitant with these changes in peroxisomes, p33 and resident peroxisomal membrane proteins are relocalized to the peroxisomal endoplasmic reticulum (pER) subdomain. This sorting of p33 is disrupted by the coexpression of a dominant-negative mutant of ADP-ribosylation factor1, implicating coatomer in vesicle formation at peroxisomes. Mutational analysis of p33 revealed that its intracellular sorting is also mediated by several targeting signals, including three peroxisomal targeting elements that function cooperatively, plus a pER targeting signal resembling an Arg-based motif responsible for vesicle-mediated retrieval of escaped ER membrane proteins from the Golgi. These results provide insight into virus-induced intracellular rearrangements and reveal a peroxisome-to-pER sorting pathway, raising new mechanistic questions regarding the biogenesis of peroxisomes in plants.
Collapse
Affiliation(s)
- Andrew W McCartney
- Department of Molecular and Cellular Biology, University of Guelph, Ontario, Canada
| | | | | | | | | |
Collapse
|
42
|
Abstract
The abundance and size of cellular organelles vary depending on the cell type and metabolic needs. Peroxisomes constitute a class of cellular organelles renowned for their ability to adapt to cellular and environmental conditions. Together with transcriptional regulators, two groups of peroxisomal proteins have a pronounced influence on peroxisome size and abundance. Pex11-type peroxisome proliferators are involved in the proliferation of peroxisomes, defined here as an increase in size and/or number of peroxisomes. Dynamin-related proteins have recently been suggested to be required for the scission of peroxisomal membranes. This review surveys the function of Pex11-type peroxisome proliferators and dynamin-related proteins in peroxisomal proliferation and division.
Collapse
Affiliation(s)
- Sven Thoms
- Ruhr-University-Bochum, Medical Faculty, Institute of Physiological Chemistry, Bochum, Germany
| | | |
Collapse
|
43
|
Sparkes IA, Hawes C, Baker A. AtPEX2 and AtPEX10 are targeted to peroxisomes independently of known endoplasmic reticulum trafficking routes. PLANT PHYSIOLOGY 2005; 139:690-700. [PMID: 16169966 PMCID: PMC1255988 DOI: 10.1104/pp.105.065094] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Controversy exists in the literature over the involvement of the endoplasmic reticulum (ER) in the delivery of membrane proteins to peroxisomes. In this study, the involvement of the ER in the trafficking of two Arabidopsis (Arabidopsis thaliana) peroxisomal membrane proteins was investigated using confocal laser scanning microscopy of living cells expressing fusions between enhanced yellow fluorescent protein (eYFP) and AtPEX2 and AtPEX10. The fusion proteins were always detected in peroxisomes and cytosol irrespective of the location of the eYFP tag or the level of expression. The cytosolic fluorescence was not due to cleavage of the eYFP reporter from the C-terminal fusion proteins. Blocking known ER transport routes using the fungal metabolite Brefeldin A or expressing dominant negative mutants of Sar1 or RabD2a had no effect on the trafficking of AtPEX2 and AtPEX10 to peroxisomes. We conclude that AtPEX2 and AtPEX10 are inserted into peroxisome membranes directly from the cytosol.
Collapse
|
44
|
Koch A, Yoon Y, Bonekamp NA, McNiven MA, Schrader M. A role for Fis1 in both mitochondrial and peroxisomal fission in mammalian cells. Mol Biol Cell 2005; 16:5077-86. [PMID: 16107562 PMCID: PMC1266408 DOI: 10.1091/mbc.e05-02-0159] [Citation(s) in RCA: 231] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The mammalian dynamin-like protein DLP1/Drp1 has been shown to mediate both mitochondrial and peroxisomal fission. In this study, we have examined whether hFis1, a mammalian homologue of yeast Fis1, which has been shown to participate in mitochondrial fission by an interaction with DLP1/Drp1, is also involved in peroxisomal growth and division. We show that hFis1 localizes to peroxisomes in addition to mitochondria. Through differential tagging and deletion experiments, we demonstrate that the transmembrane domain and the short C-terminal tail of hFis1 is both necessary and sufficient for its targeting to peroxisomes and mitochondria, whereas the N-terminal region is required for organelle fission. hFis1 promotes peroxisome division upon ectopic expression, whereas silencing of Fis1 by small interfering RNA inhibited fission and caused tubulation of peroxisomes. These findings provide the first evidence for a role of Fis1 in peroxisomal fission and suggest that the fission machinery of mitochondria and peroxisomes shares common components.
Collapse
Affiliation(s)
- Annett Koch
- Department of Cell Biology and Cell Pathology, University of Marburg, 35037 Marburg, Germany
| | | | | | | | | |
Collapse
|
45
|
Lay D, L Grosshans B, Heid H, Gorgas K, Just WW. Binding and functions of ADP-ribosylation factor on mammalian and yeast peroxisomes. J Biol Chem 2005; 280:34489-99. [PMID: 16100119 DOI: 10.1074/jbc.m503497200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have analyzed in vitro the binding characteristics of members of the ADP-ribosylation factor (ARF) family of proteins to a highly purified rat liver peroxisome preparation void of Golgi membranes and studied in vivo a role these proteins play in the proliferation of yeast peroxisomes. Although both ARF1 and ARF6 were found on peroxisomes, coatomer recruitment only depended on ARF1-GTP. Recruitment of ARF1 and coatomer to peroxisomes was significantly affected both by pretreating the animals with peroxisome proliferators and by ATP and a cytosolic fraction designated the intermediate pool fraction depleted of ARF and coatomer. In the presence of ATP, the concentrations of ARF1 and coatomer on peroxisomes were reduced, whereas intermediate pool fraction led to a concentration-dependent decrease in ARF and increase in coatomer. Brefeldin A, a fungal toxin that is known to reduce ARF1 binding to Golgi membranes, did not affect ARF1 binding to peroxisomes. In Saccharomyces cerevisiae, both ScARF1 and ScARF3, the yeast orthologs of mammalian ARF1 and ARF6, were implicated in the control of peroxisome proliferation. ScARF1 regulated this process in a positive manner, and ScARF3 regulated it in a negative manner.
Collapse
Affiliation(s)
- Dorothee Lay
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | | | | | | | | |
Collapse
|
46
|
Gondcaille C, Depreter M, Fourcade S, Lecca MR, Leclercq S, Martin PGP, Pineau T, Cadepond F, ElEtr M, Bertrand N, Beley A, Duclos S, De Craemer D, Roels F, Savary S, Bugaut M. Phenylbutyrate up-regulates the adrenoleukodystrophy-related gene as a nonclassical peroxisome proliferator. ACTA ACUST UNITED AC 2005; 169:93-104. [PMID: 15809314 PMCID: PMC2171887 DOI: 10.1083/jcb.200501036] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
X-linked adrenoleukodystrophy (X-ALD) is a demyelinating disease due to mutations in the ABCD1 (ALD) gene, encoding a peroxisomal ATP-binding cassette transporter (ALDP). Overexpression of adrenoleukodystrophy-related protein, an ALDP homologue encoded by the ABCD2 (adrenoleukodystrophy-related) gene, can compensate for ALDP deficiency. 4-Phenylbutyrate (PBA) has been shown to induce both ABCD2 expression and peroxisome proliferation in human fibroblasts. We show that peroxisome proliferation with unusual shapes and clusters occurred in liver of PBA-treated rodents in a PPARα-independent way. PBA activated Abcd2 in cultured glial cells, making PBA a candidate drug for therapy of X-ALD. The Abcd2 induction observed was partially PPARα independent in hepatocytes and totally independent in fibroblasts. We demonstrate that a GC box and a CCAAT box of the Abcd2 promoter are the key elements of the PBA-dependent Abcd2 induction, histone deacetylase (HDAC)1 being recruited by the GC box. Thus, PBA is a nonclassical peroxisome proliferator inducing pleiotropic effects, including effects at the peroxisomal level mainly through HDAC inhibition.
Collapse
Affiliation(s)
- Catherine Gondcaille
- Laboratoire de Biologie Moléculaire et Cellulaire, Faculté des Sciences Gabriel, 21000 Dijon, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Koch A, Schneider G, Lüers GH, Schrader M. Peroxisome elongation and constriction but not fission can occur independently of dynamin-like protein 1. J Cell Sci 2005; 117:3995-4006. [PMID: 15286177 DOI: 10.1242/jcs.01268] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mammalian dynamin-like protein DLP1 belongs to the dynamin family of large GTPases, which have been implicated in tubulation and fission events of cellular membranes. We have previously shown that the expression of a dominant-negative DLP1 mutant deficient in GTP hydrolysis (K38A) inhibited peroxisomal division in mammalian cells. In this study, we conducted RNA interference experiments to 'knock down' the expression of DLP1 in COS-7 cells stably expressing a GFP construct bearing the C-terminal peroxisomal targeting signal 1. The peroxisomes in DLP1-silenced cells were highly elongated with a segmented morphology. Ultrastructural and quantitative studies confirmed that the tubular peroxisomes induced by DLP1-silencing retained the ability to constrict their membranes but were not able to divide into spherical organelles. Co-transfection of DLP1 siRNA with Pex11pbeta, a peroxisomal membrane protein involved in peroxisome proliferation, induced further elongation and network formation of the peroxisomal compartment. Time-lapse microscopy of living cells silenced for DLP1 revealed that the elongated peroxisomes moved in a microtubule-dependent manner and emanated tubular projections. DLP1-silencing in COS-7 cells also resulted in a pronounced elongation of mitochondria, and in more dispersed, elongated Golgi structures, whereas morphological changes of the rER, lysosomes and the cytoskeleton were not detected. These observations clearly demonstrate that DLP1 acts on multiple membranous organelles. They further indicate that peroxisomal elongation, constriction and fission require distinct sets of proteins, and that the dynamin-like protein DLP1 functions primarily in the latter process.
Collapse
Affiliation(s)
- Annett Koch
- Department of Cell Biology and Cell Pathology, Robert Koch Strasse 6, University of Marburg, Marburg, 35037, Germany
| | | | | | | |
Collapse
|
48
|
Marelli M, Smith JJ, Jung S, Yi E, Nesvizhskii AI, Christmas RH, Saleem RA, Tam YYC, Fagarasanu A, Goodlett DR, Aebersold R, Rachubinski RA, Aitchison JD. Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane. J Cell Biol 2004; 167:1099-112. [PMID: 15596542 PMCID: PMC2172632 DOI: 10.1083/jcb.200404119] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2004] [Accepted: 11/10/2004] [Indexed: 11/22/2022] Open
Abstract
We have combined classical subcellular fractionation with large-scale quantitative mass spectrometry to identify proteins that enrich specifically with peroxisomes of Saccharomyces cerevisiae. In two complementary experiments, isotope-coded affinity tags and tandem mass spectrometry were used to quantify the relative enrichment of proteins during the purification of peroxisomes. Mathematical modeling of the data from 306 quantified proteins led to a prioritized list of 70 candidates whose enrichment scores indicated a high likelihood of them being peroxisomal. Among these proteins, eight novel peroxisome-associated proteins were identified. The top novel peroxisomal candidate was the small GTPase Rho1p. Although Rho1p has been shown to be tethered to membranes of the secretory pathway, we show that it is specifically recruited to peroxisomes upon their induction in a process dependent on its interaction with the peroxisome membrane protein Pex25p. Rho1p regulates the assembly state of actin on the peroxisome membrane, thereby controlling peroxisome membrane dynamics and biogenesis.
Collapse
|
49
|
Petriv OI, Tang L, Titorenko VI, Rachubinski RA. A new definition for the consensus sequence of the peroxisome targeting signal type 2. J Mol Biol 2004; 341:119-34. [PMID: 15312767 DOI: 10.1016/j.jmb.2004.05.064] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2004] [Revised: 05/05/2004] [Accepted: 05/22/2004] [Indexed: 10/26/2022]
Abstract
All organisms except the nematode Caenorhabditis elegans have been shown to possess an import system for peroxisomal proteins containing a peroxisome targeting signal type 2 (PTS2). The currently accepted consensus sequence for this amino-terminal nonapeptide is -(R/K)(L/V/I)X(5)(H/Q)(L/A)-. Some C.elegans proteins contain putative PTS2 motifs, including the ortholog (CeMeK) of human mevalonate kinase, an enzyme known to be targeted by PTS2 to mammalian peroxisomes. We cloned the gene for CeMeK (open reading frame Y42G9A.4) and examined the subcellular localization of CeMeK and of two other proteins with putative PTS2s at their amino termini encoded by the open reading frames D1053.2 and W10G11.11. All three proteins localized to the cytosol, confirming and extending the finding that C.elegans lacks PTS2-dependent peroxisomal protein import. The putative PTS2s of the proteins encoded by D1053.2 and W10G11.11 did not function in targeting to peroxisomes in yeast or mammalian cells, suggesting that the current PTS2 consensus sequence is too broad. Analysis of available experimental data on both functional and nonfunctional PTS2s led to two re-evaluated PTS2 consensus sequences: -R(L/V/I/Q)XX(L/V/I/H)(L/S/G/A)X(H/Q)(L/A)-, describes the most common variants of PTS2, while -(R/K)(L/V/I/Q)XX(L/V/I/H/Q)(L/S/G/A/K)X(H/Q)(L/A/F)-, describes essentially all variants of PTS2. These redefined PTS2 consensus sequences will facilitate the identification of proteins of unknown cellular localization as possible peroxisomal proteins.
Collapse
Affiliation(s)
- Oleh I Petriv
- Department of Cell Biology, University of Alberta, Medical Sciences Building 5-14, Edmonton, Alta., Canada T6G 2H7
| | | | | | | |
Collapse
|
50
|
Abstract
Peroxisomes are metabolic organelles with enzymatic content that are found in virtually all cells and are involved in beta-oxidation of fatty acids, hydrogen peroxide-based respiration and defence against oxidative stress. The steps of their biogenesis involves "peroxins", proteins encoded by PEX genes. Peroxins are involved in three key stages of peroxisome development: (1). import of peroxisomal membrane proteins; (2). import of peroxisomal matrix proteins and (3). peroxisome proliferation. Of these three areas, peroxisomal matrix-protein import is by far the best understood and accounts for most of the available published data on peroxisome biogenesis. Defects in peroxisome biogenesis result in peroxisome biogenesis disorders (PBDs), which although rare, have no known cure to-date. This review explores current understanding of each key area in peroxisome biogenesis, paying particular attention to the role of protein import.
Collapse
Affiliation(s)
- Laura-Anne Brown
- Centre for Plant Sciences, University of Leeds, Leeds, United Kingdom
| | | |
Collapse
|