1
|
Chen AS, Liu H, Wu Y, Luo S, Patz EF, Glass C, Su L, Du M, Christiani DC, Wei Q. Genetic variants in DDO and PEX5L in peroxisome-related pathways predict non-small cell lung cancer survival. Mol Carcinog 2022; 61:619-628. [PMID: 35502931 DOI: 10.1002/mc.23400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 03/05/2022] [Accepted: 03/10/2022] [Indexed: 01/14/2023]
Abstract
Peroxisomes play a role in lipid metabolism and regulation of reactive oxygen species, but its role in development and progression of non-small cell lung cancer (NSCLC) is not well understood. Here, we investigated the associations between 9708 single-nucleotide polymorphisms (SNPs) in 113 genes in the peroxisome-related pathways and survival of NSCLC patients from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) and the Harvard Lung Cancer Susceptibility (HLCS) study. In 1185 NSCLC patients from the PLCO trial, we found that 213 SNPs were significantly associated with NSCLC overall survival (OS) (p ≤ 0.05, Bayesian false discovery probability [BFDP] ≤ 0.80), of which eight SNPs were validated in the HLCS data set. In a multivariate Cox proportional hazards regression model, two independent SNPs (rs9384742 DDO and rs9825224 PEX5L) were significantly associated with NSCLC survival (hazards ratios [HR] of 1.17 with 95% CI [confidence interval] of 1.06-1.28 and 0.86 with 95% CI of 0.77-0.96, respectively). Patients with one or two protective genotypes had a significantly higher OS (HR: 0.787 [95% CI: 0.620-0.998] and 0.691 [95% CI: 0.543-0.879], respectively). Further expression quantitative trait loci analysis using whole blood and lung tissue showed that the minor allele of rs9384742 DDO was significantly associated with decreased messenger RNA (mRNA) expression levels and that DDO expression was also decreased in NSCLC tumor tissue. Additionally, high PEX5L expression levels were significantly associated with lower survival of NSCLC. Our data suggest that variants in these peroxisome-related genes may influence gene regulation and are potential predictors of NSCLC OS, once validated by additional studies.
Collapse
Affiliation(s)
- Allan S Chen
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Yufeng Wu
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Edward F Patz
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Departments of Radiology, Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, USA
| | - Carolyn Glass
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Pathology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Li Su
- Departments of Environmental Health and Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Mulong Du
- Departments of Environmental Health and Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - David C Christiani
- Departments of Environmental Health and Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA.,Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| |
Collapse
|
2
|
Nuebel E, Morgan JT, Fogarty S, Winter JM, Lettlova S, Berg JA, Chen YC, Kidwell CU, Maschek JA, Clowers KJ, Argyriou C, Chen L, Wittig I, Cox JE, Roh-Johnson M, Braverman N, Bonkowsky J, Gygi SP, Rutter J. The biochemical basis of mitochondrial dysfunction in Zellweger Spectrum Disorder. EMBO Rep 2021; 22:e51991. [PMID: 34351705 DOI: 10.15252/embr.202051991] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 06/21/2021] [Accepted: 07/12/2021] [Indexed: 01/09/2023] Open
Abstract
Peroxisomal biogenesis disorders (PBDs) are genetic disorders of peroxisome biogenesis and metabolism that are characterized by profound developmental and neurological phenotypes. The most severe class of PBDs-Zellweger spectrum disorder (ZSD)-is caused by mutations in peroxin genes that result in both non-functional peroxisomes and mitochondrial dysfunction. It is unclear, however, how defective peroxisomes contribute to mitochondrial impairment. In order to understand the molecular basis of this inter-organellar relationship, we investigated the fate of peroxisomal mRNAs and proteins in ZSD model systems. We found that peroxins were still expressed and a subset of them accumulated on the mitochondrial membrane, which resulted in gross mitochondrial abnormalities and impaired mitochondrial metabolic function. We showed that overexpression of ATAD1, a mitochondrial quality control factor, was sufficient to rescue several aspects of mitochondrial function in human ZSD fibroblasts. Together, these data suggest that aberrant peroxisomal protein localization is necessary and sufficient for the devastating mitochondrial morphological and metabolic phenotypes in ZSDs.
Collapse
Affiliation(s)
- Esther Nuebel
- Howard Hughes Medical Institute, Salt Lake City, UT, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.,Department of Biomedical Sciences, Noorda College of Osteopathic Medicine, Provo, USA
| | - Jeffrey T Morgan
- Howard Hughes Medical Institute, Salt Lake City, UT, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Sarah Fogarty
- Howard Hughes Medical Institute, Salt Lake City, UT, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Jacob M Winter
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Sandra Lettlova
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Jordan A Berg
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Yu-Chan Chen
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Chelsea U Kidwell
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - J Alan Maschek
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.,Diabetes & Metabolism Research Center, University of Utah, Salt Lake City, UT, USA.,Metabolomics, Proteomics and Mass Spectrometry Core Research Facilities, University of Utah, Salt Lake City, UT, USA
| | - Katie J Clowers
- Department of Cell Biology, Harvard University School of Medicine, Boston, MA, USA
| | | | - Lingxiao Chen
- Department of Pathology, McGill University, Montreal, ON, Canada
| | - Ilka Wittig
- Functional Proteomics, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - James E Cox
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.,Diabetes & Metabolism Research Center, University of Utah, Salt Lake City, UT, USA.,Metabolomics, Proteomics and Mass Spectrometry Core Research Facilities, University of Utah, Salt Lake City, UT, USA
| | - Minna Roh-Johnson
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Nancy Braverman
- Department of Human Genetics, McGill University, Montreal, ON, Canada.,Department of Pediatrics, Research Institute of the McGill University Health Centre, Montreal, ON, Canada
| | - Joshua Bonkowsky
- Primary Children's Hospital, University of Utah, Salt Lake City, UT, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard University School of Medicine, Boston, MA, USA
| | - Jared Rutter
- Howard Hughes Medical Institute, Salt Lake City, UT, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.,Diabetes & Metabolism Research Center, University of Utah, Salt Lake City, UT, USA
| |
Collapse
|
3
|
Yu W, Lin M, Peng M, Yan H, Wang J, Zhou J, Lu G, Wang Z, Shim WB. Fusarium verticillioides FvPex8 Is a Key Component of the Peroxisomal Docking/Translocation Module That Serves Important Roles in Fumonisin Biosynthesis but Not in Virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:803-814. [PMID: 33749306 DOI: 10.1094/mpmi-10-20-0273-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Peroxisomes are ubiquitous organelles in eukaryotes that fulfill various important metabolic functions. In this study, we investigated the role of docking/translocation module (DTM) peroxins, mainly FvPex8, FvPex13, FvPex14, and FvPex33, in Fusarium verticillioides development, virulence, and fumonisin B1 (FB1) biosynthesis. Protein interaction experiments suggested that FvPex13 serves as the central DTM subunit in F. verticillioides. Notably, FvPex8 and FvPex14 did not show direct interaction in our experiments. We generated gene-deletion mutants (ΔFvpex8, ΔFvpex13, ΔFvpex14, ΔFvpex33, ΔFvpex33/14) and further examined the functional role of these peroxins. Deletion mutants exhibited disparity in carbon nutrient utilization and defect in cell-wall integrity when stress agents were applied. Under nutrient starvation, mutants also showed higher levels of lipid droplet accumulation. Particularly, ΔFvpex8 mutant showed significant FB1 reduction and altered expression of key FB1 biosynthesis genes. However, FvPex13 was primarily responsible for asexual conidia reproduction and virulence, while the ΔFvpex33/14 double mutant also showed a virulence defect. In summary, our study suggests that FvPex13 is the central component of DTM, with direct physical interaction with other DTM peroxins, and regulates peroxisome membrane biogenesis as well as PTS1- and PTS2-mediated transmembrane cargo transportation. Importantly, we also characterized FvPex8 as a key component in F. verticillioides DTM that affects peroxisome function and FB1 biosynthesis.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Wenying Yu
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mei Lin
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Minghui Peng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huijuan Yan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843-2132, U.S.A
| | - Jiajia Wang
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jie Zhou
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education & Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Won Bo Shim
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843-2132, U.S.A
| |
Collapse
|
4
|
The Glyoxysomal Protease LON2 Is Involved in Fruiting-Body Development, Ascosporogenesis and Stress Resistance in Sordaria macrospora. J Fungi (Basel) 2021; 7:jof7020082. [PMID: 33530609 PMCID: PMC7911957 DOI: 10.3390/jof7020082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 01/05/2023] Open
Abstract
Microbodies, including peroxisomes, glyoxysomes and Woronin bodies, are ubiquitous dynamic organelles that play important roles in fungal development. The ATP-dependent chaperone and protease family Lon that maintain protein quality control within the organelle significantly regulate the functionality of microbodies. The filamentous ascomycete Sordaria macrospora is a model organism for studying fruiting-body development. The genome of S. macrospora encodes one Lon protease with the C-terminal peroxisomal targeting signal (PTS1) serine-arginine-leucine (SRL) for import into microbodies. Here, we investigated the function of the protease SmLON2 in sexual development and during growth under stress conditions. Localization studies revealed a predominant localization of SmLON2 in glyoxysomes. This localization depends on PTS1, since a variant without the C-terminal SRL motif was localized in the cytoplasm. A ΔSmlon2 mutant displayed a massive production of aerial hyphae, and produced a reduced number of fruiting bodies and ascospores. In addition, the growth of the ΔSmlon2 mutant was completely blocked under mild oxidative stress conditions. Most of the defects could be complemented with both variants of SmLON2, with and without PTS1, suggesting a dual function of SmLON2, not only in microbody, but also in cytosolic protein quality control.
Collapse
|
5
|
Towards the molecular architecture of the peroxisomal receptor docking complex. Proc Natl Acad Sci U S A 2020; 117:33216-33224. [PMID: 33323485 DOI: 10.1073/pnas.2009502117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Import of yeast peroxisomal matrix proteins is initiated by cytosolic receptors, which specifically recognize and bind the respective cargo proteins. At the peroxisomal membrane, the cargo-loaded receptor interacts with the docking protein Pex14p that is tightly associated with Pex17p. Previous data suggest that this interaction triggers the formation of an import pore for further translocation of the cargo. The mechanistic principles, however, are unclear, mainly because structures of higher-order assemblies are still lacking. Here, using an integrative approach, we provide the structural characterization of the major components of the peroxisomal docking complex Pex14p/Pex17p, in a native bilayer environment, and reveal its subunit organization. Our data show that three copies of Pex14p and a single copy of Pex17p assemble to form a 20-nm rod-like particle. The different subunits are arranged in a parallel manner, showing interactions along their complete sequences and providing receptor binding sites on both membrane sides. The long rod facing the cytosol is mainly formed by the predicted coiled-coil domains of Pex14p and Pex17p, possibly providing the necessary structural support for the formation of the import pore. Further implications of Pex14p/Pex17p for formation of the peroxisomal translocon are discussed.
Collapse
|
6
|
Mast FD, Rachubinski RA, Aitchison JD. Peroxisome prognostications: Exploring the birth, life, and death of an organelle. J Cell Biol 2020; 219:133827. [PMID: 32211898 PMCID: PMC7054992 DOI: 10.1083/jcb.201912100] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 02/07/2023] Open
Abstract
Peroxisomes play a central role in human health and have biochemical properties that promote their use in many biotechnology settings. With a primary role in lipid metabolism, peroxisomes share a niche with lipid droplets within the endomembrane-secretory system. Notably, factors in the ER required for the biogenesis of peroxisomes also impact the formation of lipid droplets. The dynamic interface between peroxisomes and lipid droplets, and also between these organelles and the ER and mitochondria, controls their metabolic flux and their dynamics. Here, we review our understanding of peroxisome biogenesis to propose and reframe models for understanding how peroxisomes are formed in cells. To more fully understand the roles of peroxisomes and to take advantage of their many properties that may prove useful in novel therapeutics or biotechnology applications, we recast mechanisms controlling peroxisome biogenesis in a framework that integrates inference from these models with experimental data.
Collapse
Affiliation(s)
- Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA
| | | | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA.,Department of Pediatrics, University of Washington, Seattle, WA
| |
Collapse
|
7
|
González-Robles A, González-Lázaro M, Lagunes-Guillén AE, Omaña-Molina M, Lares-Jiménez LF, Lares-Villa F, Martínez-Palomo A. Ultrastructural, Cytochemical, and Comparative Genomic Evidence of Peroxisomes in Three Genera of Pathogenic Free-Living Amoebae, Including the First Morphological Data for the Presence of This Organelle in Heteroloboseans. Genome Biol Evol 2020; 12:1734-1750. [PMID: 32602891 PMCID: PMC7549135 DOI: 10.1093/gbe/evaa129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2020] [Indexed: 12/13/2022] Open
Abstract
Peroxisomes perform various metabolic processes that are primarily related to the elimination of reactive oxygen species and oxidative lipid metabolism. These organelles are present in all major eukaryotic lineages, nevertheless, information regarding the presence of peroxisomes in opportunistic parasitic protozoa is scarce and in many cases it is still unknown whether these organisms have peroxisomes at all. Here, we performed ultrastructural, cytochemical, and bioinformatic studies to investigate the presence of peroxisomes in three genera of free-living amoebae from two different taxonomic groups that are known to cause fatal infections in humans. By transmission electron microscopy, round structures with a granular content limited by a single membrane were observed in Acanthamoeba castellanii, Acanthamoeba griffini, Acanthamoeba polyphaga, Acanthamoeba royreba, Balamuthia mandrillaris (Amoebozoa), and Naegleria fowleri (Heterolobosea). Further confirmation for the presence of peroxisomes was obtained by treating trophozoites in situ with diaminobenzidine and hydrogen peroxide, which showed positive reaction products for the presence of catalase. We then performed comparative genomic analyses to identify predicted peroxin homologues in these organisms. Our results demonstrate that a complete set of peroxins-which are essential for peroxisome biogenesis, proliferation, and protein import-are present in all of these amoebae. Likewise, our in silico analyses allowed us to identify a complete set of peroxins in Naegleria lovaniensis and three novel peroxin homologues in Naegleria gruberi. Thus, our results indicate that peroxisomes are present in these three genera of free-living amoebae and that they have a similar peroxin complement despite belonging to different evolutionary lineages.
Collapse
Affiliation(s)
- Arturo González-Robles
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Mónica González-Lázaro
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Anel Edith Lagunes-Guillén
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Maritza Omaña-Molina
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlanepantla, Estado de México, Mexico
| | - Luis Fernando Lares-Jiménez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, Mexico
| | - Fernando Lares-Villa
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, Mexico
| | - Adolfo Martínez-Palomo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| |
Collapse
|
8
|
Kempiński B, Chełstowska A, Poznański J, Król K, Rymer Ł, Frydzińska Z, Girzalsky W, Skoneczna A, Erdmann R, Skoneczny M. The Peroxisomal Targeting Signal 3 (PTS3) of the Budding Yeast Acyl-CoA Oxidase Is a Signal Patch. Front Cell Dev Biol 2020; 8:198. [PMID: 32292783 PMCID: PMC7135854 DOI: 10.3389/fcell.2020.00198] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/09/2020] [Indexed: 11/13/2022] Open
Abstract
The specificity of import of peroxisomal matrix proteins is dependent on the targeting signals encoded within their amino acid sequences. Two known import signals, peroxisomal targeting signal 1 (PTS1), positioned at the C-termini and PTS2 located close to N-termini of these proteins are recognized by the Pex5p and Pex7p receptors, respectively. However, in several yeast species, including Saccharomyces cerevisiae, proteins exist that are efficiently imported into peroxisomes despite having neither PTS1 nor PTS2 and for which no other import signal has been determined. An example of such a protein is S. cerevisiae acyl-CoA oxidase (AOx) encoded by the POX1 gene. While it is known that its import is driven by its interaction with the N-terminal segment of Pex5p, which is separate from its C-terminal PTS1-recognizing tetratricopeptide domain, to date, no AOx polypeptide region has been implicated as critical for this interaction, and thus would constitute the long-sought PTS3 signal. Using random mutagenesis combined with a two-hybrid screen, we identified single amino acid residues within the AOx polypeptide that are crucial for this interaction and for the peroxisomal import of this protein. Interestingly, while scattered throughout the primary sequence, these amino acids come close to each other within two domains of the folded AOx. Although the role of one or both of these regions as the PTS3 signal is not finally proven, our data indicate that the signal guiding AOx into peroxisomal matrix is not a linear sequence but a signal patch.
Collapse
Affiliation(s)
- Błażej Kempiński
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Chełstowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamil Król
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Łukasz Rymer
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Zuzanna Frydzińska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Wolfgang Girzalsky
- Medizinische Fakultät, Biochemie und Pathobiochemie/Systembiochemie, Ruhr-Universität Bochum, Bochum, Germany
| | - Adrianna Skoneczna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Ralf Erdmann
- Medizinische Fakultät, Biochemie und Pathobiochemie/Systembiochemie, Ruhr-Universität Bochum, Bochum, Germany
| | - Marek Skoneczny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| |
Collapse
|
9
|
Wang H, Zhao H, Sun K, Huang X, Jin L, Feng J. Evolutionary Basis of High-Frequency Hearing in the Cochleae of Echolocators Revealed by Comparative Genomics. Genome Biol Evol 2020; 12:3740-3753. [PMID: 31730196 PMCID: PMC7145703 DOI: 10.1093/gbe/evz250] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2019] [Indexed: 12/25/2022] Open
Abstract
High-frequency hearing is important for the survival of both echolocating bats and whales, but our understanding of its genetic basis is scattered and segmented. In this study, we combined RNA-Seq and comparative genomic analyses to obtain insights into the comprehensive gene expression profile of the cochlea and the adaptive evolution of hearing-related genes. A total of 144 genes were found to have been under positive selection in various species of echolocating bats and toothed whales, 34 of which were identified to be related to hearing behavior or auditory processes. Subsequently, multiple physiological processes associated with those genes were found to have adaptively evolved in echolocating bats and toothed whales, including cochlear bony development, antioxidant activity, ion balance, and homeostatic processes, along with signal transduction. In addition, abundant convergent/parallel genes and sites were detected between different pairs of echolocator species; however, no specific hearing-related physiological pathways were enriched by them and almost all of the convergent/parallel signals were selectively neutral, as previously reported. Notably, two adaptive parallel evolved sites in TECPR2 were shown to have been under positive selection, indicating their functional importance for the evolution of echolocation and high-frequency hearing in laryngeal echolocating bats. This study deepens our understanding of the genetic bases underlying high-frequency hearing in the cochlea of echolocating bats and toothed whales.
Collapse
Affiliation(s)
- Hui Wang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China.,College of Life Science, Jilin Agricultural University, Changchun, China
| | - Hanbo Zhao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Xiaobin Huang
- Vector Laboratory for Zoonosis Control and Prevention, Dali University, China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China.,College of Life Science, Jilin Agricultural University, Changchun, China
| |
Collapse
|
10
|
A defect in the peroxisomal biogenesis in germ cells induces a spermatogenic arrest at the round spermatid stage in mice. Sci Rep 2019; 9:9553. [PMID: 31267012 PMCID: PMC6606614 DOI: 10.1038/s41598-019-45991-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 06/18/2019] [Indexed: 12/14/2022] Open
Abstract
Peroxisomes are involved in the degradation of very long-chain fatty acids (VLCFAs) by β-oxidation. Besides neurological defects, peroxisomal dysfunction can also lead to testicular abnormalities. However, underlying alterations in the testes due to a peroxisomal defect are not well characterized yet. To maintain all metabolic functions, peroxisomes require an import machinery for the transport of matrix proteins. One component of this translocation machinery is PEX13. Its inactivation leads to a peroxisomal biogenesis defect. We have established a germ cell-specific KO of Pex13 to study the function of peroxisomes during spermatogenesis in mice. Exon 2 of floxed Pex13 was specifically excised in germ cells prior to meiosis by using a transgenic mouse strain carrying a STRA8 inducible Cre recombinase. Germ cell differentiation was interrupted at the round spermatid stage in Pex13 KO mice with formation of multinucleated giant cells (MNCs) and loss of mature spermatids. Due to a different cellular content in the germinal epithelium of Pex13 KO testes compared to control, whole testes biopsies were used for the analyses. Thus, differences in lipid composition and gene expression are only shown for whole testicular tissue but cannot be limited to single cells. Gas chromatography revealed an increase of shorter fatty acids and a decrease of n-6 docosapentaenoic acid (C22:5n-6) and n-3 docosahexaenoic acid (C22:6n-3), the main components of sperm plasma membranes. Representative genes of the metabolite transport and peroxisomal β-oxidation were strongly down-regulated. In addition, structural components of the blood-testis barrier (BTB) were altered. To conclude, defects in the peroxisomal compartment interfere with normal spermatogenesis.
Collapse
|
11
|
Rymer Ł, Kempiński B, Chełstowska A, Skoneczny M. The budding yeast Pex5p receptor directs Fox2p and Cta1p into peroxisomes via its N-terminal region near the FxxxW domain. J Cell Sci 2018; 131:jcs.216986. [PMID: 30131444 DOI: 10.1242/jcs.216986] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 08/07/2018] [Indexed: 01/08/2023] Open
Abstract
The import of most of peroxisomal proteins into the lumen of their target organelle is driven by C-terminal (PTS1) or N-terminal (PTS2) signals recognized by the Pex5p or Pex7p receptors, respectively. However, some proteins in budding yeast, such as acyl-CoA oxidase (AOx) and carnitine acetyltransferase (Cat2p), are imported into peroxisomes via an alternative route that does not rely on known PTS signals and involves the Pex5p receptor N-terminal region. Here, we show that two other budding yeast peroxisomal proteins, a multifunctional enzyme from the β-oxidation pathway (Fox2p) and catalase A (Cta1p), both of which contain PTS1, can be imported independently of this signal. The I264K amino acid substitution in Pex5p adjacent to its FxxxW diaromatic motif, previously shown to abolish the import of AOx and Cat2p into peroxisomes, also affects Fox2p and Cta1p import. Moreover, we demonstrate that Pex9p, a newly discovered paralog of Pex5p that was recently implicated in the import of malate synthases in budding yeast, also exhibits weak receptor activity towards Fox2p and Cta1p. These findings indicate the need to re-evaluate the peroxisomal import paradigm.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Łukasz Rymer
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland
| | - Błażej Kempiński
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland
| | - Anna Chełstowska
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland
| | - Marek Skoneczny
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland
| |
Collapse
|
12
|
Schwerter D, Grimm I, Girzalsky W, Erdmann R. Receptor recognition by the peroxisomal AAA complex depends on the presence of the ubiquitin moiety and is mediated by Pex1p. J Biol Chem 2018; 293:15458-15470. [PMID: 30097517 DOI: 10.1074/jbc.ra118.003936] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/23/2018] [Indexed: 01/14/2023] Open
Abstract
The receptor cycle of type I peroxisomal matrix protein import is completed by ubiquitination of the membrane-bound peroxisome biogenesis factor 5 (Pex5p) and its subsequent export back to the cytosol. The receptor export is the only ATP-dependent step of the whole process and is facilitated by two members of the AAA family of proteins (ATPases associated with various cellular activities), namely Pex1p and Pex6p. To gain further insight into substrate recognition by the AAA complex, we generated an N-terminally linked ubiquitin-Pex5p fusion protein. This fusion protein displayed biological activity because it is able to functionally complement a PEX5-deletion in Saccharomyces cerevisiae. In vitro assays revealed its interaction at WT level with the native cargo protein Pcs60p and Pex14p, a constituent of the receptor docking complex. We also demonstrate in vitro deubiquitination by the deubiquitinating enzyme Ubp15p. In vitro pulldown assays and cross-linking studies demonstrate that Pex5p recognition by the AAA complex depends on the presence of the ubiquitin moiety and is mediated by Pex1p.
Collapse
Affiliation(s)
- Daniel Schwerter
- From the Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Systems Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Immanuel Grimm
- From the Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Systems Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Wolfgang Girzalsky
- From the Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Systems Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Ralf Erdmann
- From the Institute of Biochemistry and Pathobiochemistry, Faculty of Medicine, Systems Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| |
Collapse
|
13
|
Chen XF, Tian MX, Sun RQ, Zhang ML, Zhou LS, Jin L, Chen LL, Zhou WJ, Duan KL, Chen YJ, Gao C, Cheng ZL, Wang F, Zhang JY, Sun YP, Yu HX, Zhao YZ, Yang Y, Liu WR, Shi YH, Xiong Y, Guan KL, Ye D. SIRT5 inhibits peroxisomal ACOX1 to prevent oxidative damage and is downregulated in liver cancer. EMBO Rep 2018; 19:embr.201745124. [PMID: 29491006 DOI: 10.15252/embr.201745124] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 02/05/2018] [Accepted: 02/08/2018] [Indexed: 12/15/2022] Open
Abstract
Peroxisomes account for ~35% of total H2O2 generation in mammalian tissues. Peroxisomal ACOX1 (acyl-CoA oxidase 1) is the first and rate-limiting enzyme in fatty acid β-oxidation and a major producer of H2O2 ACOX1 dysfunction is linked to peroxisomal disorders and hepatocarcinogenesis. Here, we show that the deacetylase sirtuin 5 (SIRT5) is present in peroxisomes and that ACOX1 is a physiological substrate of SIRT5. Mechanistically, SIRT5-mediated desuccinylation inhibits ACOX1 activity by suppressing its active dimer formation in both cultured cells and mouse livers. Deletion of SIRT5 increases H2O2 production and oxidative DNA damage, which can be alleviated by ACOX1 knockdown. We show that SIRT5 downregulation is associated with increased succinylation and activity of ACOX1 and oxidative DNA damage response in hepatocellular carcinoma (HCC). Our study reveals a novel role of SIRT5 in inhibiting peroxisome-induced oxidative stress, in liver protection, and in suppressing HCC development.
Collapse
Affiliation(s)
- Xiu-Fei Chen
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Meng-Xin Tian
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China
| | - Ren-Qiang Sun
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Meng-Li Zhang
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Li-Sha Zhou
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Lei Jin
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China
| | - Lei-Lei Chen
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Wen-Jie Zhou
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Kun-Long Duan
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Yu-Jia Chen
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Chao Gao
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhou-Li Cheng
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Fang Wang
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Jin-Ye Zhang
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Yi-Ping Sun
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong-Xiu Yu
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Yu-Zheng Zhao
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yi Yang
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Wei-Ren Liu
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China
| | - Ying-Hong Shi
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Shanghai, China
| | - Yue Xiong
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kun-Liang Guan
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Department of Pharmacology and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Dan Ye
- Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Shanghai, China .,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
14
|
Mutation in the peroxin-coding gene PEX22 contributing to high malate production in Saccharomyces cerevisiae. J Biosci Bioeng 2018; 125:211-217. [DOI: 10.1016/j.jbiosc.2017.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/10/2017] [Accepted: 08/21/2017] [Indexed: 11/22/2022]
|
15
|
Ali AM, Atmaj J, Adawy A, Lunev S, Van Oosterwijk N, Yan SR, Williams C, Groves MR. The Pex4p-Pex22p complex from Hansenula polymorpha: biophysical analysis, crystallization and X-ray diffraction characterization. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2018; 74:76-81. [PMID: 29400315 DOI: 10.1107/s2053230x17018428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/24/2017] [Indexed: 01/09/2023]
Abstract
Peroxisomes are a major cellular compartment of eukaryotic cells, and are involved in a variety of metabolic functions and pathways according to species, cell type and environmental conditions. Their biogenesis relies on conserved genes known as PEX genes that encode peroxin proteins. Peroxisomal membrane proteins and peroxisomal matrix proteins are generated in the cytosol and are subsequently imported into the peroxisome post-translationally. Matrix proteins containing a peroxisomal targeting signal type 1 (PTS1) are recognized by the cycling receptor Pex5p and transported to the peroxisomal lumen. Pex5p docking, release of the cargo into the lumen and recycling involve a number of peroxins, but a key player is the Pex4p-Pex22p complex described in this manuscript. Pex4p from the yeast Saccharomyces cerevisiae is a ubiquitin-conjugating enzyme that is anchored on the cytosolic side of the peroxisomal membrane through its binding partner Pex22p, which acts as both a docking site and a co-activator of Pex4p. As Pex5p undergoes recycling and release, the Pex4p-Pex22p complex is essential for monoubiquitination at the conserved cysteine residue of Pex5p. The absence of Pex4p-Pex22p inhibits Pex5p recycling and hence PTS1 protein import. This article reports the crystallization of Pex4p and of the Pex4p-Pex22p complex from the yeast Hansenula polymorpha, and data collection from their crystals to 2.0 and 2.85 Å resolution, respectively. The resulting structures are likely to provide important insights to understand the molecular mechanism of the Pex4p-Pex22p complex and its role in peroxisome biogenesis.
Collapse
Affiliation(s)
- Ameena M Ali
- Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Jack Atmaj
- Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Alaa Adawy
- Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Sergey Lunev
- Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Niels Van Oosterwijk
- Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Sun Rei Yan
- Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Chris Williams
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Matthew R Groves
- Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands
| |
Collapse
|
16
|
Uyama T, Tsuboi K, Ueda N. An involvement of phospholipase A/acyltransferase family proteins in peroxisome regulation and plasmalogen metabolism. FEBS Lett 2017; 591:2745-2760. [PMID: 28796890 DOI: 10.1002/1873-3468.12787] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 07/31/2017] [Accepted: 07/31/2017] [Indexed: 11/09/2022]
Abstract
The H-Ras-like suppressor (HRASLS) is a protein family consisting of five members in humans. Despite their discovery as tumor suppressors, we demonstrated that all these proteins are phospholipid-metabolizing enzymes, such as phospholipase (PL) A1 /A2 and acyltransferase. We thus proposed to rename HRASLS1-5 as PLA/acyltransferase (PLAAT)-1-5. Notably, PLAATs exhibit N-acyltransferase activity to biosynthesize N-acylated ethanolamine phospholipids, including N-acyl-plasmalogen, which serve as precursors of bioactive N-acylethanolamines. Furthermore, the overexpression of PLAAT-3 in animal cells causes disappearance of peroxisomes and a remarkable reduction in plasmalogen levels. This finding might be related to the inhibitory effect of PLAAT-3 on the chaperone activity of the peroxin PEX19. In this article, we will review our recent findings about PLAAT proteins, with special reference to their roles in peroxisome biogenesis and plasmalogen metabolism.
Collapse
Affiliation(s)
- Toru Uyama
- Department of Biochemistry, Kagawa University School of Medicine, Japan
| | - Kazuhito Tsuboi
- Department of Pharmacology, Kawasaki Medical School, Kurashiki, Japan
| | - Natsuo Ueda
- Department of Biochemistry, Kagawa University School of Medicine, Japan
| |
Collapse
|
17
|
Blomqvist M, Ahlberg K, Lindgren J, Ferdinandusse S, Asin-Cayuela J. Identification of a novel mutation in PEX10 in a patient with attenuated Zellweger spectrum disorder: a case report. J Med Case Rep 2017; 11:218. [PMID: 28784167 PMCID: PMC5547663 DOI: 10.1186/s13256-017-1365-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 06/23/2017] [Indexed: 12/05/2022] Open
Abstract
Background The peroxisome biogenesis disorders, which are caused by mutations in any of 13 different PEX genes, include the Zellweger spectrum disorders. Severe defects in one of these PEX genes result in the absence of functional peroxisomes which is seen in classical Zellweger syndrome. These patients present with hypotonia and seizures shortly after birth. Other typical symptoms are dysmorphic features, liver disease, retinal degeneration, sensorineural deafness, polycystic kidneys, and the patient does not reach any developmental milestones. Case presentation We report a case of a patient with Zellweger spectrum disorder due to a novel mutation in the PEX10 gene, presenting with a mild late-onset neurological phenotype. The patient, an Assyrian girl originating from Iraq, presented with sensorineural hearing impairment at the age of 5 followed by sensorimotor polyneuropathy, cognitive delay, impaired gross and fine motor skills, and tremor and muscle weakness in her teens. Analyses of biochemical markers for peroxisomal disease suggested a mild peroxisomal defect and functional studies in fibroblasts confirmed the existence of a peroxisome biogenesis disorder. Diagnosis was confirmed by next generation sequencing analysis, which showed a novel homozygous mutation (c.530 T > G (p.Leu177Arg) (NM_153818.1)) in the PEX10 gene predicted to be pathogenic. Conclusions This case highlights the importance of performing biochemical, functional, and genetic peroxisomal screening in patients with clinical presentations milder than those usually observed in Zellweger spectrum disorders.
Collapse
Affiliation(s)
- Maria Blomqvist
- Institute of Biomedicine, Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden.
| | - Karin Ahlberg
- Paediatric Clinic, Central Hospital, S-65185, Karlstad, Sweden
| | - Julia Lindgren
- Institute of Biomedicine, Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Academic Medical Center, Amsterdam, The Netherlands
| | - Jorge Asin-Cayuela
- Institute of Biomedicine, Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| |
Collapse
|
18
|
Emmanouilidis L, Gopalswamy M, Passon DM, Wilmanns M, Sattler M. Structural biology of the import pathways of peroxisomal matrix proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:804-13. [DOI: 10.1016/j.bbamcr.2015.09.034] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 09/29/2015] [Accepted: 09/30/2015] [Indexed: 11/28/2022]
|
19
|
Konkoľová J, Petrovič R, Chandoga J, Halasová E, Jungová P, Böhmer D. A novel mutation in the PEX12 gene causing a peroxisomal biogenesis disorder. Mol Biol Rep 2015; 42:1359-63. [PMID: 26094004 DOI: 10.1007/s11033-015-3885-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 06/17/2015] [Indexed: 11/24/2022]
Abstract
The peroxisomal biogenesis disorders are autosomal recessive diseases morphologically characterised by lacking peroxisomes, biochemically by generalised deficiency of peroxisomal constituent and clinically manifested by serious health problems. Genes involved in the peroxisomal biogenesis are defined as the PEX genes encoding proteins called the peroxins. These peroxins are required for function in assembly of the peroxisomal membrane or in import of the enzymes into the peroxisomes. In this study we present a full overview of the clinical presentation, biochemical and molecular data of patient with Zellweger syndrome from Slovakia. We investigated biochemical metabolites using gas chromatography/mass spectrometry. The presence of causal ins/del mutations we identified by a Sanger sequencing and RFLP. We reported that the patient was a compound heterozygote for mutations in the gene PEX12: a 2-bp insertion (c.767_768dupAT) and a 2-bp deletion (c.887_888delTC). The first one mentioned is a novel mutation, which has not been reported before. Both mutations create a frameshift of the open reading frame which result a premature STOP codon and generate a complete loss of the C-terminal RING finger domain that is crucial for the correct import of proteins into peroxisomes. We found causal mutations responsible for a severe phenotype, and moreover we noted a novel mutation c.767_768dupAT that has not been reported before. The presence of mutations was studied in all family members, and the resulting data were successfully utilized for prenatal diagnosis.
Collapse
Affiliation(s)
- Jana Konkoľová
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine & University Hospital Bratislava, Comenius University, Sasinkova 4, 811 08, Bratislava, Slovakia,
| | | | | | | | | | | |
Collapse
|
20
|
Kunze M, Malkani N, Maurer-Stroh S, Wiesinger C, Schmid JA, Berger J. Mechanistic insights into PTS2-mediated peroxisomal protein import: the co-receptor PEX5L drastically increases the interaction strength between the cargo protein and the receptor PEX7. J Biol Chem 2014; 290:4928-4940. [PMID: 25538232 DOI: 10.1074/jbc.m114.601575] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The destination of peroxisomal matrix proteins is encoded by short peptide sequences, which have been characterized as peroxisomal targeting signals (PTS) residing either at the C terminus (PTS1) or close to the N terminus (PTS2). PTS2-carrying proteins interact with their cognate receptor protein PEX7 that mediates their transport to peroxisomes by a concerted action with a co-receptor protein, which in mammals is the PTS1 receptor PEX5L. Using a modified version of the mammalian two-hybrid assay, we demonstrate that the interaction strength between cargo and PEX7 is drastically increased in the presence of the co-receptor PEX5L. In addition, cargo binding is a prerequisite for the interaction between PEX7 and PEX5L and ectopic overexpression of PTS2-carrying cargo protein drastically increases the formation of PEX7-PEX5L complexes in this assay. Consistently, we find that the peroxisomal transfer of PEX7 depends on cargo binding and that ectopic overexpression of cargo protein stimulates this process. Thus, the sequential formation of a highly stable trimeric complex involving cargo protein, PEX7 and PEX5L stabilizes cargo binding and is a prerequisite for PTS2-mediated peroxisomal import.
Collapse
Affiliation(s)
- Markus Kunze
- Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria,.
| | - Naila Malkani
- Department of Vascular Biology and Thrombosis Research, Medical University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Singapore 138671; School of Biological Sciences (SBS), Nanyang Technological University (NTU), 8 Medical Drive, Singapore 117597
| | - Christoph Wiesinger
- Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
| | - Johannes A Schmid
- Department of Vascular Biology and Thrombosis Research, Medical University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Johannes Berger
- Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
| |
Collapse
|
21
|
Kim DH, Park MJ, Gwon GH, Silkov A, Xu ZY, Yang EC, Song S, Song K, Kim Y, Yoon HS, Honig B, Cho W, Cho Y, Hwang I. An ankyrin repeat domain of AKR2 drives chloroplast targeting through coincident binding of two chloroplast lipids. Dev Cell 2014; 30:598-609. [PMID: 25203210 DOI: 10.1016/j.devcel.2014.07.026] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 05/22/2014] [Accepted: 07/31/2014] [Indexed: 10/24/2022]
Abstract
In organellogenesis of the chloroplast from endosymbiotic cyanobacteria, the establishment of protein-targeting mechanisms to the chloroplast should have been pivotal. However, it is still mysterious how these mechanisms were established and how they work in plant cells. Here we show that AKR2A, the cytosolic targeting factor for chloroplast outer membrane (COM) proteins, evolved from the ankyrin repeat domain (ARD) of the host cell by stepwise extensions of its N-terminal domain and that two lipids, monogalactosyldiacylglycerol (MGDG) and phosphatidylglycerol (PG), of the endosymbiont were selected to function as the AKR2A receptor. Structural analysis, molecular modeling, and mutational analysis of the ARD identified two adjacent sites for coincidental and synergistic binding of MGDG and PG. Based on these findings, we propose that the targeting mechanism of COM proteins was established using components from both the endosymbiont and host cell through a modification of the protein-protein-interacting ARD into a lipid binding domain.
Collapse
Affiliation(s)
- Dae Heon Kim
- Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Mi-Jeong Park
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Gwang Hyeon Gwon
- Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Antonina Silkov
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, NY 11032, USA
| | - Zheng-Yi Xu
- Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Eun Chan Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Korea
| | - Seohyeon Song
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Kyungyoung Song
- Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Younghyun Kim
- Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Korea
| | - Barry Honig
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, NY 11032, USA
| | - Wonhwa Cho
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, Korea; Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA.
| | - Yunje Cho
- Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea.
| | - Inhwan Hwang
- Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea; Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, Korea.
| |
Collapse
|
22
|
Karmous I, Chaoui A, Jaouani K, Sheehan D, El Ferjani E, Scoccianti V, Crinelli R. Role of the ubiquitin-proteasome pathway and some peptidases during seed germination and copper stress in bean cotyledons. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 76:77-85. [PMID: 24486582 DOI: 10.1016/j.plaphy.2013.12.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 12/30/2013] [Indexed: 05/12/2023]
Abstract
The role of the ubiquitin (Ub)-proteasome pathway and some endo- and aminopeptidases (EPs and APs, respectively) was studied in cotyledons of germinating bean seeds (Phaseolus vulgaris L.). The Ub system appeared to be important both in the early (3 days) and late (9 days) phases of germination. In the presence of copper, an increase in protein carbonylation and a decrease in reduced -SH pool occurred, indicating protein damage. This was associated with an enhancement in accumulation of malondialdehyde, a major product of lipid peroxidation, and an increase in content of hydrogen peroxide (H2O2), showing oxidative stress generation. Moreover, copper induced inactivation of the Ub-proteasome (EC 3.4.25) pathway and inhibition of leucine and proline aminopeptidase activities (EC 3.4.11.1 and EC 3.4.11.5, respectively), thus limiting their role in modulating essential metabolic processes, such as the removal of regulatory and oxidatively-damaged proteins. By contrast, total trypsin and chymotrypsin-like activities (EC 3.4.21.4 and EC 3.4.21.1, respectively) increased after copper exposure, in parallel with a decrease in their inhibitor capacities (i.e. trypsin inhibitor and chymotrypsin inhibitor activity), suggesting that these endoproteases are part of the protective mechanisms against copper stress.
Collapse
Affiliation(s)
- Inès Karmous
- Plant Toxicology and Molecular Biology of Microorganisms, Faculty of Sciences of Bizerta, 7021 Zarzouna, Tunisia.
| | - Abdelilah Chaoui
- Plant Toxicology and Molecular Biology of Microorganisms, Faculty of Sciences of Bizerta, 7021 Zarzouna, Tunisia.
| | - Khadija Jaouani
- Plant Toxicology and Molecular Biology of Microorganisms, Faculty of Sciences of Bizerta, 7021 Zarzouna, Tunisia.
| | - David Sheehan
- Proteomics Research Group, Department of Biochemistry and Environmental Research Institute University College Cork, Lee Maltings, Prospect Row, Mardyke, Cork, Ireland.
| | - Ezzedine El Ferjani
- Plant Toxicology and Molecular Biology of Microorganisms, Faculty of Sciences of Bizerta, 7021 Zarzouna, Tunisia.
| | - Valeria Scoccianti
- Dipartimento di Scienze della Terra, della Vita e dell'Ambiente, Sezione di Biologia Vegetale, Università di Urbino "Carlo Bo", Via Bramante 28, 61029 Urbino, Italy.
| | - Rita Crinelli
- Dipartimento di Scienze Biomolecolari, Sezione di Biochimica e Biologia Molecolare, Università di Urbino "Carlo Bo", Via Saffi 2, 61029 Urbino, Italy.
| |
Collapse
|
23
|
Li L, Wang J, Zhang Z, Wang Y, Liu M, Jiang H, Chai R, Mao X, Qiu H, Liu F, Sun G. MoPex19, which is essential for maintenance of peroxisomal structure and woronin bodies, is required for metabolism and development in the rice blast fungus. PLoS One 2014; 9:e85252. [PMID: 24454828 PMCID: PMC3891873 DOI: 10.1371/journal.pone.0085252] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 11/24/2013] [Indexed: 11/19/2022] Open
Abstract
Peroxisomes are present ubiquitously and make important contributions to cellular metabolism in eukaryotes. They play crucial roles in pathogenicity of plant fungal pathogens. The peroxisomal matrix proteins and peroxisomal membrane proteins (PMPs) are synthesized in the cytosol and imported post-translationally. Although the peroxisomal import machineries are generally conserved, some species-specific features were found in different types of organisms. In phytopathogenic fungi, the pathways of the matrix proteins have been elucidated, while the import machinery of PMPs remains obscure. Here, we report that MoPEX19, an ortholog of ScPEX19, was required for PMPs import and peroxisomal maintenance, and played crucial roles in metabolism and pathogenicity of the rice blast fungus Magnaporthe oryzae. MoPEX19 was expressed in a low level and Mopex19p was distributed in the cytoplasm and newly formed peroxisomes. MoPEX19 deletion led to mislocalization of peroxisomal membrane proteins (PMPs), as well peroxisomal matrix proteins. Peroxisomal structures were totally absent in Δmopex19 mutants and woronin bodies also vanished. Δmopex19 exhibited metabolic deficiency typical in peroxisomal disorders and also abnormality in glyoxylate cycle which was undetected in the known mopex mutants. The Δmopex19 mutants performed multiple disorders in fungal development and pathogenicity-related morphogenesis, and lost completely the pathogenicity on its hosts. These data demonstrate that MoPEX19 plays crucial roles in maintenance of peroxisomal and peroxisome-derived structures and makes more contributions to fungal development and pathogenicity than the known MoPEX genes in the rice blast fungus.
Collapse
Affiliation(s)
- Ling Li
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiaoyu Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhen Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yanli Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Maoxin Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hua Jiang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Rongyao Chai
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xueqin Mao
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Haiping Qiu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Fengquan Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- * E-mail: (FL); (GS)
| | - Guochang Sun
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- * E-mail: (FL); (GS)
| |
Collapse
|
24
|
Dolze E, Chigri F, Höwing T, Hierl G, Isono E, Vothknecht UC, Gietl C. Calmodulin-like protein AtCML3 mediates dimerization of peroxisomal processing protease AtDEG15 and contributes to normal peroxisome metabolism. PLANT MOLECULAR BIOLOGY 2013; 83:607-24. [PMID: 23943091 PMCID: PMC3830196 DOI: 10.1007/s11103-013-0112-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 07/17/2013] [Indexed: 05/22/2023]
Abstract
Matrix enzymes are imported into peroxisomes and glyoxysomes, a subclass of peroxisomes involved in lipid mobilization. Two peroxisomal targeting signals (PTS), the C-terminal PTS1 and the N-terminal PTS2, mediate the translocation of proteins into the organelle. PTS2 processing upon import is conserved in higher eukaryotes, and in watermelon the glyoxysomal processing protease (GPP) was shown to catalyse PTS2 processing. GPP and its ortholog, the peroxisomal DEG protease from Arabidopsis thaliana (AtDEG15), belong to the Deg/HtrA family of ATP-independent serine proteases with Escherichia coli DegP as their prototype. GPP existes in monomeric and dimeric forms. Their equilibrium is shifted towards the monomer upon Ca(2+)-removal and towards the dimer upon Ca(2+)-addition, which is accompanied by a change in substrate specificity from a general protease (monomer) to the specific cleavage of the PTS2 (dimer). We describe the Ca(2+)/calmodulin (CaM) mediated dimerization of AtDEG15. Dimerization is mediated by the CaM-like protein AtCML3 as shown by yeast two and three hybrid analyses. The binding of AtCML3 occurs within the first 25 N-terminal amino acids of AtDEG15, a domain containing a predicted CaM-binding motif. Biochemical analysis of AtDEG15 deletion constructs in planta support the requirement of the CaM-binding domain for PTS2 processing. Phylogenetic analyses indicate that the CaM-binding site is conserved in peroxisomal processing proteases of higher plants (dicots, monocots) but not present in orthologs of animals or cellular slime molds. Despite normal PTS2 processing activity, an atcml3 mutant exhibited reduced 2,4-DB sensitivity, a phenotype previously reported for the atdeg15 mutant, indicating similarly impaired peroxisome metabolism.
Collapse
Affiliation(s)
- Esther Dolze
- Institute of Botany, Center of Life and Food Sciences Weihenstephan, TU Munich, Emil-Ramann-Str. 4, 85350 Freising, Germany
| | - Fatima Chigri
- Department of Biology, Center of Integrated Protein Science, LMU Munich, 82152 Martinsried, Germany
| | - Timo Höwing
- Institute of Botany, Center of Life and Food Sciences Weihenstephan, TU Munich, Emil-Ramann-Str. 4, 85350 Freising, Germany
| | - Georg Hierl
- Institute of Botany, Center of Life and Food Sciences Weihenstephan, TU Munich, Emil-Ramann-Str. 4, 85350 Freising, Germany
| | - Erika Isono
- Department of Plant Systems Biology, Center of Life and Food Sciences Weihenstephan, TU Munich, 85350 Freising, Germany
| | - Ute C. Vothknecht
- Department of Biology, Center of Integrated Protein Science, LMU Munich, 82152 Martinsried, Germany
| | - Christine Gietl
- Institute of Botany, Center of Life and Food Sciences Weihenstephan, TU Munich, Emil-Ramann-Str. 4, 85350 Freising, Germany
| |
Collapse
|
25
|
Vamecq J, Cherkaoui-Malki M, Andreoletti P, Latruffe N. The human peroxisome in health and disease: the story of an oddity becoming a vital organelle. Biochimie 2013; 98:4-15. [PMID: 24075875 DOI: 10.1016/j.biochi.2013.09.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 09/18/2013] [Indexed: 12/18/2022]
Abstract
Since the first report by Rhodin in 1954, our knowledge on mammalian microbodies/peroxisomes has known several periods. An initial two decades period (1954-1973) has contributed to the biochemical individualisation of peroxisomes as a new class of subcellular organelles (de Duve, 1965). The corresponding research period failed to define a clear role of mammalian peroxisomes in vital functions and intermediary metabolism, explaining why feeling that peroxisomes might be in the human cell oddities has prevailed during several decades. The period standing from 1973 to nowadays has progressively removed this cell oddity view of peroxisomes by highlighting vital function and metabolic role of peroxisomes in health and disease along with genetic and metabolic regulation of peroxisomal protein content, organelle envelope formation and protein signal targeting mechanisms. Research on peroxisomes and their response to various drugs and metabolites, dietary and physiological conditions has also played a key role in the discovery of peroxisome proliferator activated receptors (PPARs) belonging to the nuclear hormone receptor superfamily and for which impact in science and medicine goes now by far beyond that of the peroxisomes.
Collapse
Affiliation(s)
- Joseph Vamecq
- INSERM, Laboratory of Biochemistry and Molecular Biology, Hormonology-Metabolism-Nutrition-Oncology, Centre of Biology and Pathology (CBP), CHU Lille, France.
| | - Mustapha Cherkaoui-Malki
- Laboratory of Biochemistry of Peroxisome, Inflammation & Lipids Metabolism (BioPeroxIL-EA7270), University of Burgundy, 21000 Dijon, France
| | - Pierre Andreoletti
- Laboratory of Biochemistry of Peroxisome, Inflammation & Lipids Metabolism (BioPeroxIL-EA7270), University of Burgundy, 21000 Dijon, France
| | - Norbert Latruffe
- Laboratory of Biochemistry of Peroxisome, Inflammation & Lipids Metabolism (BioPeroxIL-EA7270), University of Burgundy, 21000 Dijon, France
| |
Collapse
|
26
|
Abstract
PMPs (peroxisome membrane proteins) play essential roles in organelle biogenesis and in co-ordinating peroxisomal metabolism with pathways in other subcellular compartments through transport of metabolites and the operation of redox shuttles. Although the import of soluble proteins into the peroxisome matrix has been well studied, much less is known about the trafficking of PMPs. Pex3 and Pex19 (and Pex16 in mammals) were identified over a decade ago as critical components of PMP import; however, it has proved surprisingly difficult to produce a unified model for their function in PMP import and peroxisome biogenesis. It has become apparent that each of these peroxins has multiple functions and in the present review we focus on both the classical and the more recently identified roles of Pex19 and Pex3 as informed by structural, biochemical and live cell imaging studies. We consider the different models proposed for peroxisome biogenesis and the role of PMP import within them, and propose that the differences may be more perceived than real and may reflect the highly dynamic nature of peroxisomes.
Collapse
|
27
|
Farnesyl diphosphate synthase, the target for nitrogen-containing bisphosphonate drugs, is a peroxisomal enzyme in the model system Dictyostelium discoideum. Biochem J 2012; 447:353-61. [PMID: 22849378 PMCID: PMC3465988 DOI: 10.1042/bj20120750] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
NBP (nitrogen-containing bisphosphonate) drugs protect against excessive osteoclast-mediated bone resorption. After binding to bone mineral, they are taken up selectively by the osteoclasts and inhibit the essential enzyme FDPS (farnesyl diphosphate synthase). NBPs inhibit also growth of amoebae of Dictyostelium discoideum in which their target is again FDPS. A fusion protein between FDPS and GFP (green fluorescent protein) was found, in D. discoideum, to localize to peroxisomes and to confer resistance to the NBP alendronate. GFP was also directed to peroxisomes by a fragment of FDPS comprising amino acids 1–22. This contains a sequence of nine amino acids that closely resembles the nonapeptide PTS2 (peroxisomal targeting signal type 2): there is only a single amino acid mismatch between the two sequences. Mutation analysis confirmed that the atypical PTS2 directs FDPS into peroxisomes. Furthermore, expression of the D. discoideum FDPS–GFP fusion protein in strains of Saccharomyces cerevisiae defective in peroxisomal protein import demonstrated that import of FDPS into peroxisomes was blocked in a strain lacking the PTS2-dependent import pathway. The peroxisomal location of FDPS in D. discoideum indicates that NBPs have to cross the peroxisomal membrane before they can bind to their target.
Collapse
|
28
|
Pieuchot L, Jedd G. Peroxisome Assembly and Functional Diversity in Eukaryotic Microorganisms. Annu Rev Microbiol 2012; 66:237-63. [DOI: 10.1146/annurev-micro-092611-150126] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Laurent Pieuchot
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 117604 Singapore; ,
| | - Gregory Jedd
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 117604 Singapore; ,
| |
Collapse
|
29
|
Finley D, Ulrich HD, Sommer T, Kaiser P. The ubiquitin-proteasome system of Saccharomyces cerevisiae. Genetics 2012; 192:319-60. [PMID: 23028185 PMCID: PMC3454868 DOI: 10.1534/genetics.112.140467] [Citation(s) in RCA: 301] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 07/28/2012] [Indexed: 12/14/2022] Open
Abstract
Protein modifications provide cells with exquisite temporal and spatial control of protein function. Ubiquitin is among the most important modifiers, serving both to target hundreds of proteins for rapid degradation by the proteasome, and as a dynamic signaling agent that regulates the function of covalently bound proteins. The diverse effects of ubiquitylation reflect the assembly of structurally distinct ubiquitin chains on target proteins. The resulting ubiquitin code is interpreted by an extensive family of ubiquitin receptors. Here we review the components of this regulatory network and its effects throughout the cell.
Collapse
Affiliation(s)
- Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Helle D. Ulrich
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, EN6 3LD, United Kingdom
| | - Thomas Sommer
- Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Peter Kaiser
- Department of Biological Chemistry, University of California, Irvine, California 92697
| |
Collapse
|
30
|
Baes M, Van Veldhoven PP. Mouse models for peroxisome biogenesis defects and β-oxidation enzyme deficiencies. Biochim Biophys Acta Mol Basis Dis 2012; 1822:1489-500. [DOI: 10.1016/j.bbadis.2012.03.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Revised: 02/22/2012] [Accepted: 03/06/2012] [Indexed: 12/26/2022]
|
31
|
Xiao Y, Karnati S, Qian G, Nenicu A, Fan W, Tchatalbachev S, Höland A, Hossain H, Guillou F, Lüers GH, Baumgart-Vogt E. Cre-mediated stress affects sirtuin expression levels, peroxisome biogenesis and metabolism, antioxidant and proinflammatory signaling pathways. PLoS One 2012; 7:e41097. [PMID: 22829911 PMCID: PMC3400606 DOI: 10.1371/journal.pone.0041097] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 06/21/2012] [Indexed: 11/28/2022] Open
Abstract
Cre-mediated excision of loxP sites is widely used in mice to manipulate gene function in a tissue-specific manner. To analyze phenotypic alterations related to Cre-expression, we have used AMH-Cre-transgenic mice as a model system. Different Cre expression levels were obtained by investigation of C57BL/6J wild type as well as heterozygous and homozygous AMH-Cre-mice. Our results indicate that Cre-expression itself in Sertoli cells already has led to oxidative stress and lipid peroxidation (4-HNE lysine adducts), inducing PPARα/γ, peroxisome proliferation and alterations of peroxisome biogenesis (PEX5, PEX13 and PEX14) as well as metabolic proteins (ABCD1, ABCD3, MFP1, thiolase B, catalase). In addition to the strong catalase increase, a NRF2- and FOXO3-mediated antioxidative response (HMOX1 of the endoplasmic reticulum and mitochondrial SOD2) and a NF-κB activation were noted. TGFβ1 and proinflammatory cytokines like IL1, IL6 and TNFα were upregulated and stress-related signaling pathways were induced. Sertoli cell mRNA-microarray analysis revealed an increase of TNFR2-signaling components. 53BP1 recruitment and expression levels for DNA repair genes as well as for p53 were elevated and the ones for related sirtuin deacetylases affected (SIRT 1, 3-7) in Sertoli cells. Under chronic Cre-mediated DNA damage conditions a strong downregulation of Sirt1 was observed, suggesting that the decrease of this important coordinator between DNA repair and metabolic signaling might induce the repression release of major transcription factors regulating metabolic and cytokine-mediated stress pathways. Indeed, caspase-3 was activated and increased germ cell apoptosis was observed, suggesting paracrine effects. In conclusion, the observed wide stress-induced effects and metabolic alterations suggest that it is essential to use the correct control animals (Cre/Wt) with matched Cre expression levels to differentiate between Cre-mediated and specific gene-knock out-mediated effects.
Collapse
Affiliation(s)
- Yu Xiao
- Institute for Anatomy and Cell Biology II, Justus Liebig University Giessen, Giessen, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Cryptic peroxisomal targeting via alternative splicing and stop codon read-through in fungi. Nature 2012; 485:522-5. [PMID: 22622582 DOI: 10.1038/nature11051] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 03/21/2012] [Indexed: 11/09/2022]
Abstract
Peroxisomes are eukaryotic organelles important for the metabolism of long-chain fatty acids. Here we show that in numerous fungal species, several core enzymes of glycolysis, including glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and 3-phosphoglycerate kinase (PGK), reside in both the cytoplasm and peroxisomes. We detected in these enzymes cryptic type 1 peroxisomal targeting signals (PTS1), which are activated by post-transcriptional processes. Notably, the molecular mechanisms that generate the peroxisomal isoforms vary considerably among different species. In the basidiomycete plant pathogen Ustilago maydis, peroxisomal targeting of Pgk1 results from ribosomal read-through, whereas alternative splicing generates the PTS1 of Gapdh. In the filamentous ascomycete Aspergillus nidulans, peroxisomal targeting of these enzymes is achieved by exactly the opposite mechanisms. We also detected PTS1 motifs in the glycolytic enzymes triose-phosphate isomerase and fructose-bisphosphate aldolase. U. maydis mutants lacking the peroxisomal isoforms of Gapdh or Pgk1 showed reduced virulence. In addition, mutational analysis suggests that GAPDH, together with other peroxisomal NADH-dependent dehydrogenases, has a role in redox homeostasis. Owing to its hidden nature, partial peroxisomal targeting of well-studied cytoplasmic enzymes has remained undetected. Thus, we anticipate that further bona fide cytoplasmic proteins exhibit similar dual targeting.
Collapse
|
33
|
|
34
|
Mignarri A, Vinciguerra C, Giorgio A, Ferdinandusse S, Waterham H, Wanders R, Bertini E, Dotti MT, Federico A. Zellweger Spectrum Disorder with Mild Phenotype Caused by PEX2 Gene Mutations. JIMD Rep 2012; 6:43-6. [PMID: 23430938 DOI: 10.1007/8904_2011_102] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 09/30/2011] [Accepted: 09/30/2011] [Indexed: 12/12/2022] Open
Abstract
The Zellweger spectrum disorders (ZSDs) are known to be severe disorders with onset in the newborn period or later in childhood, frequently resulting in death during childhood or adolescence. Here, we report a case of ZSD due to mutations in the PEX2 gene, with very mild phenotype. A 51-year-old Italian man was referred to us because of a clinical picture characterized by ataxia, areflexia, nystagmus, and strabismus, with childhood onset and slowly progressive course. The patient showed no cognitive impairment. Neurological examination revealed gait ataxia, dysarthria, dysmetria, areflexia, and bilateral pes cavus. Nerve conduction studies indicated a severe axonal sensorimotor polyneuropathy. Brain MRI showed marked cerebellar atrophy and absence of white matter involvement. MR spectroscopy uncovered a decreased N-acetyl aspartate peak. Biochemical analyses suggested a mild peroxisomal defect. Sequence analysis of the PEX2 gene identified two heterozygous mutations. The clinical phenotype of our patient differs from previously reported ZSD patients with PEX2 gene mutations and suggests that genetic screening of PEX2 is warranted in children and adults with otherwise unexplained autosomal recessive ataxia. MRI findings diverged from the "classic" spectrum observed in ZSDs. The moderate impairment in peroxisome biogenesis seems to affect predominantly neuronal cells in cerebellum, leading to cerebellar atrophy.
Collapse
Affiliation(s)
- Andrea Mignarri
- Department of Neurological, Neurosurgical and Behavioural Sciences, Medical School, University of Siena, Viale Bracci 2, Siena, 53100, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Grimm I, Saffian D, Platta HW, Erdmann R. The AAA-type ATPases Pex1p and Pex6p and their role in peroxisomal matrix protein import in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:150-8. [DOI: 10.1016/j.bbamcr.2011.09.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 09/02/2011] [Accepted: 09/03/2011] [Indexed: 12/25/2022]
|
36
|
Uyama T, Ichi I, Kono N, Inoue A, Tsuboi K, Jin XH, Araki N, Aoki J, Arai H, Ueda N. Regulation of peroxisomal lipid metabolism by catalytic activity of tumor suppressor H-rev107. J Biol Chem 2011; 287:2706-18. [PMID: 22134920 DOI: 10.1074/jbc.m111.267575] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
H-rev107 is a mammalian protein belonging to the HRAS-like suppressor family. Although the protein was originally found as a tumor suppressor, currently it is receiving considerable attention as a regulator of adipocyte lipolysis. We recently revealed that purified recombinant H-rev107 has phospholipase A(1/2) activity, releasing free fatty acids from glycerophospholipids with a preference for esterolysis at the sn-1 position. In the present study, we constitutively expressed H-rev107 in cloned HEK293 cells to examine its biological function in living cells. Initially, the cells accumulated free fatty acids. We also found a remarkable decrease in the levels of ether-type lipids, including plasmalogen and ether-type triglyceride, with a concomitant increase in fatty alcohols, substrates for the biosynthesis of ether-type lipids. Considering that peroxisomes are involved in the ether-type lipid biosynthesis, we next focused on peroxisomes and found that the peroxisomal markers 70-kDa peroxisomal membrane protein and catalase were abnormally distributed in the transfected cells. These biochemical and morphological abnormalities were not seen in HEK293 cells stably expressing a catalytically inactive mutant of H-rev107. When H-rev107 or its fusion protein with enhanced green fluorescence protein was transiently expressed in mammalian cells, both proteins were associated with peroxisomes in some of the observed cells. These results suggest that H-rev107 interferes with the biosynthesis of ether-type lipids and is responsible for the dysfunction of peroxisomes in H-rev107-expressing cells.
Collapse
Affiliation(s)
- Toru Uyama
- Department of Biochemistry, Kagawa University School of Medicine, 1750-1 Ikenobe, Miki, Kagawa 761-0793, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Liu F, Lu Y, Pieuchot L, Dhavale T, Jedd G. Import oligomers induce positive feedback to promote peroxisome differentiation and control organelle abundance. Dev Cell 2011; 21:457-68. [PMID: 21920312 DOI: 10.1016/j.devcel.2011.08.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 05/06/2011] [Accepted: 08/02/2011] [Indexed: 11/28/2022]
Abstract
A fundamental question in cell biology is how cells control organelle composition and abundance. Woronin bodies are fungal peroxisomes centered on a crystalline core of the self-assembled HEX protein. Despite using the canonical peroxisome import machinery for biogenesis, Woronin bodies are scarce compared to the overall peroxisome population. Here, we show that HEX oligomers promote the differentiation of a subpopulation of peroxisomes, which become enlarged and highly active in matrix protein import. HEX physically associates with the essential matrix import peroxin, PEX26, and promotes its enrichment in the membrane of differentiated peroxisomes. In addition, a PEX26 mutant that disrupts differentiation produces increased numbers of aberrantly small Woronin bodies. Our data suggest a mechanism where HEX oligomers recruit a key component of the import machinery, which promotes the import of additional HEX. This type of positive feedback provides a basic mechanism for the production of an organelle subpopulation of distinct composition and abundance.
Collapse
Affiliation(s)
- Fangfang Liu
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, Singapore
| | | | | | | | | |
Collapse
|
38
|
Nuttall JM, Motley A, Hettema EH. Peroxisome biogenesis: recent advances. Curr Opin Cell Biol 2011; 23:421-6. [PMID: 21689915 DOI: 10.1016/j.ceb.2011.05.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 04/27/2011] [Accepted: 05/17/2011] [Indexed: 11/27/2022]
Abstract
In recent years, it has become evident that peroxisomes form part of the endomembrane system. Peroxisomes can form from the ER via a maturation process and they can multiply by growth and division, whereby the ER provides membrane for growth and ongoing fission (Figure 1). Until very recently, it was widely accepted that most peroxisomal membrane proteins (PMPs) insert directly into peroxisomes, whereas a small subset of PMPs traffic via the ER. In this minireview, we focus mainly on PMP biogenesis, and highlight recent advances in peroxisomal matrix protein import, fission and segregation in yeast.
Collapse
Affiliation(s)
- James M Nuttall
- Dept. Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom
| | | | | |
Collapse
|
39
|
Peraza-Reyes L, Arnaise S, Zickler D, Coppin E, Debuchy R, Berteaux-Lecellier V. The importomer peroxins are differentially required for peroxisome assembly and meiotic development in Podospora anserina: insights into a new peroxisome import pathway. Mol Microbiol 2011; 82:365-77. [PMID: 21895788 DOI: 10.1111/j.1365-2958.2011.07816.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Peroxisome biogenesis relies on two known peroxisome matrix protein import pathways that are mediated by the receptors PEX5 and PEX7. These pathways converge at the importomer, a peroxisome-membrane complex that is required for protein translocation into peroxisomes and consists of docking and RING-finger subcomplexes. In the fungus Podospora anserina, the RING-finger peroxins are crucial for meiocyte formation, while PEX5, PEX7 or the docking peroxin PEX14 are not. Here we show that PEX14 and the PEX14-related protein PEX14/17 are differentially involved in peroxisome import during development. PEX14/17 activity does not compensate for loss of PEX14 function, and elimination of both proteins has no effect on meiocyte differentiation. In contrast, the docking peroxin PEX13, and the peroxins implicated in peroxisome membrane biogenesis PEX3 and PEX19, are required for meiocyte formation. Remarkably, the PTS2 coreceptor PEX20 is also essential for meiocyte differentiation and this function does not require PEX5 or PEX7. This finding suggests that PEX20 can mediate the import receptor activity of specific peroxisome matrix proteins. Our results suggest a new pathway for peroxisome import, which relies on PEX20 as import receptor and which seems critically required for specific developmental processes, like meiocyte differentiation in P. anserina.
Collapse
Affiliation(s)
- Leonardo Peraza-Reyes
- Institut de Génétique et Microbiologie, Univ. Paris-Sud, UMR8621, F-91405 Orsay, France.
| | | | | | | | | | | |
Collapse
|
40
|
Dastig S, Nenicu A, Otte DM, Zimmer A, Seitz J, Baumgart-Vogt E, Lüers GH. Germ cells of male mice express genes for peroxisomal metabolic pathways implicated in the regulation of spermatogenesis and the protection against oxidative stress. Histochem Cell Biol 2011; 136:413-25. [PMID: 21898072 DOI: 10.1007/s00418-011-0832-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2011] [Indexed: 12/21/2022]
Abstract
Peroxisomes are organelles with main functions in the metabolism of lipids and of reactive oxygen species. Within the testis, they have different functional profiles depending on the cell types. A dysfunction of peroxisomes interferes with regular spermatogenesis and can lead to infertility due to spermatogenic arrest. However, so far only very little is known about the functions of peroxisomes in germ cells. We have therefore analyzed the peroxisomal compartment in germ cells and its alterations during spermatogenesis by fluorescence and electron microscopy as well as by expression profiling of peroxisome-related genes in purified cell populations isolated from mouse testis. We could show that peroxisomes are present in all germ cells of the germinal epithelium. During late spermiogenesis, the peroxisomes form large clusters that are segregated from the spermatozoa into the residual bodies upon release from the germinal epithelium. Germ cells express genes for proteins involved in numerous metabolic pathways of peroxisomes. Based on the expression profile, we conclude that newly identified functions of germ cell peroxisomes are the synthesis of plasmalogens as well as the metabolism of retinoids, polyunsaturated fatty acids and polyamines. Thus, germ cell peroxisomes are involved in the regulation of the homeostasis of signaling molecules regulating spermatogenesis and they contribute to the protection of germ cells against oxidative stress.
Collapse
Affiliation(s)
- Sandra Dastig
- Department of Anatomy and Cell Biology, University of Marburg, Marburg, Germany
| | | | | | | | | | | | | |
Collapse
|
41
|
Zhang X, De Marcos Lousa C, Schutte-Lensink N, Ofman R, Wanders RJ, Baldwin SA, Baker A, Kemp S, Theodoulou FL. Conservation of targeting but divergence in function and quality control of peroxisomal ABC transporters: an analysis using cross-kingdom expression. Biochem J 2011; 436:547-57. [PMID: 21476988 DOI: 10.1042/bj20110249] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
ABC (ATP-binding cassette) subfamily D transporters are found in all eukaryotic kingdoms and are known to play essential roles in mammals and plants; however, their number, organization and physiological contexts differ. Via cross-kingdom expression experiments, we have explored the conservation of targeting, protein stability and function between mammalian and plant ABCD transporters. When expressed in tobacco epidermal cells, the mammalian ABCD proteins ALDP (adrenoleukodystrophy protein), ALDR (adrenoleukodystrophy-related protein) and PMP70 (70 kDa peroxisomal membrane protein) targeted faithfully to peroxisomes and P70R (PMP70-related protein) targeted to the ER (endoplasmic reticulum), as in the native host. The Arabidopsis thaliana peroxin AtPex19_1 interacted with human peroxisomal ABC transporters both in vivo and in vitro, providing an explanation for the fidelity of targeting. The fate of X-linked adrenoleukodystrophy disease-related mutants differed between fibroblasts and plant cells. In fibroblasts, levels of ALDP in some 'protein-absent' mutants were increased by low-temperature culture, in some cases restoring function. In contrast, all mutant ALDP proteins examined were stable and correctly targeted in plant cells, regardless of their fate in fibroblasts. ALDR complemented the seed germination defect of the Arabidopsis cts-1 mutant which lacks the peroxisomal ABCD transporter CTS (Comatose), but neither ALDR nor ALDP was able to rescue the defect in fatty acid β-oxidation in establishing seedlings. Taken together, our results indicate that the mechanism for trafficking of peroxisomal membrane proteins is shared between plants and mammals, but suggest differences in the sensing and turnover of mutant ABC transporter proteins and differences in substrate specificity and/or function.
Collapse
Affiliation(s)
- Xuebin Zhang
- Biological Chemistry Department, Rothamsted Research, Harpenden, Herts. AL5 2JQ, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Mast FD, Li J, Virk MK, Hughes SC, Simmonds AJ, Rachubinski RA. A Drosophila model for the Zellweger spectrum of peroxisome biogenesis disorders. Dis Model Mech 2011; 4:659-72. [PMID: 21669930 PMCID: PMC3180231 DOI: 10.1242/dmm.007419] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Human peroxisome biogenesis disorders are lethal genetic diseases in which abnormal peroxisome assembly compromises overall peroxisome and cellular function. Peroxisomes are ubiquitous membrane-bound organelles involved in several important biochemical processes, notably lipid metabolism and the use of reactive oxygen species for detoxification. Using cultured cells, we systematically characterized the peroxisome assembly phenotypes associated with dsRNA-mediated knockdown of 14 predicted Drosophila homologs of PEX genes (encoding peroxins; required for peroxisome assembly and linked to peroxisome biogenesis disorders), and confirmed that at least 13 of them are required for normal peroxisome assembly. We also demonstrate the relevance of Drosophila as a genetic model for the early developmental defects associated with the human peroxisome biogenesis disorders. Mutation of the PEX1 gene is the most common cause of peroxisome biogenesis disorders and is one of the causes of the most severe form of the disease, Zellweger syndrome. Inherited mutations in Drosophila Pex1 correlate with reproducible defects during early development. Notably, Pex1 mutant larvae exhibit abnormalities that are analogous to those exhibited by Zellweger syndrome patients, including developmental delay, poor feeding, severe structural abnormalities in the peripheral and central nervous systems, and early death. Finally, microarray analysis defined several clusters of genes whose expression varied significantly between wild-type and mutant larvae, implicating peroxisomal function in neuronal development, innate immunity, lipid and protein metabolism, gamete formation, and meiosis.
Collapse
Affiliation(s)
- Fred D Mast
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | | | | | | | | | | |
Collapse
|
43
|
Cepińska MN, Veenhuis M, van der Klei IJ, Nagotu S. Peroxisome Fission is Associated with Reorganization of Specific Membrane Proteins. Traffic 2011; 12:925-37. [DOI: 10.1111/j.1600-0854.2011.01198.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
44
|
Autosomal recessive cerebellar ataxia caused by mutations in the PEX2 gene. Orphanet J Rare Dis 2011; 6:8. [PMID: 21392394 PMCID: PMC3064617 DOI: 10.1186/1750-1172-6-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Accepted: 03/10/2011] [Indexed: 01/13/2023] Open
Abstract
Objective To expand the spectrum of genetic causes of autosomal recessive cerebellar ataxia (ARCA). Case report Two brothers are described who developed progressive cerebellar ataxia at 3 1/2 and 18 years, respectively. After ruling out known common genetic causes of ARCA, analysis of blood peroxisomal markers strongly suggested a peroxisomal biogenesis disorder. Sequencing of candidate PEX genes revealed a homozygous c.865_866insA mutation in the PEX2 gene leading to a frameshift 17 codons upstream of the stop codon. PEX gene mutations usually result in a severe neurological phenotype (Zellweger spectrum disorders). Conclusions Genetic screening of PEX2 and other PEX genes involved in peroxisomal biogenesis is warranted in children and adults with ARCA.
Collapse
|
45
|
Abstract
Despite their distinct biological functions, there is a surprising similarity between the composition of the machinery that imports proteins into peroxisomes and the machinery that degrades endoplasmic reticulum (ER)-associated proteins. The basis of this similarity lies in the fact that both machineries make use of the same basic mechanistic principle: the tagging of a substrate by monoubiquitylation or polyubiquitylation and its subsequent recognition and ATP-dependent removal from a membrane by ATPases of the ATPases associated with diverse cellular activities (AAA) family of proteins. We propose that the ER-associated protein degradation (ERAD)-like removal of the peroxisomal import receptor is mechanically coupled to protein translocation into the organelle, giving rise to a new concept of export-driven import.
Collapse
|
46
|
Schmidt F, Treiber N, Zocher G, Bjelic S, Steinmetz MO, Kalbacher H, Stehle T, Dodt G. Insights into peroxisome function from the structure of PEX3 in complex with a soluble fragment of PEX19. J Biol Chem 2010; 285:25410-7. [PMID: 20554521 PMCID: PMC2919104 DOI: 10.1074/jbc.m110.138503] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 05/17/2010] [Indexed: 11/06/2022] Open
Abstract
The human peroxins PEX3 and PEX19 play a central role in peroxisomal membrane biogenesis. The membrane-anchored PEX3 serves as the receptor for cytosolic PEX19, which in turn recognizes newly synthesized peroxisomal membrane proteins. After delivering these proteins to the peroxisomal membrane, PEX19 is recycled to the cytosol. The molecular mechanisms underlying these processes are not well understood. Here, we report the crystal structure of the cytosolic domain of PEX3 in complex with a PEX19-derived peptide. PEX3 adopts a novel fold that is best described as a large helical bundle. A hydrophobic groove at the membrane-distal end of PEX3 engages the PEX19 peptide with nanomolar affinity. Mutagenesis experiments identify phenylalanine 29 in PEX19 as critical for this interaction. Because key PEX3 residues involved in complex formation are highly conserved across species, the observed binding mechanism is of general biological relevance.
Collapse
Affiliation(s)
- Friederike Schmidt
- From the Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Nora Treiber
- the Institute for Organic Chemistry and Biochemistry, University of Freiburg, 79106 Freiburg, Germany
| | - Georg Zocher
- From the Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Sasa Bjelic
- the Laboratory of Biomolecular Research, Structural Biology, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland, and
| | - Michel O. Steinmetz
- the Laboratory of Biomolecular Research, Structural Biology, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland, and
| | - Hubert Kalbacher
- From the Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Thilo Stehle
- From the Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
- the Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Gabriele Dodt
- From the Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| |
Collapse
|
47
|
Rucktäschel R, Halbach A, Girzalsky W, Rottensteiner H, Erdmann R. De novo synthesis of peroxisomes upon mitochondrial targeting of Pex3p. Eur J Cell Biol 2010; 89:947-54. [PMID: 20655617 DOI: 10.1016/j.ejcb.2010.06.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Peroxisomes can form either by growth and division of pre-existing peroxisomes or by de novo synthesis from the endoplasmic reticulum. Pex3p is the key component for both pathways and its targeting to the ER is thought to initiate the de novo formation of peroxisomes. Here, we addressed the question whether Pex3p also can induce peroxisome formation from mitochondrial membranes. Pex3p was targeted to mitochondria by fusion with the mitochondrial targeting signal of Tom20p. The Tom20p-Pex3p-fusion protein was expressed in Pex3p-deficient cells, which are characterized by the lack of peroxisomal membranes. De novo formation of import-competent peroxisomes was observed upon expression of the mitochondrial Pex3p in the mutant cells. This de novo synthesis is independent of the GTPases Vps1p and Dnm1p, two proteins required for peroxisome fission. We conclude that natural or artificial targeting of Pex3p to any endomembrane may initiate peroxisome formation and that also Pex3p-containing mitochondria can serve as source for the de novo synthesis of peroxisomes.
Collapse
Affiliation(s)
- Robert Rucktäschel
- Institut für Physiologische Chemie, Abteilung für Systembiochemie, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | | | | | | | | |
Collapse
|
48
|
Williams CP, Stanley WA. Peroxin 5: a cycling receptor for protein translocation into peroxisomes. Int J Biochem Cell Biol 2010; 42:1771-4. [PMID: 20633695 DOI: 10.1016/j.biocel.2010.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Revised: 07/05/2010] [Accepted: 07/06/2010] [Indexed: 11/26/2022]
Abstract
Peroxins are proteins that regulate the biogenesis of peroxisomes-small vesicular subcellular organelles essential for human life and health. A key peroxin - to date the best studied - is peroxin 5. Structurally, peroxin 5 is a bi-domain protein of about 70 kDa containing both globular and non-globular segments and displaying conformational flexibility. Functionally, it is a cycling receptor for importing essential enzymes into the peroxisome lumen, facilitated by highly promiscuous interactions with numerous proteins and possibly lipids. Peroxin 5 has medical significance in that (i) congenital defects can lead to fatal peroxisome biogenesis disorders, (ii) inefficient peroxisome targeting is linked to disease and aging and (iii) differences between human peroxin 5 and homologues in pathogens may be exploited in the development of therapeutics.
Collapse
Affiliation(s)
- Chris P Williams
- European Molecular Biology Laboratory, c/o DESY, Hamburg, Germany
| | | |
Collapse
|
49
|
Islinger M, Cardoso MJR, Schrader M. Be different--the diversity of peroxisomes in the animal kingdom. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:881-97. [PMID: 20347886 DOI: 10.1016/j.bbamcr.2010.03.013] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 03/15/2010] [Accepted: 03/18/2010] [Indexed: 10/19/2022]
Abstract
Peroxisomes represent so-called "multipurpose organelles" as they contribute to various anabolic as well as catabolic pathways. Thus, with respect to the physiological specialization of an individual organ or animal species, peroxisomes exhibit a functional diversity, which is documented by significant variations in their proteome. These differences are usually regarded as an adaptational response to the nutritional and environmental life conditions of a specific organism. Thus, human peroxisomes can be regarded as an in part physiologically unique organellar entity fulfilling metabolic functions that differ from our animal model systems. In line with this, a profound understanding on how peroxisomes acquired functional heterogeneity in terms of an evolutionary and mechanistic background is required. This review summarizes our current knowledge on the heterogeneity of peroxisomal physiology, providing insights into the genetic and cell biological mechanisms, which lead to the differential localization or expression of peroxisomal proteins and further gives an overview on peroxisomal biochemical pathways, which are specialized in different animal species and organs. Moreover, it addresses the impact of proteome studies on our understanding of differential peroxisome function describing the utility of mass spectrometry and computer-assisted algorithms to identify peroxisomal target sequences for the detection of new organ- or species-specific peroxisomal proteins.
Collapse
Affiliation(s)
- M Islinger
- Department of Anatomy and Cell Biology, Ruprecht-Karls University, 69120 Heidelberg, Germany
| | | | | |
Collapse
|
50
|
Mast FD, Fagarasanu A, Rachubinski R. The peroxisomal protein importomer: a bunch of transients with expanding waistlines. Nat Cell Biol 2010; 12:203-5. [DOI: 10.1038/ncb0310-203] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|