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Waterham HR, Koster J, Ebberink MS, Ješina P, Zeman J, Nosková L, Kmoch S, Devic P, Cheillan D, Wanders RJA, Ferdinandusse S. Autosomal dominant Zellweger spectrum disorder caused by de novo variants in PEX14 gene. Genet Med 2023; 25:100944. [PMID: 37493040 DOI: 10.1016/j.gim.2023.100944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 07/27/2023] Open
Abstract
PURPOSE Zellweger spectrum disorders (ZSDs) are known as autosomal recessive disorders caused by defective peroxisome biogenesis due to bi-allelic pathogenic variants in any of at least 13 different PEX genes. Here, we report 2 unrelated patients who present with an autosomal dominant ZSD. METHODS We performed biochemical and genetic studies in blood and skin fibroblasts of the patients and demonstrated the pathogenicity of the identified PEX14 variants by functional cell studies. RESULTS We identified 2 different single heterozygous de novo variants in the PEX14 genes of 2 patients diagnosed with ZSD. Both variants cause messenger RNA mis-splicing, leading to stable expression of similar C-terminally truncated PEX14 proteins. Functional studies indicated that the truncated PEX14 proteins lost their function in peroxisomal matrix protein import and cause increased degradation of peroxisomes, ie, pexophagy, thus exerting a dominant-negative effect on peroxisome functioning. Inhibition of pexophagy by different autophagy inhibitors or genetic knockdown of the peroxisomal autophagy receptor NBR1 resulted in restoration of peroxisomal functions in the patients' fibroblasts. CONCLUSION Our finding of an autosomal dominant ZSD expands the genetic repertoire of ZSDs. Our study underscores that single heterozygous variants should not be ignored as possible genetic cause of diseases with an established autosomal recessive mode of inheritance.
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Affiliation(s)
- Hans R Waterham
- Amsterdam UMC - AMC, Department of Laboratory Medicine, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Amsterdam Reproduction & Development, Amsterdam, The Netherlands; United for Metabolic Diseases, The Netherlands.
| | - Janet Koster
- Amsterdam UMC - AMC, Department of Laboratory Medicine, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Merel S Ebberink
- Amsterdam UMC - AMC, Department of Laboratory Medicine, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Pavel Ješina
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague 2, Czech Republic
| | - Jiri Zeman
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague 2, Czech Republic
| | - Lenka Nosková
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague 2, Czech Republic
| | - Stanislav Kmoch
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague 2, Czech Republic
| | - Perrine Devic
- Centre Hospitalier Universitaire de Lyon, CHU Lyon·U 301, Hopital Neurologique, Bron, France
| | - David Cheillan
- Service Biochimie et Biologie Moléculaire Grand Est, UM Pathologies Métaboliques, Erythrocytaires et Dépistage Périnatal, Centre de Biologie et de Pathologie Est, Groupement Hospitalier Est - Hospices Civils de Lyon, Bron Cedex, France
| | - Ronald J A Wanders
- Amsterdam UMC - AMC, Department of Laboratory Medicine, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Amsterdam Reproduction & Development, Amsterdam, The Netherlands; United for Metabolic Diseases, The Netherlands
| | - Sacha Ferdinandusse
- Amsterdam UMC - AMC, Department of Laboratory Medicine, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
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2
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Baker A, Lin CC, Lett C, Karpinska B, Wright MH, Foyer CH. Catalase: A critical node in the regulation of cell fate. Free Radic Biol Med 2023; 199:56-66. [PMID: 36775107 DOI: 10.1016/j.freeradbiomed.2023.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/19/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
Abstract
Catalase (CAT) is an extensively studied if somewhat enigmatic enzyme that is at the heart of eukaryotic antioxidant systems with a canonical role in peroxisomal function. The CAT family of proteins exert control over a wide range of plant growth and defence processes. CAT proteins are subject to many types of post-translational modification (PTM), which modify activity, ligand binding, stability, compartmentation and function. The CAT interactome involves many cytosolic and nuclear proteins that appear to be essential for protein functions. Hence, the CAT network of roles extends far beyond those associated with peroxisomal metabolism. Some pathogen effector proteins are able to redirect CAT to the nucleus and recent evidence indicates CAT can traffic to the nucleus in the absence of exogenous proteins. While the mechanisms that target CAT to the nucleus are not understood, CAT activity in the cytosol and nucleus is promoted by interactions with nucleoredoxin. Here we discuss recent findings that have been pivotal in generating a step change in our understanding of CAT functions in plant cells.
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Affiliation(s)
- Alison Baker
- Centre for Plant Sciences and School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Chi-Chuan Lin
- Centre for Plant Sciences and School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Casey Lett
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Barbara Karpinska
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Megan H Wright
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK
| | - Christine H Foyer
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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3
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Bittner E, Stehlik T, Freitag J. Sharing the wealth: The versatility of proteins targeted to peroxisomes and other organelles. Front Cell Dev Biol 2022; 10:934331. [PMID: 36225313 PMCID: PMC9549241 DOI: 10.3389/fcell.2022.934331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Peroxisomes are eukaryotic organelles with critical functions in cellular energy and lipid metabolism. Depending on the organism, cell type, and developmental stage, they are involved in numerous other metabolic and regulatory pathways. Many peroxisomal functions require factors also relevant to other cellular compartments. Here, we review proteins shared by peroxisomes and at least one different site within the cell. We discuss the mechanisms to achieve dual targeting, their regulation, and functional consequences. Characterization of dual targeting is fundamental to understand how peroxisomes are integrated into the metabolic and regulatory circuits of eukaryotic cells.
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4
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Role of C-terminal domain in a manganese-catalase from Geobacillus thermopakistaniensis. J Biosci Bioeng 2022; 134:203-212. [PMID: 35811183 DOI: 10.1016/j.jbiosc.2022.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/03/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022]
Abstract
Catalases catalyze the decomposition of hydrogen peroxide into water and oxygen. We have characterized two manganese-catalases from Geobacillus thermopakistaniensis, CatGt and Cat-IIGt, which exhibited significant variation in their sequence, structure and properties. There was only 23% sequence identity between the two. The striking structural difference was the presence of an extended C-terminal domain in CatGt. Molecular modelling and docking studies revealed that deletion of the C-terminal domain removes non-specific binding, which results in increased substrate affinity. To verify experimentally, a C-terminal truncated version of CatGt, named as CatGt-ΔC, was produced in Escherichia coli and effects of deletion were analyzed. There was no significant difference in optimal pH, optimal temperature and substrate specificity of CatGt and CatGt-ΔC. However, Km value was reduced from 259 to 157 mM and CatGt-ΔC exhibited ∼1.5-fold higher catalytic efficiency as compared to CatGt. Furthermore, removal of the C-terminal domain converted the tetrameric nature to monomeric, and reduced the thermostability of the truncated protein. These results demonstrate that C-terminal domain of CatGt might have little role in maintaining enzyme function but provides additional structural stability to the protein, which is a desired property for industrial applications.
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5
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Insights into the Structure and Function of the Pex1/Pex6 AAA-ATPase in Peroxisome Homeostasis. Cells 2022; 11:cells11132067. [PMID: 35805150 PMCID: PMC9265785 DOI: 10.3390/cells11132067] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/25/2022] [Accepted: 06/26/2022] [Indexed: 02/01/2023] Open
Abstract
The AAA-ATPases Pex1 and Pex6 are required for the formation and maintenance of peroxisomes, membrane-bound organelles that harbor enzymes for specialized metabolism. Together, Pex1 and Pex6 form a heterohexameric AAA-ATPase capable of unfolding substrate proteins via processive threading through a central pore. Here, we review the proposed roles for Pex1/Pex6 in peroxisome biogenesis and degradation, discussing how the unfolding of potential substrates contributes to peroxisome homeostasis. We also consider how advances in cryo-EM, computational structure prediction, and mechanisms of related ATPases are improving our understanding of how Pex1/Pex6 converts ATP hydrolysis into mechanical force. Since mutations in PEX1 and PEX6 cause the majority of known cases of peroxisome biogenesis disorders such as Zellweger syndrome, insights into Pex1/Pex6 structure and function are important for understanding peroxisomes in human health and disease.
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6
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Monic S, Lamy A, Thonnus M, Bizarra-Rebelo T, Bringaud F, Smith TK, Figueiredo LM, Rivière L. A novel lipase with dual localisation in Trypanosoma brucei. Sci Rep 2022; 12:4766. [PMID: 35306507 PMCID: PMC8934347 DOI: 10.1038/s41598-022-08546-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/03/2022] [Indexed: 12/05/2022] Open
Abstract
Phospholipases are esterases involved in lipid catabolism. In pathogenic micro-organisms (bacteria, fungi, parasites) they often play a critical role in virulence and pathogenicity. A few phospholipases (PL) have been characterised so far at the gene and protein level in unicellular parasites including African trypanosomes (AT). They could play a role in different processes such as host–pathogen interaction, antigenic variation, intermediary metabolism. By mining the genome database of AT we found putative new phospholipase candidate genes and here we provided biochemical evidence that one of these has lipolytic activity. This protein has a unique non-canonical glycosome targeting signal responsible for its dual localisation in the cytosol and the peroxisomes-related organelles named glycosomes. We also show that this new phospholipase is excreted by these pathogens and that antibodies directed against this protein are generated during an experimental infection with T. brucei gambiense, a subspecies responsible for infection in humans. This feature makes this protein a possible tool for diagnosis.
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7
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Kataya A, Gautam N, Jamshed M, Muench DG, Samuel MA, Thelen JJ, Moorhead GB. Identification of Arabidopsis Protein Kinases That Harbor Functional Type 1 Peroxisomal Targeting Signals. Front Cell Dev Biol 2022; 10:745883. [PMID: 35242755 PMCID: PMC8886021 DOI: 10.3389/fcell.2022.745883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/25/2022] [Indexed: 12/25/2022] Open
Abstract
Peroxisomes are eukaryotic specific organelles that perform diverse metabolic functions including fatty acid β-oxidation, reactive species metabolism, photorespiration, and responses to stress. However, the potential regulation of these functions by post-translational modifications, including protein phosphorylation, has had limited study. Recently, we identified and catalogued a large number of peroxisomal phosphorylated proteins, implicating the presence of protein kinases in this organelle. Here, we employed available prediction models coupled with sequence conservation analysis to identify 31 protein kinases from the Arabidopsis kinome (all protein kinases) that contain a putative, non-canonical peroxisomal targeting signal type 1 (PTS1). From this, twelve C-terminal domain-PTS1s were demonstrated to be functional in vivo, targeting enhanced yellow fluorescent protein to peroxisomes, increasing the list of presumptive peroxisomal protein kinases to nineteen. Of the twelve protein kinases with functional PTS1s, we obtained full length clones for eight and demonstrated that seven target to peroxisomes in vivo. Screening homozygous mutants of the presumptive nineteen protein kinases revealed one candidate (GPK1) that harbors a sugar-dependence phenotype, suggesting it is involved in regulating peroxisomal fatty acid β-oxidation. These results present new opportunities for investigating the regulation of peroxisome functions.
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Affiliation(s)
- Amr Kataya
- Department of Chemistry, Bioscience, and Environmental Engineering, University of Stavanger, Stavanger, Norway.,Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.,Christopher S. Bond Life Sciences Center, Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Nitija Gautam
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Muhammad Jamshed
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Marcus A Samuel
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jay J Thelen
- Christopher S. Bond Life Sciences Center, Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Greg B Moorhead
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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8
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Kamoshita M, Kumar R, Anteghini M, Kunze M, Islinger M, Martins dos Santos V, Schrader M. Insights Into the Peroxisomal Protein Inventory of Zebrafish. Front Physiol 2022; 13:822509. [PMID: 35295584 PMCID: PMC8919083 DOI: 10.3389/fphys.2022.822509] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/07/2022] [Indexed: 12/19/2022] Open
Abstract
Peroxisomes are ubiquitous, oxidative subcellular organelles with important functions in cellular lipid metabolism and redox homeostasis. Loss of peroxisomal functions causes severe disorders with developmental and neurological abnormalities. Zebrafish are emerging as an attractive vertebrate model to study peroxisomal disorders as well as cellular lipid metabolism. Here, we combined bioinformatics analyses with molecular cell biology and reveal the first comprehensive inventory of Danio rerio peroxisomal proteins, which we systematically compared with those of human peroxisomes. Through bioinformatics analysis of all PTS1-carrying proteins, we demonstrate that D. rerio lacks two well-known mammalian peroxisomal proteins (BAAT and ZADH2/PTGR3), but possesses a putative peroxisomal malate synthase (Mlsl) and verified differences in the presence of purine degrading enzymes. Furthermore, we revealed novel candidate peroxisomal proteins in D. rerio, whose function and localisation is discussed. Our findings confirm the suitability of zebrafish as a vertebrate model for peroxisome research and open possibilities for the study of novel peroxisomal candidate proteins in zebrafish and humans.
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Affiliation(s)
- Maki Kamoshita
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Rechal Kumar
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Marco Anteghini
- LifeGlimmer GmbH, Berlin, Germany
- Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Markus Kunze
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Markus Islinger
- Institute of Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Vítor Martins dos Santos
- LifeGlimmer GmbH, Berlin, Germany
- Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
- *Correspondence: Michael Schrader,
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9
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Dubreuil MM, Morgens DW, Okumoto K, Honsho M, Contrepois K, Lee-McMullen B, Traber GM, Sood RS, Dixon SJ, Snyder MP, Fujiki Y, Bassik MC. Systematic Identification of Regulators of Oxidative Stress Reveals Non-canonical Roles for Peroxisomal Import and the Pentose Phosphate Pathway. Cell Rep 2021; 30:1417-1433.e7. [PMID: 32023459 DOI: 10.1016/j.celrep.2020.01.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/07/2019] [Accepted: 01/02/2020] [Indexed: 12/13/2022] Open
Abstract
Reactive oxygen species (ROS) play critical roles in metabolism and disease, yet a comprehensive analysis of the cellular response to oxidative stress is lacking. To systematically identify regulators of oxidative stress, we conducted genome-wide Cas9/CRISPR and shRNA screens. This revealed a detailed picture of diverse pathways that control oxidative stress response, ranging from the TCA cycle and DNA repair machineries to iron transport, trafficking, and metabolism. Paradoxically, disrupting the pentose phosphate pathway (PPP) at the level of phosphogluconate dehydrogenase (PGD) protects cells against ROS. This dramatically alters metabolites in the PPP, consistent with rewiring of upper glycolysis to promote antioxidant production. In addition, disruption of peroxisomal import unexpectedly increases resistance to oxidative stress by altering the localization of catalase. Together, these studies provide insights into the roles of peroxisomal matrix import and the PPP in redox biology and represent a rich resource for understanding the cellular response to oxidative stress.
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Affiliation(s)
- Michael M Dubreuil
- Program in Cancer Biology, Stanford University, Stanford, CA 94305-5120, USA; Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - David W Morgens
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Kanji Okumoto
- Department of Biology, Faculty of Sciences, Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masanori Honsho
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kévin Contrepois
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | | | | | - Ria S Sood
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Scott J Dixon
- Program in Cancer Biology, Stanford University, Stanford, CA 94305-5120, USA; Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305-5120, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
| | - Yukio Fujiki
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | - Michael C Bassik
- Program in Cancer Biology, Stanford University, Stanford, CA 94305-5120, USA; Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA; Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305-5120, USA.
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10
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Crowe LP, Wilkinson CL, Nicholson KR, Morris MT. Trypanosoma brucei Pex13.2 Is an Accessory Peroxin That Functions in the Import of Peroxisome Targeting Sequence Type 2 Proteins and Localizes to Subdomains of the Glycosome. mSphere 2020; 5:e00744-19. [PMID: 32075879 PMCID: PMC7031615 DOI: 10.1128/msphere.00744-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/30/2020] [Indexed: 01/30/2023] Open
Abstract
Kinetoplastid parasites, including Trypanosoma brucei, Trypanosoma cruzi, and Leishmania, harbor unique organelles known as glycosomes, which are evolutionarily related to peroxisomes. Glycosome/peroxisome biogenesis is mediated by proteins called peroxins that facilitate organelle formation, proliferation, and degradation and import of proteins housed therein. Import of matrix proteins occurs via one of two pathways that are dictated by their peroxisome targeting sequence (PTS). In PTS1 import, a C-terminal tripeptide sequence, most commonly SKL, is recognized by the soluble receptor Pex5. In PTS2 import, a less conserved N-terminal sequence is recognized by Pex7. The soluble receptors deliver their cargo to the import channel consisting minimally of Pex13 and Pex14. While much of the import process is conserved, kinetoplastids are the only organisms to have two Pex13s, Pex13.1 and Pex13.2. It is unclear why trypanosomes require two Pex13s when one is sufficient for most eukaryotes. To interrogate the role of Pex13.2, we have employed biochemical approaches to partially resolve the composition of the Pex13/Pex14 import complexes in T. brucei and characterized glycosome morphology and protein import in Pex13.2-deficient parasites. Here, we show that Pex13.2 is an integral glycosome membrane protein that interacts with Pex13.1 and Pex14. The N terminus of Pex13.2 faces the cytoplasmic side of the membrane, where it can facilitate interactions required for protein import. Two-dimensional gel electrophoresis revealed three glycosome membrane complexes containing combinations of Pex13.1, Pex13.2, and Pex14. The silencing of Pex13.2 resulted in parasites with fewer, larger glycosomes and disrupted glycosome protein import, suggesting the protein is involved in glycosome biogenesis as well as protein import. Furthermore, superresolution microscopy demonstrated that Pex13.2 localizes to discrete foci in the glycosome periphery, indicating that the glycosome periphery is not homogenous.IMPORTANCETrypanosoma brucei causes human African trypanosomiasis and a wasting disease called Nagana in livestock. Current treatments are expensive, toxic, and difficult to administer. Because of this, the search for new drug targets is essential. T. brucei has glycosomes that are essential to parasite survival; however, our ability to target them in drug development is hindered by our lack of understanding about how these organelles are formed and maintained. This work forwards our understanding of how the parasite-specific protein Pex13.2 functions in glycosome protein import and lays the foundation for future studies focused on blocking Pex13.2 function, which would be lethal to bloodstream-form parasites that reside in the mammalian bloodstream.
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Affiliation(s)
- Logan P Crowe
- Eukaryotic Innovations Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Christina L Wilkinson
- Eukaryotic Innovations Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Kathleen R Nicholson
- Eukaryotic Innovations Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Meredith T Morris
- Eukaryotic Innovations Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
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11
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Fujikawa Y, Suekawa M, Endo S, Fukami Y, Mano S, Nishimura M, Esaka M. Effect of mutation of C-terminal and heme binding region of Arabidopsis catalase on the import to peroxisomes. Biosci Biotechnol Biochem 2018; 83:322-325. [PMID: 30295129 DOI: 10.1080/09168451.2018.1530094] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We evaluated the import of Arabidopsis catalase to peroxisomes under homogenous transient expression. The amino acids at -11 to -4 from the C-terminus are necessary for catalase import. The results are in agreement with the previous work under stable expression. We first demonstrate that heme-binding sites are important for peroxisomal import, suggesting the importance of catalase folding. Abbreviations: AtCat: Arabidopsis catalase; PTS: peroxisomal targeting signal; PEX: Peroxin.
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Affiliation(s)
- Yukichi Fujikawa
- a Graduate School of Biosphere Sciences , Hiroshima University , Higashi-Hiroshima , Japan
| | - Marina Suekawa
- a Graduate School of Biosphere Sciences , Hiroshima University , Higashi-Hiroshima , Japan
| | - Satoshi Endo
- a Graduate School of Biosphere Sciences , Hiroshima University , Higashi-Hiroshima , Japan
| | - Youjirou Fukami
- a Graduate School of Biosphere Sciences , Hiroshima University , Higashi-Hiroshima , Japan
| | - Shoji Mano
- b Department of Cell Biology , National Institute for Basic Biology , Okazaki , Japan.,c Department of Basic Biology , School of Life Science, SOKENDAI (The Graduate University for Advanced Studies) , Okazaki , Japan
| | - Mikio Nishimura
- d Department of Biology, Faculty of Science and Engineering , Konan University , Kobe , Japan
| | - Muneharu Esaka
- a Graduate School of Biosphere Sciences , Hiroshima University , Higashi-Hiroshima , Japan
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12
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Karnati S, Oruqaj G, Janga H, Tumpara S, Colasante C, Van Veldhoven PP, Braverman N, Pilatz A, Mariani TJ, Baumgart-Vogt E. PPARα-mediated peroxisome induction compensates PPARγ-deficiency in bronchiolar club cells. PLoS One 2018; 13:e0203466. [PMID: 30212482 PMCID: PMC6136741 DOI: 10.1371/journal.pone.0203466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 08/21/2018] [Indexed: 11/18/2022] Open
Abstract
Despite the important functions of PPARγ in various cell types of the lung, PPARγ-deficiency in club cells induces only mild emphysema. Peroxisomes are distributed in a similar way as PPARγ in the lung and are mainly enriched in club and AECII cells. To date, the effects of PPARγ-deficiency on the overall peroxisomal compartment and its metabolic alterations in pulmonary club cells are unknown. Therefore, we characterized wild-type and club cell-specific PPARγ knockout-mice lungs and used C22 cells to investigate the peroxisomal compartment and its metabolic roles in the distal airway epithelium by means of 1) double-immunofluorescence labelling for peroxisomal proteins, 2) laser-assisted microdissection of the bronchiolar epithelium and subsequent qRT-PCR, 3) siRNA-transfection of PPARγand PPRE dual-luciferase reporter activity in C22 cells, 4) PPARg inhibition by GW9662, 5) GC-MS based lipid analysis. Our results reveal elevated levels of fatty acids, increased expression of PPARα and PPRE activity, a strong overall upregulation of the peroxisomal compartment and its associated gene expression (biogenesis, α-oxidation, β-oxidation, and plasmalogens) in PPARγ-deficient club cells. Interestingly, catalase was significantly increased and mistargeted into the cytoplasm, suggestive for oxidative stress by the PPARγ-deficiency in club cells. Taken together, PPARα-mediated metabolic induction and proliferation of peroxisomes via a PPRE-dependent mechanism could compensate PPARγ-deficiency in club cells.
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Affiliation(s)
- Srikanth Karnati
- Institute for Anatomy and Cell Biology II, Division of Medical Cell Biology, Justus Liebig University, Giessen, Germany
- * E-mail: ,
| | - Gani Oruqaj
- Institute for Anatomy and Cell Biology II, Division of Medical Cell Biology, Justus Liebig University, Giessen, Germany
| | - Harshavardhan Janga
- Institute for Anatomy and Cell Biology II, Division of Medical Cell Biology, Justus Liebig University, Giessen, Germany
| | - Srinu Tumpara
- Institute for Anatomy and Cell Biology II, Division of Medical Cell Biology, Justus Liebig University, Giessen, Germany
| | - Claudia Colasante
- Institute for Anatomy and Cell Biology II, Division of Medical Cell Biology, Justus Liebig University, Giessen, Germany
| | - Paul P. Van Veldhoven
- Laboratory of Lipid Biochemistry and Protein Interactions, KU Leuven, Leuven, Belgium
| | - Nancy Braverman
- Depts. of Human Genetics and Pediatrics, McGill University-Montreal Children’s Hospital Research Institute, Montreal, Canada
| | - Adrian Pilatz
- Department of Urology, Pediatric Urology and Andrology, Justus Liebig University Giessen, Giessen, Germany
| | - Thomas J. Mariani
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Eveline Baumgart-Vogt
- Institute for Anatomy and Cell Biology II, Division of Medical Cell Biology, Justus Liebig University, Giessen, Germany
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13
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Tyutereva EV, Dobryakova KS, Schiermeyer A, Shishova MF, Pawlowski K, Demidchik V, Reumann S, Voitsekhovskaja OV. The levels of peroxisomal catalase protein and activity modulate the onset of cell death in tobacco BY-2 cells via reactive oxygen species levels and autophagy. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:247-258. [PMID: 32291039 DOI: 10.1071/fp16418] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 04/03/2017] [Indexed: 06/11/2023]
Abstract
In plant cells, peroxisomes participate in the metabolism of reactive oxygen species (ROS). One of the major regulators of cellular ROS levels - catalase (CAT) - occurs exclusively in peroxisomes. CAT activity is required for immunity-triggered autophagic programmed cell death (PCD). Autophagy has been recently demonstrated to represent a route for degradation of peroxisomes in plant cells. In the present study, the dynamics of the cellular peroxisome pool in tobacco BY-2 cell suspension cultures were used to analyse the effects of inhibition of basal autophagy with special attention to CAT activity. Numbers of peroxisomes per cell, levels of CAT protein and activity, cell viability, ROS levels and expression levels of genes encoding components of antioxidant system were analysed upon application of 3-methyladenine (3-MA), an inhibitor of autophagy, and/or aminotriazole (AT), an inhibitor of CAT. When applied separately, 3-MA and AT led to an increase in cell death, but this effect was attenuated by their simultaneous application. The obtained data suggest that both the levels of CAT protein in peroxisomes as well as CAT activity modulate the onset of cell death in tobacco BY-2 cells via ROS levels and autophagy.
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Affiliation(s)
- Elena V Tyutereva
- Laboratory of Molecular and Ecological Physiology, Komarov Botanical Institute, Russian Academy of Sciences, ul. Professora Popova 2, 197376 Saint Petersburg, Russia
| | - Ksenia S Dobryakova
- Laboratory of Molecular and Ecological Physiology, Komarov Botanical Institute, Russian Academy of Sciences, ul. Professora Popova 2, 197376 Saint Petersburg, Russia
| | - Andreas Schiermeyer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Department of Plant Biotechnology, Forckenbeckstrasse 6, D-52074 Aachen, Germany
| | - Maria F Shishova
- Department of Physiology and Biochemistry of Plants, Saint Petersburg State University, Universitetskaya em., 7/9, 199034 Saint Petersburg, Russia
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Vadim Demidchik
- Laboratory of Molecular and Ecological Physiology, Komarov Botanical Institute, Russian Academy of Sciences, ul. Professora Popova 2, 197376 Saint Petersburg, Russia
| | - Sigrun Reumann
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University of Goettingen, Justus-von-Liebig Weg 11, D-37077, Goettingen, Germany
| | - Olga V Voitsekhovskaja
- Laboratory of Molecular and Ecological Physiology, Komarov Botanical Institute, Russian Academy of Sciences, ul. Professora Popova 2, 197376 Saint Petersburg, Russia
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14
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Bersch K, Lobos Matthei I, Thoms S. Multiple Localization by Functional Translational Readthrough. Subcell Biochem 2018; 89:201-219. [PMID: 30378024 DOI: 10.1007/978-981-13-2233-4_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In a compartmentalized cell, correct protein localization is crucial for function of virtually all cellular processes. From the cytoplasm as a starting point, proteins are imported into organelles by specific targeting signals. Many proteins, however, act in more than one cellular compartment. In this chapter, we discuss mechanisms by which proteins can be targeted to multiple organelles with a focus on a novel gene regulatory mechanism, functional translational readthrough, that permits multiple targeting of proteins to the peroxisome and other organelles. In mammals, lactate and malate dehydrogenase are the best-characterized enzymes whose targeting is controlled by functional translational readthrough.
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Affiliation(s)
- Kristina Bersch
- Department of Child and Adolescent Health, University Medical Center Göttingen, University of Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Ignacio Lobos Matthei
- Department of Child and Adolescent Health, University Medical Center Göttingen, University of Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Sven Thoms
- Department of Child and Adolescent Health, University Medical Center Göttingen, University of Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.
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15
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Walton PA, Brees C, Lismont C, Apanasets O, Fransen M. The peroxisomal import receptor PEX5 functions as a stress sensor, retaining catalase in the cytosol in times of oxidative stress. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:1833-1843. [PMID: 28760655 DOI: 10.1016/j.bbamcr.2017.07.013] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 07/03/2017] [Accepted: 07/27/2017] [Indexed: 02/08/2023]
Abstract
Accumulating evidence indicates that peroxisome functioning, catalase localization, and cellular oxidative balance are intimately interconnected. Nevertheless, it remains largely unclear why modest increases in the cellular redox state especially interfere with the subcellular localization of catalase, the most abundant peroxisomal antioxidant enzyme. This study aimed at gaining more insight into this phenomenon. Therefore, we first established a simple and powerful approach to study peroxisomal protein import and protein-protein interactions in living cells in response to changes in redox state. By employing this approach, we confirm and extend previous observations that Cys-11 of human PEX5, the shuttling import receptor for peroxisomal matrix proteins containing a C-terminal peroxisomal targeting signal (PTS1), functions as a redox switch that modulates the protein's activity in response to intracellular oxidative stress. In addition, we show that oxidative stress affects the import of catalase, a non-canonical PTS1-containing protein, more than the import of a reporter protein containing a canonical PTS1. Furthermore, we demonstrate that changes in the local redox state do not affect PEX5-substrate binding and that human PEX5 does not oligomerize in cellulo, not even when the cells are exposed to oxidative stress. Finally, we present evidence that catalase retained in the cytosol can protect against H2O2-mediated redox changes in a manner that peroxisomally targeted catalase does not. Together, these findings lend credit to the idea that inefficient catalase import, when coupled with the role of PEX5 as a redox-regulated import receptor, constitutes a cellular defense mechanism to combat oxidative insults of extra-peroxisomal origin.
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Affiliation(s)
- Paul A Walton
- Laboratory of Lipid Biochemistry and Protein Interactions, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, Box 601, B-3000 Leuven, Belgium; Department of Anatomy and Cell Biology, University of Western Ontario, 474 Medical Sciences Building, London, Ontario ON N6A 3K7, Canada
| | - Chantal Brees
- Laboratory of Lipid Biochemistry and Protein Interactions, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, Box 601, B-3000 Leuven, Belgium
| | - Celien Lismont
- Laboratory of Lipid Biochemistry and Protein Interactions, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, Box 601, B-3000 Leuven, Belgium
| | - Oksana Apanasets
- Laboratory of Lipid Biochemistry and Protein Interactions, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, Box 601, B-3000 Leuven, Belgium
| | - Marc Fransen
- Laboratory of Lipid Biochemistry and Protein Interactions, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, Box 601, B-3000 Leuven, Belgium.
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16
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Chen N, Teng XL, Xiao XG. Subcellular Localization of a Plant Catalase-Phenol Oxidase, AcCATPO, from Amaranthus and Identification of a Non-canonical Peroxisome Targeting Signal. FRONTIERS IN PLANT SCIENCE 2017; 8:1345. [PMID: 28824680 PMCID: PMC5539789 DOI: 10.3389/fpls.2017.01345] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/18/2017] [Indexed: 05/03/2023]
Abstract
AcCATPO is a plant catalase-phenol oxidase recently identified from red amaranth. Its physiological function remains unexplored. As the starting step of functional analysis, here we report its subcellular localization and a non-canonical targeting signal. Commonly used bioinformatics programs predicted a peroxisomal localization for AcCATPO, but failed in identification of canonical peroxisomal targeting signals (PTS). The C-terminal GFP tagging led the fusion protein AcCATPO-GFP to the cytosol and the nucleus, but N-terminal tagging directed the GFP-AcCATPO to peroxisomes and nuclei, in transgenic tobacco. Deleting the tripeptide (PTM) at the extreme C-terminus almost ruled out the peroxisomal localization of GFP-AcCATPOΔ3, and removing the C-terminal decapeptide completely excluded peroxisomes as the residence of GFP-AcCATPOΔ10. Furthermore, this decapeptide as a targeting signal could import GFP-10aa to the peroxisome exclusively. Taken together, these results demonstrate that AcCATPO is localized to the peroxisome and the nucleus, and its peroxisomal localization is attributed to a non-canonical PTS1, the C-terminal decapeptide which contains an internal SRL motif and a conserved tripeptide P-S/T-I/M at the extreme of C-terminus. This work may further the study as to the physiological function of AcCATPO, especially clarify its involvement in betalain biosynthesis, and provide a clue to elucidate more non-canonic PTS.
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17
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Reumann S, Chowdhary G, Lingner T. Characterization, prediction and evolution of plant peroxisomal targeting signals type 1 (PTS1s). BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1863:790-803. [PMID: 26772785 DOI: 10.1016/j.bbamcr.2016.01.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 01/01/2016] [Accepted: 01/04/2016] [Indexed: 12/22/2022]
Abstract
Our knowledge of the proteome of plant peroxisomes and their functional plasticity is far from being complete, primarily due to major technical challenges in experimental proteome research of the fragile cell organelle. Several unexpected novel plant peroxisome functions, for instance in biotin and phylloquinone biosynthesis, have been uncovered recently. Nevertheless, very few regulatory and membrane proteins of plant peroxisomes have been identified and functionally described up to now. To define the matrix proteome of plant peroxisomes, computational methods have emerged as important powerful tools. Novel prediction approaches of high sensitivity and specificity have been developed for peroxisome targeting signals type 1 (PTS1) and have been validated by in vivo subcellular targeting analyses and thermodynamic binding studies with the cytosolic receptor, PEX5. Accordingly, the algorithms allow the correct prediction of many novel peroxisome-targeted proteins from plant genome sequences and the discovery of additional organelle functions. In this review, we provide an overview of methodologies, capabilities and accuracies of available prediction algorithms for PTS1 carrying proteins. We also summarize and discuss recent quantitative, structural and mechanistic information of the interaction of PEX5 with PTS1 carrying proteins in relation to in vivo import efficiency. With this knowledge, we develop a model of how proteins likely evolved peroxisomal targeting signals in the past and still nowadays, in which order the two import pathways might have evolved in the ancient eukaryotic cell, and how the secondary loss of the PTS2 pathway probably happened in specific organismal groups.
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Affiliation(s)
- S Reumann
- Department of Plant Biochemistry and Infection Biology, Biocentre Klein Flottbek, University of Hamburg, D-22609 Hamburg, Germany; Centre for Organelle Research, University of Stavanger, N-4036 Stavanger, Norway.
| | - G Chowdhary
- Centre for Organelle Research, University of Stavanger, N-4036 Stavanger, Norway; KIIT School of Biotechnology, Campus XI, KIIT University, I-751024 Bhubaneswar, India.
| | - T Lingner
- Department of Bioinformatics, Institute for Microbiology and Genetics, D-37077 Goettingen, Germany.
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18
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DeLoache WC, Russ ZN, Dueber JE. Towards repurposing the yeast peroxisome for compartmentalizing heterologous metabolic pathways. Nat Commun 2016; 7:11152. [PMID: 27025684 PMCID: PMC5476825 DOI: 10.1038/ncomms11152] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/23/2016] [Indexed: 11/29/2022] Open
Abstract
Compartmentalization of enzymes into organelles is a promising strategy for limiting metabolic crosstalk and improving pathway efficiency, but improved tools and design rules are needed to make this strategy available to more engineered pathways. Here we focus on the Saccharomyces cerevisiae peroxisome and develop a sensitive high-throughput assay for peroxisomal cargo import. We identify an enhanced peroxisomal targeting signal type 1 (PTS1) for rapidly sequestering non-native cargo proteins. Additionally, we perform the first systematic in vivo measurements of nonspecific metabolite permeability across the peroxisomal membrane using a polymer exclusion assay. Finally, we apply these new insights to compartmentalize a two-enzyme pathway in the peroxisome and characterize the expression regimes where compartmentalization leads to improved product titre. This work builds a foundation for using the peroxisome as a synthetic organelle, highlighting both promise and future challenges on the way to realizing this goal. Compartmentalization of enzymes into cellular organelles is a promising strategy for improving pathway efficiency. Here, the authors use a high-throughput assay to identify enhanced peroxisomal targeting signals in yeast, and study the effects of peroxisomal compartmentalization on the performance of a model pathway.
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Affiliation(s)
- William C DeLoache
- UC Berkeley and UCSF Graduate Program in Bioengineering, University of California, Berkeley (UC Berkeley), Berkeley, California 94720, USA.,Department of Bioengineering, UC Berkeley, Berkeley, California 94720, USA
| | - Zachary N Russ
- UC Berkeley and UCSF Graduate Program in Bioengineering, University of California, Berkeley (UC Berkeley), Berkeley, California 94720, USA.,Department of Bioengineering, UC Berkeley, Berkeley, California 94720, USA
| | - John E Dueber
- Department of Bioengineering, UC Berkeley, Berkeley, California 94720, USA
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19
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Fernández-Fernández ÁD, Corpas FJ. In Silico Analysis of Arabidopsis thaliana Peroxisomal 6-Phosphogluconate Dehydrogenase. SCIENTIFICA 2016; 2016:3482760. [PMID: 27034898 PMCID: PMC4789532 DOI: 10.1155/2016/3482760] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 02/08/2016] [Indexed: 05/21/2023]
Abstract
NADPH, whose regeneration is critical for reductive biosynthesis and detoxification pathways, is an essential component in cell redox homeostasis. Peroxisomes are subcellular organelles with a complex biochemical machinery involved in signaling and stress processes by molecules such as hydrogen peroxide (H2O2) and nitric oxide (NO). NADPH is required by several peroxisomal enzymes involved in β-oxidation, NO, and glutathione (GSH) generation. Plants have various NADPH-generating dehydrogenases, one of which is 6-phosphogluconate dehydrogenase (6PGDH). Arabidopsis contains three 6PGDH genes that probably are encoded for cytosolic, chloroplastic/mitochondrial, and peroxisomal isozymes, although their specific functions remain largely unknown. This study focuses on the in silico analysis of the biochemical characteristics and gene expression of peroxisomal 6PGDH (p6PGDH) with the aim of understanding its potential function in the peroxisomal NADPH-recycling system. The data show that a group of plant 6PGDHs contains an archetypal type 1 peroxisomal targeting signal (PTS), while in silico gene expression analysis using affymetrix microarray data suggests that Arabidopsis p6PGDH appears to be mainly involved in xenobiotic response, growth, and developmental processes.
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Affiliation(s)
- Álvaro D. Fernández-Fernández
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Apartado 419, 18080 Granada, Spain
| | - Francisco J. Corpas
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Apartado 419, 18080 Granada, Spain
- *Francisco J. Corpas:
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20
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Reglinski K, Keil M, Altendorf S, Waithe D, Eggeling C, Schliebs W, Erdmann R. Peroxisomal Import Reduces the Proapoptotic Activity of Deubiquitinating Enzyme USP2. PLoS One 2015; 10:e0140685. [PMID: 26484888 PMCID: PMC4617714 DOI: 10.1371/journal.pone.0140685] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/28/2015] [Indexed: 12/15/2022] Open
Abstract
The human deubiquitinating enzyme ubiquitin-specific protease 2 (USP2) regulates multiple cellular pathways, including cell proliferation and apoptosis. As a result of alternative splicing four USP2 isoenzymes are expressed in human cells of which all contain a weak peroxisome targeting signal of type 1 (PTS1) at their C-termini. Here, we systematically analyzed apoptotic effects induced by overexpression and intracellular localization for each isoform. All isoforms exhibit proapoptotic activity and are post-translationally imported into the matrix of peroxisomes in a PEX5-dependent manner. However, a significant fraction of the USP2 pool resides in the cytosol due to a weaker PTS1 and thus low affinity to the PTS receptor PEX5. Blocking of peroxisomal import did not interfere with the proapoptotic activity of USP2, suggesting that the enzyme performs its critical function outside of this compartment. Instead, increase of the efficiency of USP2 import into peroxisomes either by optimization of its peroxisomal targeting signal or by overexpression of the PTS1 receptor did result in a reduction of the apoptotic rate of transfected cells. Our studies suggest that peroxisomal import of USP2 provides additional control over the proapoptotic activity of cytosolic USP2 by spatial separation of the deubiquitinating enzymes from their interaction partners in the cytosol and nucleus.
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Affiliation(s)
- Katharina Reglinski
- Institut für Biochemie und Pathobiochemie, Abteilung Systembiochemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Marina Keil
- Institut für Biochemie und Pathobiochemie, Abteilung Systembiochemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Sabrina Altendorf
- Institut für Biochemie und Pathobiochemie, Abteilung Systembiochemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Dominic Waithe
- Wolfson Imaging Centre, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
| | - Christian Eggeling
- Wolfson Imaging Centre, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
| | - Wolfgang Schliebs
- Institut für Biochemie und Pathobiochemie, Abteilung Systembiochemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Ralf Erdmann
- Institut für Biochemie und Pathobiochemie, Abteilung Systembiochemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
- * E-mail:
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21
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Schrader M, Costello J, Godinho LF, Islinger M. Peroxisome-mitochondria interplay and disease. J Inherit Metab Dis 2015; 38:681-702. [PMID: 25687155 DOI: 10.1007/s10545-015-9819-7] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/21/2015] [Accepted: 01/26/2015] [Indexed: 12/16/2022]
Abstract
Peroxisomes and mitochondria are ubiquitous, highly dynamic organelles with an oxidative type of metabolism in eukaryotic cells. Over the years, substantial evidence has been provided that peroxisomes and mitochondria exhibit a close functional interplay which impacts on human health and development. The so-called "peroxisome-mitochondria connection" includes metabolic cooperation in the degradation of fatty acids, a redox-sensitive relationship, an overlap in key components of the membrane fission machineries and cooperation in anti-viral signalling and defence. Furthermore, combined peroxisome-mitochondria disorders with defects in organelle division have been revealed. In this review, we present the latest progress in the emerging field of peroxisomal and mitochondrial interplay in mammals with a particular emphasis on cooperative fatty acid β-oxidation, redox interplay, organelle dynamics, cooperation in anti-viral signalling and the resulting implications for disease.
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Affiliation(s)
- Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK,
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22
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Skoulding NS, Chowdhary G, Deus MJ, Baker A, Reumann S, Warriner SL. Experimental validation of plant peroxisomal targeting prediction algorithms by systematic comparison of in vivo import efficiency and in vitro PTS1 binding affinity. J Mol Biol 2014; 427:1085-101. [PMID: 25498386 DOI: 10.1016/j.jmb.2014.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/30/2014] [Accepted: 12/04/2014] [Indexed: 01/19/2023]
Abstract
Most peroxisomal matrix proteins possess a C-terminal targeting signal type 1 (PTS1). Accurate prediction of functional PTS1 sequences and their relative strength by computational methods is essential for determination of peroxisomal proteomes in silico but has proved challenging due to high levels of sequence variability of non-canonical targeting signals, particularly in higher plants, and low levels of availability of experimentally validated non-canonical examples. In this study, in silico predictions were compared with in vivo targeting analyses and in vitro thermodynamic binding of mutated variants within the context of one model targeting sequence. There was broad agreement between the methods for entire PTS1 domains and position-specific single amino acid residues, including residues upstream of the PTS1 tripeptide. The hierarchy Leu>Met>Ile>Val at the C-terminal position was determined for all methods but both experimental approaches suggest that Tyr is underweighted in the prediction algorithm due to the absence of this residue in the positive training dataset. A combination of methods better defines the score range that discriminates a functional PTS1. In vitro binding to the PEX5 receptor could discriminate among strong targeting signals while in vivo targeting assays were more sensitive, allowing detection of weak functional import signals that were below the limit of detection in the binding assay. Together, the data provide a comprehensive assessment of the factors driving PTS1 efficacy and provide a framework for the more quantitative assessment of the protein import pathway in higher plants.
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Affiliation(s)
- Nicola S Skoulding
- School of Chemistry and the Astbury Centre, University of Leeds, Leeds LS2 9JT, UK
| | - Gopal Chowdhary
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Richard Johansens Gate 4, N-4021 Stavanger, Norway; KIIT School of Biotechnology, Campus XI, KIIT University, I-751024 Bhubaneswar, India
| | - Mara J Deus
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Richard Johansens Gate 4, N-4021 Stavanger, Norway
| | - Alison Baker
- Centre for Plant Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sigrun Reumann
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Richard Johansens Gate 4, N-4021 Stavanger, Norway; Department of Biology, Biocentre Klein Flottbek, University of Hamburg, D-22609 Hamburg, Germany
| | - Stuart L Warriner
- School of Chemistry and the Astbury Centre, University of Leeds, Leeds LS2 9JT, UK.
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23
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Fodor K, Wolf J, Reglinski K, Passon DM, Lou Y, Schliebs W, Erdmann R, Wilmanns M. Ligand-Induced Compaction of the PEX5 Receptor-Binding Cavity Impacts Protein Import Efficiency into Peroxisomes. Traffic 2014; 16:85-98. [DOI: 10.1111/tra.12238] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/03/2014] [Accepted: 11/03/2014] [Indexed: 01/22/2023]
Affiliation(s)
- Krisztián Fodor
- Hamburg Unit; European Molecular Biology Laboratory Hamburg Unit; Hamburg Germany
| | - Janina Wolf
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum; Bochum Germany
| | - Katharina Reglinski
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum; Bochum Germany
| | - Daniel M. Passon
- Hamburg Unit; European Molecular Biology Laboratory Hamburg Unit; Hamburg Germany
| | - Ye Lou
- Hamburg Unit; European Molecular Biology Laboratory Hamburg Unit; Hamburg Germany
| | - Wolfgang Schliebs
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum; Bochum Germany
| | - Ralf Erdmann
- Department of Systems Biochemistry, Faculty of Medicine, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum; Bochum Germany
| | - Matthias Wilmanns
- Hamburg Unit; European Molecular Biology Laboratory Hamburg Unit; Hamburg Germany
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24
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Sooch BS, Kauldhar BS, Puri M. Recent insights into microbial catalases: Isolation, production and purification. Biotechnol Adv 2014; 32:1429-47. [DOI: 10.1016/j.biotechadv.2014.09.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 09/10/2014] [Accepted: 09/18/2014] [Indexed: 01/08/2023]
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25
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Choudhry SK, Kawałek A, van der Klei IJ. Peroxisomal quality control mechanisms. Curr Opin Microbiol 2014; 22:30-7. [PMID: 25305535 DOI: 10.1016/j.mib.2014.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/08/2014] [Accepted: 09/12/2014] [Indexed: 10/24/2022]
Abstract
Peroxisomes are ubiquitous organelles that harbor diverse metabolic pathways, which are essential for normal cell performance. Conserved functions of these organelles are hydrogen peroxide metabolism and β-oxidation. Cells employ multiple quality control mechanisms to ensure proper peroxisome function and to protect peroxisomes from damage. These involve the function of molecular chaperones, a peroxisomal Lon protease and autophagic removal of dysfunctional organelles. In addition, multiple mechanisms exist to combat peroxisomal oxidative stress. Here, we outline recent advances in our understanding of peroxisomal quality control, focussing on yeast and filamentous fungi.
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Affiliation(s)
- Sanjeev K Choudhry
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, P.O. Box 11103, 9300CC Groningen, The Netherlands
| | - Adam Kawałek
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, P.O. Box 11103, 9300CC Groningen, The Netherlands
| | - Ida J van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, Systems Biology Centre for Energy Metabolism and Ageing, University of Groningen, P.O. Box 11103, 9300CC Groningen, The Netherlands.
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26
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Lanyon-Hogg T, Hooper J, Gunn S, Warriner SL, Baker A. PEX14 binding to Arabidopsis PEX5 has differential effects on PTS1 and PTS2 cargo occupancy of the receptor. FEBS Lett 2014; 588:2223-9. [PMID: 24879895 PMCID: PMC4065332 DOI: 10.1016/j.febslet.2014.05.038] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 04/16/2014] [Accepted: 05/15/2014] [Indexed: 12/11/2022]
Abstract
The interaction between Arabidopsis PEX5 and PEX14N is independent of cargo binding. The affinity of a PTS1 peptide for PEX5 is unaffected by PEX14N binding. Arabidopsis PEX5 complexes PTS1 and PTS2 cargoes. PEX5 and 7 co-isolate with PEX14N, but the PTS2 cargo thiolase does not. PEX14N does not unload canonical PTS1 cargo peptide in vitro but may play a role in PTS2 release.
PEX5 acts as a cycling receptor for import of PTS1 proteins into peroxisomes and as a co-receptor for PEX7, the PTS2 receptor, but the mechanism of cargo unloading has remained obscure. Using recombinant protein domains we show PEX5 binding to the PEX14N-terminal domain (PEX14N) has no effect on the affinity of PEX5 for a PTS1 containing peptide. PEX5 can form a complex containing both recombinant PTS1 cargo and endogenous PEX7-thiolase simultaneously but isolation of the complex via the PEX14 construct resulted in an absence of thiolase, suggesting a possible role for PEX14 in the unloading of PTS2 cargos. pMDH1physically interacts with PEX5 by pull down (View interaction) PEX5Cbinds to PEX14N by filter binding (View interaction) PEX14Nbinds to PEX5C by pull down (View interaction) PEX14Nphysically interacts with PEX7 by pull down (View interaction) PEX5physically interacts with PEX7 by pull down (View interaction) DCI1physically interacts with PEX5 by pull down (View interaction) PEX5physically interacts with thiolase PTS2-cargo by pull down (View interaction) pMDH1physically interacts with PEX7 by pull down (View interaction) DCI1physically interacts with thiolase PTS2-cargo by pull down (View interaction) DCI1physically interacts with PEX7 by pull down (View interaction) PEX14Nphysically interacts with PEX5 by pull down (View interaction)
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Affiliation(s)
- Thomas Lanyon-Hogg
- Centre for Plant Sciences, Irene Manton Building, University of Leeds, Leeds LS2 9JT, UK; School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - Jacob Hooper
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - Sarah Gunn
- Centre for Plant Sciences, Irene Manton Building, University of Leeds, Leeds LS2 9JT, UK; School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | | | - Alison Baker
- Centre for Plant Sciences, Irene Manton Building, University of Leeds, Leeds LS2 9JT, UK.
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27
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Abstract
Peroxisomes carry out various oxidative reactions that are tightly regulated to adapt to the changing needs of the cell and varying external environments. Accordingly, they are remarkably fluid and can change dramatically in abundance, size, shape and content in response to numerous cues. These dynamics are controlled by multiple aspects of peroxisome biogenesis that are coordinately regulated with each other and with other cellular processes. Ongoing studies are deciphering the diverse molecular mechanisms that underlie biogenesis and how they cooperate to dynamically control peroxisome utility. These important challenges should lead to an understanding of peroxisome dynamics that can be capitalized upon for bioengineering and the development of therapies to improve human health.
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Affiliation(s)
- Jennifer J Smith
- 1] Seattle Biomedical Research Institute, 307 Westlake Avenue North, 98109-5240, USA. [2] Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5219, USA
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Ast J, Stiebler AC, Freitag J, Bölker M. Dual targeting of peroxisomal proteins. Front Physiol 2013; 4:297. [PMID: 24151469 PMCID: PMC3798809 DOI: 10.3389/fphys.2013.00297] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 09/28/2013] [Indexed: 01/08/2023] Open
Abstract
Cellular compartmentalization into organelles serves to separate biological processes within the environment of a single cell. While some metabolic reactions are specific to a single organelle, others occur in more than one cellular compartment. Specific targeting of proteins to compartments inside of eukaryotic cells is mediated by defined sequence motifs. To achieve multiple targeting to different compartments cells use a variety of strategies. Here, we focus on mechanisms leading to dual targeting of peroxisomal proteins. In many instances, isoforms of peroxisomal proteins with distinct intracellular localization are encoded by separate genes. But also single genes can give rise to differentially localized proteins. Different isoforms can be generated by use of alternative transcriptional start sites, by differential splicing or ribosomal read-through of stop codons. In all these cases different peptide variants are produced, of which only one carries a peroxisomal targeting signal. Alternatively, peroxisomal proteins contain additional signals that compete for intracellular targeting. Dual localization of proteins residing in both the cytoplasm and in peroxisomes may also result from use of inefficient targeting signals. The recent observation that some bona fide cytoplasmic enzymes were also found in peroxisomes indicates that dual targeting of proteins to both the cytoplasm and the peroxisome might be more widespread. Although current knowledge of proteins exhibiting only partial peroxisomal targeting is far from being complete, we speculate that the metabolic capacity of peroxisomes might be larger than previously assumed.
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Affiliation(s)
- Julia Ast
- Department of Biology, Philipps University Marburg Marburg, Germany
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29
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Manivannan S, de Boer R, Veenhuis M, van der Klei IJ. Lumenal peroxisomal protein aggregates are removed by concerted fission and autophagy events. Autophagy 2013; 9:1044-56. [PMID: 23614977 DOI: 10.4161/auto.24543] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We demonstrated that in the yeast Hansenula polymorpha peroxisome fission and degradation are coupled processes that are important to remove intra-organellar protein aggregates. Protein aggregates were formed in peroxisomes upon synthesis of a mutant catalase variant. We showed that the introduction of these aggregates in the peroxisomal lumen had physiological disadvantages as it affected growth and caused enhanced levels of reactive oxygen species. Formation of the protein aggregates was followed by asymmetric peroxisome fission to separate the aggregate from the mother organelle. Subsequently, these small, protein aggregate-containing organelles were degraded by autophagy. In line with this observation we showed that the degradation of the protein aggregates was strongly reduced in dnm1 and pex11 cells in which peroxisome fission is reduced. Moreover, this process was dependent on Atg1 and Atg11.
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