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Guo X, Zhou J, La Yan, Liu X, Yuan Y, Ye J, Zhang Z, Chen H, Ma Y, Zhong Z, Luo G, Chen H. Very long-chain fatty acids control peroxisome dynamics via a feedback loop in intestinal stem cells during gut regeneration. Dev Cell 2024:S1534-5807(24)00398-8. [PMID: 39047737 DOI: 10.1016/j.devcel.2024.06.020] [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: 10/13/2023] [Revised: 04/19/2024] [Accepted: 06/25/2024] [Indexed: 07/27/2024]
Abstract
Peroxisome dynamics are crucial for intestinal stem cell (ISC) differentiation and gut regeneration. However, the precise mechanisms that govern peroxisome dynamics within ISCs during gut regeneration remain unknown. Using mouse colitis and Drosophila intestine models, we have identified a negative-feedback control mechanism involving the transcription factors peroxisome proliferator-activated receptors (PPARs) and SOX21. This feedback mechanism effectively regulates peroxisome abundance during gut regeneration. Following gut injury, the released free very long-chain fatty acids (VLCFAs) increase peroxisome abundance by stimulating PPARs-PEX11s signaling. PPARs act to stimulate peroxisome fission and inhibit pexophagy. SOX21, which acts downstream of peroxisomes during ISC differentiation, induces peroxisome elimination through pexophagy while repressing PPAR expression. Hence, PPARs and SOX21 constitute a finely tuned negative-feedback loop that regulates peroxisome dynamics. These findings shed light on the complex molecular mechanisms underlying peroxisome regulation in ISCs, contributing to our understanding of gut renewal and repair.
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Affiliation(s)
- Xiaoxin Guo
- West China Centre of Excellence for Pancreatitis and Laboratory of Stem Cell and Anti-Aging Research, National Clinical Research Center for Geriatrics and State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Juanyu Zhou
- West China Centre of Excellence for Pancreatitis and Laboratory of Stem Cell and Anti-Aging Research, National Clinical Research Center for Geriatrics and State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - La Yan
- West China Centre of Excellence for Pancreatitis and Laboratory of Stem Cell and Anti-Aging Research, National Clinical Research Center for Geriatrics and State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xingzhu Liu
- West China Centre of Excellence for Pancreatitis and Laboratory of Stem Cell and Anti-Aging Research, National Clinical Research Center for Geriatrics and State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yu Yuan
- West China Centre of Excellence for Pancreatitis and Laboratory of Stem Cell and Anti-Aging Research, National Clinical Research Center for Geriatrics and State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jinbao Ye
- West China Centre of Excellence for Pancreatitis and Laboratory of Stem Cell and Anti-Aging Research, National Clinical Research Center for Geriatrics and State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zehong Zhang
- West China Centre of Excellence for Pancreatitis and Laboratory of Stem Cell and Anti-Aging Research, National Clinical Research Center for Geriatrics and State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Haiou Chen
- West China Centre of Excellence for Pancreatitis and Laboratory of Stem Cell and Anti-Aging Research, National Clinical Research Center for Geriatrics and State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yongxin Ma
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan 610041, China
| | - Zhendong Zhong
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Guanzheng Luo
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Haiyang Chen
- West China Centre of Excellence for Pancreatitis and Laboratory of Stem Cell and Anti-Aging Research, National Clinical Research Center for Geriatrics and State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
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2
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Chou SE, Kalel VC, Erdmann R. Biochemical Fractionation of Trypanosomes for the Analysis of Glycosomal Protein Import Defects. Methods Mol Biol 2023; 2643:445-453. [PMID: 36952205 DOI: 10.1007/978-1-0716-3048-8_32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Insect-transmitted trypanosomatid parasite infections cause life-threatening neglected tropical diseases (NTDs), including African sleeping sickness, Chagas disease and leishmaniasis. In these parasites, glycosomes are unique organelles that are essential for the parasite survival. Proper biogenesis of glycosomes is crucial to ensure correct compartmentation of the glycosomal metabolism. Genetic or chemical disruption of the glycosome biogenesis leads to a mislocalization of the glycosomal enzymes into the cytosol, which results in toxicity to the parasites. Here, we describe a detailed protocol for biochemical fractionation of Trypanosoma brucei parasites to detect mislocalization of glycosomal proteins to the cytosol. This approach utilizes increasing concentrations of digitonin that first permeabilizes the plasma membrane, followed by permeabilization of other organelles, depending on their cholesterol content. Fractionated samples can be further analyzed using immunoblotting for specific marker proteins or quantified by the specific enzyme activities.
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Affiliation(s)
- Shih-En Chou
- Institute for Biochemistry and Pathobiochemistry Department of Systems Biochemistry, Faculty of Medicine, Ruhr University of Bochum, Bochum, Germany
| | - Vishal C Kalel
- Institute for Biochemistry and Pathobiochemistry Department of Systems Biochemistry, Faculty of Medicine, Ruhr University of Bochum, Bochum, Germany.
| | - Ralf Erdmann
- Institute for Biochemistry and Pathobiochemistry Department of Systems Biochemistry, Faculty of Medicine, Ruhr University of Bochum, Bochum, Germany.
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3
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Spatial-temporal regulation of fatty alcohol biosynthesis in yeast. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:141. [PMID: 36527110 PMCID: PMC9758912 DOI: 10.1186/s13068-022-02242-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Construction of efficient microbial cell factories is one of the core steps for establishing green bio-manufacturing processes. However, the complex metabolic regulation makes it challenging in driving the metabolic flux toward the product biosynthesis. Dynamically coupling the biosynthetic pathways with the cellular metabolism at spatial-temporal manner should be helpful for improving the production with alleviating the cellular stresses. RESULTS In this study, we observed the mismatch between fatty alcohol biosynthesis and cellular metabolism, which compromised the fatty alcohol production in Saccharomyces cerevisiae. To enhance the fatty alcohol production, we spatial-temporally regulated fatty alcohol biosynthetic pathway by peroxisomal compartmentalization (spatial) and dynamic regulation of gene expression (temporal). In particular, fatty acid/acyl-CoA responsive promoters were identified by comparative transcriptional analysis, which helped to dynamically regulate the expression of acyl-CoA reductase gene MaFAR1 and improved fatty alcohol biosynthesis by 1.62-fold. Furthermore, enhancing the peroxisomal supply of acyl-CoA and NADPH further improved fatty alcohol production to 282 mg/L, 2.52 times higher than the starting strain. CONCLUSIONS This spatial-temporal regulation strategy partially coordinated fatty alcohol biosynthesis with cellular metabolism including peroxisome biogenesis and precursor supply, which should be applied for production of other products in microbes.
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Han M, Chen Z, He P, Li Z, Chen Q, Tong Z, Wang M, Du H, Zhang H. YgiM may act as a trigger in the sepsis caused by Klebsiella pneumoniae through the membrane-associated ceRNA network. Front Genet 2022; 13:973145. [PMID: 36212144 PMCID: PMC9537587 DOI: 10.3389/fgene.2022.973145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/07/2022] [Indexed: 11/27/2022] Open
Abstract
Sepsis is one of the diseases that can cause serious mortality. In E. coli, an inner membrane protein YgiM encoded by gene ygiM can target the eukaryotic peroxisome. Peroxisome is a membrane-enclosed organelle associated with the ROS metabolism and was reported to play the key role in immune responses and inflammation during the development of sepsis. Klebsiella pneumoniae (K. pneumoniae) is one of the important pathogens causing sepsis. However, the function of gene vk055_4013 which is highly homologous to ygiM of E. coli has not been demonstrated in K. pneumoniae. In this study, we prepared ΔygiM of K. pneumoniae ATCC43816, and found that the deletion of ygiM did not affect bacterial growth and mouse mortality in the mouse infection model. Interestingly, ΔygiM not only resulted in reduced bacterial resistance to macrophages, but also attenuated pathological manifestations in mouse organs. Furthermore, based on the data of Gene Expression Omnibus, the expression profiles of micro RNAs (miRNAs) and messenger RNAs (mRNAs) in the serum of 44 sepsis patients caused by K. pneumoniae infection were analyzed, and 11 differently expressed miRNAs and 8 DEmRNAs associated with the membrane function were found. Finally, the membrane-associated competing endogenous RNAs (ceRNAs) network was constructed. In this ceRNAs network, DEmiRNAs (hsa-miR-7108-5p, hsa-miR-6780a-5p, hsa-miR-6756-5p, hsa-miR-4433b-3p, hsa-miR-3652, hsa-miR-342-3p, hsa-miR-32-5p) and their potential downstream target DEmRNAs (VNN1, CEACAM8, PGLYRP1) were verified in the cell model infected by wild type and ΔygiM of K. pneumoniae, respectively. Taken together, YgiM may trigger the sepsis caused by K. pneumoniae via membrane-associated ceRNAs. This study provided new insights into the role of YgiM in the process of K. pneumoniae induced sepsis.
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Affiliation(s)
- Mingxiao Han
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhihao Chen
- Department of Orthopedics, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Department of Musculoskeletal Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Ping He
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Department of Clinical Laboratory, Sichuan Province Science City Hospital, Chengdu, China
| | - Ziyuan Li
- Department of Orthopedics, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Qi Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Zelei Tong
- Department of Orthopedics, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Min Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Haifang Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
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5
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Tarafdar S, Chowdhary G. Translating the Arabidopsis thaliana Peroxisome Proteome Insights to Solanum lycopersicum: Consensus Versus Diversity. Front Cell Dev Biol 2022; 10:909604. [PMID: 35912119 PMCID: PMC9328179 DOI: 10.3389/fcell.2022.909604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022] Open
Abstract
Peroxisomes are small, single-membrane specialized organelles present in all eukaryotic organisms. The peroxisome is one of the nodal centers of reactive oxygen species homeostasis in plants, which are generated in a high amount due to various stress conditions. Over the past decade, there has been extensive study on peroxisomal proteins and their signaling pathways in the model plant Arabidopsis thaliana, and a lot has been deciphered. However, not much impetus has been given to studying the peroxisome proteome of economically important crops. Owing to the significance of peroxisomes in the physiology of plants during normal and stress conditions, understating its proteome is of much importance. Hence, in this paper, we have made a snapshot of putative peroxisomal matrix proteins in the economically important vegetable crop tomato (Solanum lycopersicum, (L.) family Solanaceae). First, a reference peroxisomal matrix proteome map was generated for Arabidopsis thaliana using the available proteomic and localization studies, and proteins were categorized into various groups as per their annotations. This was used to create the putative peroxisomal matrix proteome map for S. lycopersicum. The putative peroxisome proteome in S. lycopersicum retains the basic framework: the bulk of proteins had peroxisomal targeting signal (PTS) type 1, a minor group had PTS2, and the catalase family retained its characteristic internal PTS. Apart from these, a considerable number of S. lycopersicum orthologs did not contain any "obvious" PTS. The number of PTS2 isoforms was found to be reduced in S. lycopersicum. We further investigated the PTS1s in the case of both the plant species and generated a pattern for canonical and non-canonical PTS1s. The number of canonical PTS1 proteins was comparatively lesser in S. lycopersicum. The non-canonical PTS1s were found to be comparable in both the plant species; however, S. lycopersicum showed greater diversity in the composition of the signal tripeptide. Finally, we have tried to address the lacunas and probable strategies to fill those gaps.
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Affiliation(s)
| | - Gopal Chowdhary
- Plant Molecular Biology Laboratory, School of Biotechnology, KIIT, Bhubaneswar, India
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Vasilev J, Mix AK, Heimerl T, Maier UG, Moog D. Inferred Subcellular Localization of Peroxisomal Matrix Proteins of Guillardia theta Suggests an Important Role of Peroxisomes in Cryptophytes. FRONTIERS IN PLANT SCIENCE 2022; 13:889662. [PMID: 35783940 PMCID: PMC9244630 DOI: 10.3389/fpls.2022.889662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Peroxisomes participate in several important metabolic processes in eukaryotic cells, such as the detoxification of reactive oxygen species (ROS) or the degradation of fatty acids by β-oxidation. Recently, the presence of peroxisomes in the cryptophyte Guillardia theta and other "chromalveolates" was revealed by identifying proteins for peroxisomal biogenesis. Here, we investigated the subcellular localization of candidate proteins of G. theta in the diatom Phaeodactylum tricornutum, either possessing a putative peroxisomal targeting signal type 1 (PTS1) sequence or factors lacking a peroxisomal targeting signal but known to be involved in β-oxidation. Our results indicate important contributions of the peroxisomes of G. theta to the carbohydrate, ether phospholipid, nucleotide, vitamin K, ROS, amino acid, and amine metabolisms. Moreover, our results suggest that in contrast to many other organisms, the peroxisomes of G. theta are not involved in the β-oxidation of fatty acids, which exclusively seems to occur in the cryptophyte's mitochondria.
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Affiliation(s)
- Jana Vasilev
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Ann-Kathrin Mix
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Uwe G. Maier
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Daniel Moog
- Laboratory for Cell Biology, Department of Biology, Philipps-University Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
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7
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Yaakoub H, Mina S, Calenda A, Bouchara JP, Papon N. Oxidative stress response pathways in fungi. Cell Mol Life Sci 2022; 79:333. [PMID: 35648225 PMCID: PMC11071803 DOI: 10.1007/s00018-022-04353-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/21/2022] [Accepted: 05/05/2022] [Indexed: 11/03/2022]
Abstract
Fungal response to any stress is intricate, specific, and multilayered, though it employs only a few evolutionarily conserved regulators. This comes with the assumption that one regulator operates more than one stress-specific response. Although the assumption holds true, the current understanding of molecular mechanisms that drive response specificity and adequacy remains rudimentary. Deciphering the response of fungi to oxidative stress may help fill those knowledge gaps since it is one of the most encountered stress types in any kind of fungal niche. Data have been accumulating on the roles of the HOG pathway and Yap1- and Skn7-related pathways in mounting distinct and robust responses in fungi upon exposure to oxidative stress. Herein, we review recent and most relevant studies reporting the contribution of each of these pathways in response to oxidative stress in pathogenic and opportunistic fungi after giving a paralleled overview in two divergent models, the budding and fission yeasts. With the concept of stress-specific response and the importance of reactive oxygen species in fungal development, we first present a preface on the expanding domain of redox biology and oxidative stress.
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Affiliation(s)
- Hajar Yaakoub
- Univ Angers, Univ Brest, IRF, SFR ICAT, 49000, Angers, France
| | - Sara Mina
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | | | | | - Nicolas Papon
- Univ Angers, Univ Brest, IRF, SFR ICAT, 49000, Angers, France.
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8
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AoPEX1 and AoPEX6 Are Required for Mycelial Growth, Conidiation, Stress Response, Fatty Acid Utilization, and Trap Formation in Arthrobotrys oligospora. Microbiol Spectr 2022; 10:e0027522. [PMID: 35323036 PMCID: PMC9045386 DOI: 10.1128/spectrum.00275-22] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Arthrobotrys oligospora (A. oligospora) is a typical nematode-trapping (NT) fungus that can capture nematodes by producing adhesive networks. Peroxisomes are single membrane-bound organelles that perform multiple physiological functions in filamentous fungi. Peroxisome biogenesis proteins are encoded by PEX genes, and the functions of PEX genes in A. oligospora and other NT fungi remain largely unknown. Here, our results demonstrated that two PEX genes (AoPEX1 and AoPEX6) are essential for mycelial growth, conidiation, fatty acid utilization, stress tolerance, and pathogenicity in A. oligospora. AoPEX1 and AoPEX6 knockout resulted in a failure to produce traps, conidia, peroxisomes, and Woronin bodies and damaged cell walls, reduced autophagosome levels, and increased lipid droplet size. Transcriptome data analysis showed that AoPEX1 and AoPEX6 deletion resulted in the upregulation of the proteasome, membranes, ribosomes, DNA replication, and cell cycle functions, and the downregulation of MAPK signaling and nitrogen metabolism. In summary, our results provide novel insights into the functions of PEX genes in the growth, development, and pathogenicity of A. oligospora and contribute to the elucidation of the regulatory mechanism of peroxisomes in trap formation and lifestyle switching in NT fungi. IMPORTANCE Nematode-trapping (NT) fungi are important resources for the biological control of plant-parasitic nematodes. They are widely distributed in various ecological environments and capture nematodes by producing unique predatory organs (traps). However, the molecular mechanisms of trap formation and lifestyle switching in NT fungi are still unclear. Here, we provided experimental evidence that the AoPEX1 and AoPEX6 genes could regulate mycelial growth and development, trap formation, and nematode predation of A. oligospora. We further analyzed the global transcription level changes of wild-type and mutant strains using RNA-seq. This study highlights the important role of peroxisome biogenesis genes in vegetative growth, conidiation, trap formation, and pathogenicity, which contribute to probing the mechanism of organelle development and trap formation of NT fungi and lays a foundation for developing high-efficiency nematode biocontrol agents.
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9
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Infant T, Deb R, Ghose S, Nagotu S. Post-translational modifications of proteins associated with yeast peroxisome membrane: An essential mode of regulatory mechanism. Genes Cells 2021; 26:843-860. [PMID: 34472666 PMCID: PMC9291962 DOI: 10.1111/gtc.12892] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022]
Abstract
Peroxisomes are single membrane‐bound organelles important for the optimum functioning of eukaryotic cells. Seminal discoveries in the field of peroxisomes are made using yeast as a model. Several proteins required for the biogenesis and function of peroxisomes are identified to date. As with proteins involved in other major cellular pathways, peroxisomal proteins are also subjected to regulatory post‐translational modifications. Identification, characterization and mapping of these modifications to specific amino acid residues on proteins are critical toward understanding their functional significance. Several studies have tried to identify post‐translational modifications of peroxisomal proteins and determine their impact on peroxisome structure and function. In this manuscript, we provide an overview of the various post‐translational modifications that govern the peroxisome dynamics in yeast.
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Affiliation(s)
- Terence Infant
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Rachayeeta Deb
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Suchetana Ghose
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
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10
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Liu Y, Weaver CM, Sen Y, Eitzen G, Simmonds AJ, Linchieh L, Lurette O, Hebert-Chatelain E, Rachubinski RA, Di Cara F. The Nitric Oxide Donor, S-Nitrosoglutathione, Rescues Peroxisome Number and Activity Defects in PEX1G843D Mild Zellweger Syndrome Fibroblasts. Front Cell Dev Biol 2021; 9:714710. [PMID: 34434934 PMCID: PMC8382563 DOI: 10.3389/fcell.2021.714710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/20/2021] [Indexed: 02/04/2023] Open
Abstract
Peroxisome biogenesis disorders (PBDs) are a group of metabolic developmental diseases caused by mutations in one or more genes encoding peroxisomal proteins. Zellweger syndrome spectrum (PBD-ZSS) results from metabolic dysfunction caused by damaged or non-functional peroxisomes and manifests as a multi-organ syndrome with significant morbidity and mortality for which there is no current drug therapy. Mild PBD-ZSS patients can exhibit a more progressive disease course and could benefit from the identification of drugs to improve the quality of life and extend the lifespan of affected individuals. Our study used a high-throughput screen of FDA-approved compounds to identify compounds that improve peroxisome function and biogenesis in human fibroblast cells carrying the mild PBD-ZSS variant, PEX1G843D. Our screen identified the nitrogen oxide donor, S-nitrosoglutathione (GSNO), as a potential therapeutic for this mild form of PBD-ZSS. Further biochemical characterization showed that GSNO enhances both peroxisome number and function in PEX1G843D mutant fibroblasts and leads to increased survival and longer lifespan in an in vivo humanized Drosophila model carrying the PEX1G843D mutation. GSNO is therefore a strong candidate to be translated to clinical trials as a potential therapeutic for mild PBD-ZSS.
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Affiliation(s)
- Yidi Liu
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Ceileigh M Weaver
- Department of Microbiology and Immunology, IWK Research Centre, Dalhousie University, Halifax, NS, Canada
| | - Yarina Sen
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Gary Eitzen
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Lilliana Linchieh
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Olivier Lurette
- Department of Biology, University of Moncton, Moncton, NB, Canada
| | | | | | - Francesca Di Cara
- Department of Microbiology and Immunology, IWK Research Centre, Dalhousie University, Halifax, NS, Canada
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11
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Meyer MT, Watermann C, Dreyer T, Wagner S, Wittekindt C, Klussmann JP, Ergün S, Baumgart-Vogt E, Karnati S. Differential Expression of Peroxisomal Proteins in Distinct Types of Parotid Gland Tumors. Int J Mol Sci 2021; 22:7872. [PMID: 34360635 PMCID: PMC8345988 DOI: 10.3390/ijms22157872] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022] Open
Abstract
Salivary gland cancers are rare but aggressive tumors that have poor prognosis and lack effective cure. Of those, parotid tumors constitute the majority. Functioning as metabolic machinery contributing to cellular redox balance, peroxisomes have emerged as crucial players in tumorigenesis. Studies on murine and human cells have examined the role of peroxisomes in carcinogenesis with conflicting results. These studies either examined the consequences of altered peroxisomal proliferators or compared their expression in healthy and neoplastic tissues. None, however, examined such differences exclusively in human parotid tissue or extended comparison to peroxisomal proteins and their associated gene expressions. Therefore, we examined differences in peroxisomal dynamics in parotid tumors of different morphologies. Using immunofluorescence and quantitative PCR, we compared the expression levels of key peroxisomal enzymes and proliferators in healthy and neoplastic parotid tissue samples. Three parotid tumor subtypes were examined: pleomorphic adenoma, mucoepidermoid carcinoma and acinic cell carcinoma. We observed higher expression of peroxisomal matrix proteins in neoplastic samples with exceptional down regulation of certain enzymes; however, the degree of expression varied between tumor subtypes. Our findings confirm previous experimental results on other organ tissues and suggest peroxisomes as possible therapeutic targets or markers in all or certain subtypes of parotid neoplasms.
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Affiliation(s)
- Malin Tordis Meyer
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Klinikstrasse 33, Ebene-1, D-35392 Gießen, Germany; (M.T.M.); (C.W.); (S.W.); (C.W.); (J.P.K.)
| | - Christoph Watermann
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Klinikstrasse 33, Ebene-1, D-35392 Gießen, Germany; (M.T.M.); (C.W.); (S.W.); (C.W.); (J.P.K.)
| | - Thomas Dreyer
- Institute of Pathology, Justus Liebig University, Langhansstrasse 10, D-35392 Gießen, Germany;
| | - Steffen Wagner
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Klinikstrasse 33, Ebene-1, D-35392 Gießen, Germany; (M.T.M.); (C.W.); (S.W.); (C.W.); (J.P.K.)
| | - Claus Wittekindt
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Klinikstrasse 33, Ebene-1, D-35392 Gießen, Germany; (M.T.M.); (C.W.); (S.W.); (C.W.); (J.P.K.)
| | - Jens Peter Klussmann
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Klinikstrasse 33, Ebene-1, D-35392 Gießen, Germany; (M.T.M.); (C.W.); (S.W.); (C.W.); (J.P.K.)
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University of Cologne, D-50931 Cologne, Germany
| | - Süleyman Ergün
- Institute for Anatomy and Cell Biology, Julius-Maximilians-University Würzburg, Koellikerstrasse 6, D-97070 Würzburg, Germany;
| | - Eveline Baumgart-Vogt
- Institute for Anatomy and Cell Biology II, Medical Cell Biology, Justus Liebig University, D-35385 Gießen, Germany;
| | - Srikanth Karnati
- Institute for Anatomy and Cell Biology, Julius-Maximilians-University Würzburg, Koellikerstrasse 6, D-97070 Würzburg, Germany;
- Institute for Anatomy and Cell Biology II, Medical Cell Biology, Justus Liebig University, D-35385 Gießen, Germany;
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12
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Wu PC, Chen YK, Yago JI, Chung KR. Peroxisomes Implicated in the Biosynthesis of Siderophores and Biotin, Cell Wall Integrity, Autophagy, and Response to Hydrogen Peroxide in the Citrus Pathogenic Fungus Alternaria alternata. Front Microbiol 2021; 12:645792. [PMID: 34262533 PMCID: PMC8273606 DOI: 10.3389/fmicb.2021.645792] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Little is known about the roles of peroxisomes in the necrotrophic fungal plant pathogens. In the present study, a Pex6 gene encoding an ATPase-associated protein was characterized by analysis of functional mutations in the tangerine pathotype of Alternaria alternata, which produces a host-selective toxin. Peroxisomes were observed in fungal cells by expressing a mCherry fluorescent protein tagging with conserved tripeptides serine-lysing-leucine and transmission electron microscopy. The results indicated that Pex6 plays no roles in peroxisomal biogenesis but impacts protein import into peroxisomes. The number of peroxisomes was affected by nutritional conditions and H2O2, and their degradation was mediated by an autophagy-related machinery termed pexophagy. Pex6 was shown to be required for the formation of Woronin bodies, the biosynthesis of biotin, siderophores, and toxin, the uptake and accumulation of H2O2, growth, and virulence, as well as the Slt2 MAP kinase-mediated maintenance of cell wall integrity. Adding biotin, oleate, and iron in combination fully restored the growth of the pex6-deficient mutant (Δpex6), but failed to restore Δpex6 virulence to citrus. Adding purified toxin could only partially restore Δpex6 virulence even in the presence of biotin, oleate, and iron. Sensitivity assays revealed that Pex6 plays no roles in resistance to H2O2 and superoxide, but plays a negative role in resistance to 2-chloro-5-hydroxypyridine (a hydroxyl radical-generating compound), eosin Y and rose Bengal (singlet oxygen-generating compounds), and 2,3,5-triiodobenzoic acid (an auxin transport inhibitor). The diverse functions of Pex6 underscore the importance of peroxisomes in physiology, pathogenesis, and development in A. alternata.
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Affiliation(s)
- Pei-Ching Wu
- Department of Plant Pathology, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Kun Chen
- Department of Plant Pathology, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Jonar I. Yago
- Plant Science Department, College of Agriculture, Nueva Vizcaya State University, Bayombong, Philippines
| | - Kuang-Ren Chung
- Department of Plant Pathology, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
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13
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Yamashita K, Tamura S, Honsho M, Yada H, Yagita Y, Kosako H, Fujiki Y. Mitotic phosphorylation of Pex14p regulates peroxisomal import machinery. J Cell Biol 2021; 219:152047. [PMID: 32854114 PMCID: PMC7659713 DOI: 10.1083/jcb.202001003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/28/2020] [Accepted: 07/13/2020] [Indexed: 01/27/2023] Open
Abstract
Peroxisomal matrix proteins are imported into peroxisomes via membrane-bound docking/translocation machinery. One central component of this machinery is Pex14p, a peroxisomal membrane protein involved in the docking of Pex5p, the receptor for peroxisome targeting signal type 1 (PTS1). Studies in several yeast species have shown that Pex14p is phosphorylated in vivo, whereas no function has been assigned to Pex14p phosphorylation in yeast and mammalian cells. Here, we investigated peroxisomal protein import and its dynamics in mitotic mammalian cells. In mitotically arrested cells, Pex14p is phosphorylated at Ser-232, resulting in a lower import efficiency of catalase, but not the majority of proteins including canonical PTS1 proteins. Conformational change induced by the mitotic phosphorylation of Pex14p more likely increases homomeric interacting affinity and suppresses topological change of its N-terminal part, thereby giving rise to the retardation of Pex5p export in mitotic cells. Taken together, these data show that mitotic phosphorylation of Pex14p and consequent suppression of catalase import are a mechanism of protecting DNA upon nuclear envelope breakdown at mitosis.
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Affiliation(s)
- Koichiro Yamashita
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | | | - Masanori Honsho
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.,Institute of Rheological Functions of Food, Fukuoka, Japan
| | - Hiroto Yada
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Yuichi Yagita
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, Japan
| | - Yukio Fujiki
- Division of Organelle Homeostasis, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.,Institute of Rheological Functions of Food, Fukuoka, Japan
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14
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Wu PC, Chen CW, Choo CYL, Chen YK, Yago JI, Chung KR. Proper Functions of Peroxisomes Are Vital for Pathogenesis of Citrus Brown Spot Disease Caused by Alternaria alternata. J Fungi (Basel) 2020; 6:jof6040248. [PMID: 33114679 PMCID: PMC7712655 DOI: 10.3390/jof6040248] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/14/2020] [Accepted: 10/24/2020] [Indexed: 11/27/2022] Open
Abstract
In addition to the production of a host-selective toxin, the tangerine pathotype of Alternaria alternata must conquer toxic reactive oxygen species (ROS) in order to colonize host plants. The roles of a peroxin 6-coding gene (pex6) implicated in protein import into peroxisomes was functionally characterized to gain a better understanding of molecular mechanisms in ROS resistance and fungal pathogenicity. The peroxisome is a vital organelle involved in metabolisms of fatty acids and hydrogen peroxide in eukaryotes. Targeted deletion of pex6 had no impacts on the biogenesis of peroxisomes and cellular resistance to ROS. The pex6 deficient mutant (Δpex6) reduced toxin production by 40% compared to wild type and barely induce necrotic lesions on citrus leaves. Co-inoculation of purified toxin with Δpex6 conidia on citrus leaves, however, failed to fully restore lesion formation, indicating that toxin only partially contributed to the loss of Δpex6 pathogenicity. Δpex6 conidia germinated poorly and formed fewer appressorium-like structures (nonmelanized enlargement of hyphal tips) than wild type. Δpex6 hyphae grew slowly and failed to penetrate beyond the epidermal layers. Moreover, Δpex6 had thinner cell walls and lower viability. All of these defects resulting from deletion of pex6 could also account for the loss of Δpex6 pathogenicity. Overall, our results have demonstrated that proper peroxisome functions are of vital importance to pathogenesis of the tangerine pathotype of A. alternata.
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Affiliation(s)
- Pei-Ching Wu
- Department of Plant Pathology, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 40227, Taiwan; (C.-W.C.); (C.Y.L.C.); (Y.-K.C.)
- Correspondence: (P.-C.W.); (K.-R.C.); Tel.: +886-4-22840780 (ext. 316) (P.-C.W.); +886-4-22840780 (ext. 301) (K.-R.C.)
| | - Chia-Wen Chen
- Department of Plant Pathology, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 40227, Taiwan; (C.-W.C.); (C.Y.L.C.); (Y.-K.C.)
| | - Celine Yen Ling Choo
- Department of Plant Pathology, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 40227, Taiwan; (C.-W.C.); (C.Y.L.C.); (Y.-K.C.)
| | - Yu-Kun Chen
- Department of Plant Pathology, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 40227, Taiwan; (C.-W.C.); (C.Y.L.C.); (Y.-K.C.)
| | - Jonar I. Yago
- Plant Science Department, College of Agriculture, Nueva Vizcaya State University, Bayombong, Nueva Vizcaya 3700, Philippines;
| | - Kuang-Ren Chung
- Department of Plant Pathology, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 40227, Taiwan; (C.-W.C.); (C.Y.L.C.); (Y.-K.C.)
- Correspondence: (P.-C.W.); (K.-R.C.); Tel.: +886-4-22840780 (ext. 316) (P.-C.W.); +886-4-22840780 (ext. 301) (K.-R.C.)
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15
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Mast FD, Rachubinski RA, Aitchison JD. Peroxisome prognostications: Exploring the birth, life, and death of an organelle. J Cell Biol 2020; 219:133827. [PMID: 32211898 PMCID: PMC7054992 DOI: 10.1083/jcb.201912100] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 02/07/2023] Open
Abstract
Peroxisomes play a central role in human health and have biochemical properties that promote their use in many biotechnology settings. With a primary role in lipid metabolism, peroxisomes share a niche with lipid droplets within the endomembrane-secretory system. Notably, factors in the ER required for the biogenesis of peroxisomes also impact the formation of lipid droplets. The dynamic interface between peroxisomes and lipid droplets, and also between these organelles and the ER and mitochondria, controls their metabolic flux and their dynamics. Here, we review our understanding of peroxisome biogenesis to propose and reframe models for understanding how peroxisomes are formed in cells. To more fully understand the roles of peroxisomes and to take advantage of their many properties that may prove useful in novel therapeutics or biotechnology applications, we recast mechanisms controlling peroxisome biogenesis in a framework that integrates inference from these models with experimental data.
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Affiliation(s)
- Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA
| | | | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA.,Department of Pediatrics, University of Washington, Seattle, WA
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16
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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.
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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
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17
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Nie H, Cheng C, Hua J. Mitochondrial proteomic analysis reveals that proteins relate to oxidoreductase activity play a central role in pollen fertility in cotton. J Proteomics 2020; 225:103861. [PMID: 32531408 DOI: 10.1016/j.jprot.2020.103861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/05/2020] [Accepted: 06/02/2020] [Indexed: 01/18/2023]
Abstract
Cotton (Gossypium hirsutum L.) is an important economic crop. Cytoplasm male sterility (CMS) has been used to develop hybrid system and to produce hybrid seeds in cotton, but the molecular mechanism of CMS remains unclear. Mitochondria are semi-autonomous organelles, which play an important role in the reproduction of flowering plants. Male sterility has been proved associated with mitochondrial dysfunction in plants. In present study, a new strategy of proteomic sequencing data-independent acquisition (DIA) was used to analysis protein abundance across CMS lines 2074A (cytoplasm of Gossypium harknessii, D2-2) and 2074S (cytoplasm of G. hirsutum, AD1), and their maintainer 2074B. Comparing with transcriptome results showed that there is little consistence between proteome and transcriptome. A total of 2095 protein species were identified in three materials, and 186 and 161 differentially proteins were detected in the comparisons of 2074A vs 2074B, and 2074S vs 2074B, respectively. Among them, 49 and 50 proteins were specific existed in anther, and mainly participated in oxidoreductase activity, carbohydrate metabolism, fatty acid metabolism, cell aging, wax or cutin deposition and signal transduction. Gh_A07G0770 and Gh_D05G1908 were specific up-regulated in sterility lines, and the other genes Gh_D08G1196, Gh_D12G1971, Gh_A11G1250, Gh_D08G0388 were down-regulated, which presented similar expression tendency verified by qRT-PCR, transcriptome and proteome results. These six genes related to lipid synthesis, response to oxidative stress and cell aging, suggested them being involved in CMS occurrence. Using virus-induced gene silencing (VIGS) system, sterility obtained demonstrated the silencing Gh_A11G1250 in maintainer 2074B led to partial anthers abortion. Gh_A11G1250 encoded a mitochondrial localization of peroxisomal-like protein, participated in response to reactive oxygen species (ROS). Twenty-two proteins interacting with Gh_A11G1250 mainly related to chlorophyll biosynthetic process, photoperiodism and flowering, which showed different expression pattern between the male sterile line 2074A and maintainer 2074B. This novel research based on mitochondrial proteomics comparison confirmed that DAPs related to oxidative stress are critical to pollen abortion. BIOLOGICAL SIGNIFICANCE: Cytoplasm male sterility (CMS) system is utilized widely for hybrid production in cotton. However, the genetic and molecular mechanisms of CMS still need to be further elucidated. Up till now, fewer comprehensive comparisons of the mitochondrial proteomes from cotton CMS line and maintainer line have been reported. In this study, we performed a novel comparison of mitochondrial protein profiles in two CMS lines and their common maintainer line. Based on our results, we found a potential protein related to oxidative stress led to the anthers abortion. These results accumulate data to interpret the molecular mechanisms of CMS in cotton.
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Affiliation(s)
- Hushuai Nie
- Laboratory of Cotton Genetics, Genomics and Breeding, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology; China Agricultural University, No. 2, Yuanmingyuan West Rd, Haidian District, Beijing 100193, PR China
| | - Cheng Cheng
- Laboratory of Cotton Genetics, Genomics and Breeding, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology; China Agricultural University, No. 2, Yuanmingyuan West Rd, Haidian District, Beijing 100193, PR China
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology; China Agricultural University, No. 2, Yuanmingyuan West Rd, Haidian District, Beijing 100193, PR China.
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18
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Du G, Xiong L, Li X, Zhuo Z, Zhuang X, Yu Z, Wu L, Xiao D, Liu Z, Jie M, Liu X, Luo G, Guo Z, Chen H. Peroxisome Elevation Induces Stem Cell Differentiation and Intestinal Epithelial Repair. Dev Cell 2020; 53:169-184.e11. [PMID: 32243783 DOI: 10.1016/j.devcel.2020.03.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/20/2020] [Accepted: 03/03/2020] [Indexed: 02/08/2023]
Abstract
Epithelial-repair-dependent mucosal healing (MH) is associated with a more favorable prognosis for patients with inflammatory bowel disease (IBD). MH is accomplished via repair and regeneration of the intestinal epithelium. However, the mechanism underlying MH is ill defined. We found a striking upregulation of peroxisomes in the injured crypts of IBD patients. By increasing peroxisome levels in Drosophila midguts, we found that peroxisome elevation enhanced RAB7-dependent late endosome maturation, which then promoted stem and/or progenitor-cell differentiation via modulation of Janus Kinase (JAK) and Signal Transducer and Activator of Transcription (STAT)-SOX21A signaling. This in turn enhanced ISC-mediated regeneration. Importantly, RAB7 and SOX21 were upregulated in the crypts of IBD patients. Moreover, administration of drugs that increased peroxisome levels reversed the symptoms of dextran sulfate sodium (DSS)-induced colitis in mice. This study demonstrates a peroxisome-mediated epithelial repair mechanism, which opens a therapeutic avenue for the enhancement of MH in IBD patients.
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Affiliation(s)
- Gang Du
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China; Laboratory for Stem Cell and anti-Aging Research, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Lishou Xiong
- Department of Gastroenterology and Hepatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Xiaorong Li
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Zhangpeng Zhuo
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Xiaojun Zhuang
- Department of Gastroenterology and Hepatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Zihua Yu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Lijian Wu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Danqing Xiao
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Zhiming Liu
- Laboratory for Stem Cell and anti-Aging Research, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Minwen Jie
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Xuehong Liu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Guanzheng Luo
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Zheng Guo
- Department of Medical Genetics, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Haiyang Chen
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China; Laboratory for Stem Cell and anti-Aging Research, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
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19
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Ortega-Martínez M, Gutiérrez-Dávila V, Niderhauser-García A, Salazar-Aranda R, Solís-Soto JM, Montes-de-Oca-Luna R, Jaramillo-Rangel G. Peroxisomicine A1, a potential antineoplastic agent, causes micropexophagy in addition to macropexophagy. Cell Biol Int 2020; 44:918-923. [PMID: 31814220 DOI: 10.1002/cbin.11280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022]
Abstract
Peroxisomicine A1 (PA1) is a potential antineoplastic agent with high and selective toxicity toward peroxisomes of tumor cells. Pexophagy is a selective autophagy process that degrades damaged peroxisomes; this process has been studied mainly in methylotrophic yeasts. There are two main modes of pexophagy in yeast: macropexophagy and micropexophagy. Previous studies showed that peroxisomes damaged by a prolonged exposition to PA1 are eliminated by macropexophagy. In this work, Candida boidinii was grown in methanol-containing media, and PA1 was added to the cultures at 2 µg/mL after they reached the mid-exponential growth phase. Samples were taken at 5, 10, 15, 20, and 25 min after the addition of PA1 and processed for ultrastructural analysis. Typical morphological characteristics of micropexophagy were observed: the direct engulfment of peroxisomes by the vacuolar membrane and the presence of the micropexophagic membrane apparatus (MIPA), which mediates the fusion between the opposing tips of the vacuole to complete sequestration of peroxisomes from the cytosol. In conclusion, here we report that, in addition to macropexophagy, peroxisomes damaged by PA1 can be eliminated by micropexophagy. This information is useful to deepen the knowledge of the mechanism of action of PA1 and of that of pexophagy per se.
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Affiliation(s)
- Marta Ortega-Martínez
- Department of Pathology, School of Medicine, Autonomous University of Nuevo Leon, Ave. Madero y Dr. Eduardo Aguirre P., Monterrey, Nuevo León, 64460, Mexico
| | - Vanessa Gutiérrez-Dávila
- Department of Pathology, School of Medicine, Autonomous University of Nuevo Leon, Ave. Madero y Dr. Eduardo Aguirre P., Monterrey, Nuevo León, 64460, Mexico
| | - Alberto Niderhauser-García
- Department of Pathology, School of Medicine, Autonomous University of Nuevo Leon, Ave. Madero y Dr. Eduardo Aguirre P., Monterrey, Nuevo León, 64460, Mexico
| | - Ricardo Salazar-Aranda
- Department of Analytical Chemistry, School of Medicine, Autonomous University of Nuevo Leon, Ave. Madero y Dr. Eduardo Aguirre P., Monterrey, Nuevo León, 64460, Mexico
| | - Juan M Solís-Soto
- Department of Physiology, School of Dentistry, Autonomous University of Nuevo Leon, Dr. Eduardo Aguirre P. y Silao, Monterrey, Nuevo León, 64460, Mexico
| | - Roberto Montes-de-Oca-Luna
- Department of Histology, School of Medicine, Autonomous University of Nuevo Leon, Ave. Madero y Dr. Eduardo Aguirre P., Monterrey, Nuevo León, 64460, Mexico
| | - Gilberto Jaramillo-Rangel
- Department of Pathology, School of Medicine, Autonomous University of Nuevo Leon, Ave. Madero y Dr. Eduardo Aguirre P., Monterrey, Nuevo León, 64460, Mexico
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20
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Kirkin V. History of the Selective Autophagy Research: How Did It Begin and Where Does It Stand Today? J Mol Biol 2020; 432:3-27. [PMID: 31082435 PMCID: PMC6971693 DOI: 10.1016/j.jmb.2019.05.010] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 02/07/2023]
Abstract
Autophagy, self-eating, is a pivotal catabolic mechanism that ensures homeostasis and survival of the cell in the face of stressors as different as starvation, infection, or protein misfolding. The importance of the research in this field was recognized by the general public after the Nobel Prize for Physiology or Medicine was awarded in 2016 to Yoshinori Ohsumi for discoveries of the mechanisms of autophagy using yeast as a model organism. One of the seminal findings of Ohsumi was on the role ubiquitin-like proteins (UBLs)-Atg5, Atg12, and Atg8-play in the formation of the double-membrane vesicle autophagosome, which is the functional unit of autophagy. Subsequent work by several groups demonstrated that, like the founding member of the UBL family ubiquitin, these small but versatile protein and lipid modifiers interact with a plethora of proteins, which either directly regulate autophagosome formation, for example, components of the Atg1/ULK1 complex, or are involved in cargo recognition, for example, Atg19 and p62/SQSTM1. By tethering the cargo to the UBLs present on the forming autophagosome, the latter proteins were proposed to effectively act as selective autophagy receptors. The discovery of the selective autophagy receptors brought a breakthrough in the autophagy field, supplying the mechanistic underpinning for the formation of an autophagosome selectively around the cytosolic cargo, that is, a protein aggregate, a mitochondrion, or a cytosolic bacterium. In this historical overview, I highlight key steps that the research into selective autophagy has been taking over the past 20 years. I comment on their significance and discuss current challenges in developing more detailed knowledge of the mechanisms of selective autophagy. I will conclude by introducing the new directions that this dynamic research field is taking into its third decade.
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Affiliation(s)
- Vladimir Kirkin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK.
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Pejvakin-mediated pexophagy protects auditory hair cells against noise-induced damage. Proc Natl Acad Sci U S A 2019; 116:8010-8017. [PMID: 30936319 DOI: 10.1073/pnas.1821844116] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Noise overexposure causes oxidative stress, leading to auditory hair cell damage. Adaptive peroxisome proliferation involving pejvakin, a peroxisome-associated protein from the gasdermin family, has been shown to protect against this harmful oxidative stress. However, the role of pejvakin in peroxisome dynamics and homeostasis remains unclear. Here we show that sound overstimulation induces an early and rapid selective autophagic degradation of peroxisomes (pexophagy) in auditory hair cells from wild-type, but not pejvakin-deficient (Pjvk -/-), mice. Noise overexposure triggers recruitment of the autophagosome-associated protein MAP1LC3B (LC3B; microtubule-associated protein 1 light chain 3β) to peroxisomes in wild-type, but not Pjvk -/-, mice. We also show that pejvakin-LC3B binding involves an LC3-interacting region within the predicted chaperone domain of pejvakin. In transfected cells and in vivo transduced auditory hair cells, cysteine mutagenesis experiments demonstrated the requirement for both C328 and C343, the two cysteine residues closest to the C terminus of pejvakin, for reactive oxygen species-induced pejvakin-LC3B interaction and pexophagy. The viral transduction of auditory hair cells from Pjvk -/- mice in vivo with both Pjvk and Lc3b cDNAs completely restored sound-induced pexophagy, fully prevented the development of oxidative stress, and resulted in normal levels of peroxisome proliferation, whereas Pjvk cDNA alone yielded only a partial correction of the defects. Overall, our results demonstrate that pexophagy plays a key role in noise-induced peroxisome proliferation and identify defective pexophagy as a cause of noise-induced hearing loss. They suggest that pejvakin acts as a redox-activated pexophagy receptor/adaptor, thereby identifying a previously unknown function of gasdermin family proteins.
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Knoblach B, Rachubinski RA. Determinants of the assembly, integrity and maintenance of the endoplasmic reticulum-peroxisome tether. Traffic 2019; 20:213-225. [PMID: 30597694 DOI: 10.1111/tra.12635] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 12/24/2018] [Accepted: 12/26/2018] [Indexed: 11/29/2022]
Abstract
Organelle tethering and intercommunication are crucial for proper cell function. We previously described a tether between peroxisomes and the endoplasmic reticulum (ER) that acts in peroxisome population control in the yeast, Saccharomyces cerevisiae. Components of this tether are Pex3p, an integral membrane protein of both peroxisomes and the ER and Inp1p, a connector that links peroxisomes to the ER. Here, we report the analysis of random Inp1p mutants that enabled identification of regions in Inp1p required for the assembly and maintenance of the ER-peroxisome tether. Interaction analysis between Inp1p mutants and known Inp1p-binding proteins demonstrated that Pex3p and Inp1p do not constitute the sole components of the ER-peroxisome tether. Deletion of these Inp1p interactors whose steady-state localization is outside of ER-peroxisome tethers affected peroxisome dynamics. Our findings are consistent with the presence of regulatory cues that act on ER-peroxisome tethers and point to the existence of membrane contact sites between peroxisomes and organelles other than the ER.
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Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
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Knoblach B, Rachubinski RA. Reconstitution of human peroxisomal β-oxidation in yeast. FEMS Yeast Res 2018; 18:5075582. [PMID: 30124827 DOI: 10.1093/femsyr/foy092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/14/2018] [Indexed: 11/14/2022] Open
Abstract
We report the permanent introduction of the human peroxisomal β-oxidation enzymatic machinery required for straight chain degradation of fatty acids into the yeast, Saccharomyces cerevisiae. Peroxisomal β-oxidation encompasses four sequential reactions that are confined to three enzymes. The genes encoding human acyl-CoA oxidase 1, peroxisomal multifunctional enzyme type 2 and 3-ketoacyl-CoA thiolase were introduced into the genomic loci of their yeast gene equivalents. The human β-oxidation genes were individually tagged with sequence coding for GFP and expression of the protein chimeras as well as their targeting to peroxisomes was confirmed. Functional complementation of the β-oxidation pathway was assessed by growth on media containing fatty acids of different chain lengths. Yeast cells exhibited distinctive substrate specificities depending on whether they expressed the human or their endogenous β-oxidation machinery. The genetic engineering of yeast to contain a 'humanized' organelle is a first step for the in vivo study of human peroxisome disorders in a model organism.
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Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, MSB 5-14, Edmonton, Alberta T6G 2H7, Canada
| | - Richard A Rachubinski
- Department of Cell Biology, University of Alberta, Edmonton, MSB 5-14, Edmonton, Alberta T6G 2H7, Canada
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Distinct Roles for Peroxisomal Targeting Signal Receptors Pex5 and Pex7 in Drosophila. Genetics 2018; 211:141-149. [PMID: 30389805 DOI: 10.1534/genetics.118.301628] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 10/26/2018] [Indexed: 12/26/2022] Open
Abstract
Peroxisomes are ubiquitous membrane-enclosed organelles involved in lipid processing and reactive oxygen detoxification. Mutations in human peroxisome biogenesis genes (Peroxin, PEX, or Pex) cause developmental disabilities and often early death. Pex5 and Pex7 are receptors that recognize different peroxisomal targeting signals called PTS1 and PTS2, respectively, and traffic proteins to the peroxisomal matrix. We characterized mutants of Drosophila melanogaster Pex5 and Pex7 and found that adult animals are affected in lipid processing. Pex5 mutants exhibited severe developmental defects in the embryonic nervous system and muscle, similar to what is observed in humans with PEX5 mutations, while Pex7 fly mutants were weakly affected in brain development, suggesting different roles for fly Pex7 and human PEX7. Of note, although no PTS2-containing protein has been identified in Drosophila, Pex7 from Drosophila can function as a bona fide PTS2 receptor because it can rescue targeting of the PTS2-containing protein thiolase to peroxisomes in PEX7 mutant human fibroblasts.
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Akşit A, van der Klei IJ. Yeast peroxisomes: How are they formed and how do they grow? Int J Biochem Cell Biol 2018; 105:24-34. [PMID: 30268746 DOI: 10.1016/j.biocel.2018.09.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 01/01/2023]
Abstract
Peroxisomes are single membrane enclosed cell organelles, which are present in almost all eukaryotic cells. In addition to the common peroxisomal pathways such as β-oxidation of fatty acids and decomposition of H2O2, these organelles fulfil a range of metabolic and non-metabolic functions. Peroxisomes are very important since various human disorders exist that are caused by a defect in peroxisome function. Here we describe our current knowledge on the molecular mechanisms of peroxisome biogenesis in yeast, including peroxisomal protein sorting, organelle dynamics and peroxisomal membrane contact sites.
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Affiliation(s)
- Arman Akşit
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands
| | - Ida J van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands.
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Luo M, Zhuang X. Review: Selective degradation of peroxisome by autophagy in plants: Mechanisms, functions, and perspectives. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:485-491. [PMID: 30080638 DOI: 10.1016/j.plantsci.2018.06.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/28/2018] [Accepted: 06/29/2018] [Indexed: 06/08/2023]
Abstract
Peroxisome, a single-membrane organelle conserved in eukaryotic, is responsible for a series of oxidative reactions with its specific enzymatic components. A counterbalance between peroxisome biogenesis and degradation is crucial for the homeostasis of peroxisomes. One such degradation mechanism, termed pexophagy, is a type of selective autophagic process to deliver the excess/damaged peroxisomes into the vacuole. In plants, pexophagy is involved in the remodeling of seedlings and quality control of peroxisomes. Here, we describe the recent advance in plant pexophagy, with a focus to discuss the key regulators in plants in comparison with those in yeast and mammals, as well as future directions for pexophagy studies in plants.
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Affiliation(s)
- Mengqian Luo
- Centre for Cell & Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Xiaohong Zhuang
- Centre for Cell & Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China.
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Kinoshita N, Matsuura A, Fujiki Y. Peroxisome biogenesis: a novel inducible PEX19 splicing variant is involved in early stages of peroxisome proliferation. J Biochem 2017; 161:297-308. [PMID: 28391327 DOI: 10.1093/jb/mvw075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/25/2016] [Indexed: 01/23/2023] Open
Abstract
Pex19p harbouring a prenylation CAAX box functions as a chaperone and transporter for peroxisomal membrane proteins in membrane assembly. By functional phenotype-complementation assay using a pex19 Chinese hamster ovary cell mutant ZP119, we herein cloned a rat cDNA encoding a protein similar to Pex19p, but with a C-terminal hydrophobic segment in place of the CAAX box region. The transcript of this gene was highly induced by treatment of rats with a peroxisome proliferator, clofibrate, hence termed PEX19i, while the other three less prominently inducible PEX19 variants encoded authentic Pex19p but differed in the length of 3' non-coding region. Pex19pi restored peroxisomes in ZP119 with slightly lower efficiency than Pex19p, showing apparently weaker interaction with Pex11pβ essential for peroxisome proliferation. However, the C-terminal region of Pex19p was not essential for the association of Pex19p with peroxisomal membrane and interaction with membrane assembly factors, Pex3p and Pex16p. Non-prenylated Pex19p interacted with a membrane protein cargo, Pex14p, but more weakly than Pex19pi and the farnesylated Pex19p. Thus, PEX19i most likely plays important roles involving the membrane formation at early stages, in prompt response to peroxisome proliferation. Similar types of PEX19 mRNA variants were also elevated in mouse regenerating liver.
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Affiliation(s)
- Naohiko Kinoshita
- Department of Biology, Faculty of Sciences Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Akira Matsuura
- Department of Nanobiology, Graduate School of Advanced Integration Science, Chiba University, Yayoi-cho 1-33, Inage-ku, Chiba 263-8522, Japan
| | - Yukio Fujiki
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Global Fitness Profiling Identifies Arsenic and Cadmium Tolerance Mechanisms in Fission Yeast. G3-GENES GENOMES GENETICS 2016; 6:3317-3333. [PMID: 27558664 PMCID: PMC5068951 DOI: 10.1534/g3.116.033829] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Heavy metals and metalloids such as cadmium [Cd(II)] and arsenic [As(III)] are widespread environmental toxicants responsible for multiple adverse health effects in humans. However, the molecular mechanisms underlying metal-induced cytotoxicity and carcinogenesis, as well as the detoxification and tolerance pathways, are incompletely understood. Here, we use global fitness profiling by barcode sequencing to quantitatively survey the Schizosaccharomyces pombe haploid deletome for genes that confer tolerance of cadmium or arsenic. We identified 106 genes required for cadmium resistance and 110 genes required for arsenic resistance, with a highly significant overlap of 36 genes. A subset of these 36 genes account for almost all proteins required for incorporating sulfur into the cysteine-rich glutathione and phytochelatin peptides that chelate cadmium and arsenic. A requirement for Mms19 is explained by its role in directing iron–sulfur cluster assembly into sulfite reductase as opposed to promoting DNA repair, as DNA damage response genes were not enriched among those required for cadmium or arsenic tolerance. Ubiquinone, siroheme, and pyridoxal 5′-phosphate biosynthesis were also identified as critical for Cd/As tolerance. Arsenic-specific pathways included prefoldin-mediated assembly of unfolded proteins and protein targeting to the peroxisome, whereas cadmium-specific pathways included plasma membrane and vacuolar transporters, as well as Spt–Ada–Gcn5-acetyltransferase (SAGA) transcriptional coactivator that controls expression of key genes required for cadmium tolerance. Notable differences are apparent with corresponding screens in the budding yeast Saccharomyces cerevisiae, underscoring the utility of analyzing toxic metal defense mechanisms in both organisms.
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Roles of Peroxisomes in the Rice Blast Fungus. BIOMED RESEARCH INTERNATIONAL 2016; 2016:9343417. [PMID: 27610388 PMCID: PMC5004026 DOI: 10.1155/2016/9343417] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/25/2016] [Indexed: 11/18/2022]
Abstract
The rice blast fungus, Magnaporthe oryzae, is a model plant pathogenic fungus and is a severe threat to global rice production. Over the past two decades, it has been found that the peroxisomes play indispensable roles during M. oryzae infection. Given the importance of the peroxisomes for virulence, we review recent advances of the peroxisomes roles during M. oryzae infection processes. We firstly introduce the molecular mechanisms and life cycles of the peroxisomes. And then, metabolic functions related to the peroxisomes are also discussed. Finally, we provide an overview of the relationship between peroxisomes and pathogenicity.
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Abstract
SIGNIFICANCE Peroxisomes are organelles present in most eukaryotic cells. The organs with the highest density of peroxisomes are the liver and kidneys. Peroxisomes possess more than fifty enzymes and fulfill a multitude of biological tasks. They actively participate in apoptosis, innate immunity, and inflammation. In recent years, a considerable amount of evidence has been collected to support the involvement of peroxisomes in the pathogenesis of kidney injury. RECENT ADVANCES The nature of the two most important peroxisomal tasks, beta-oxidation of fatty acids and hydrogen peroxide turnover, functionally relates peroxisomes to mitochondria. Further support for their communication and cooperation is furnished by the evidence that both organelles share the components of their division machinery. Until recently, the majority of studies on the molecular mechanisms of kidney injury focused primarily on mitochondria and neglected peroxisomes. CRITICAL ISSUES The aim of this concise review is to introduce the reader to the field of peroxisome biology and to provide an overview of the evidence about the contribution of peroxisomes to the development and progression of kidney injury. The topics of renal ischemia-reperfusion injury, endotoxin-induced kidney injury, diabetic nephropathy, and tubulointerstitial fibrosis, as well as the potential therapeutic implications of peroxisome activation, are addressed in this review. FUTURE DIRECTIONS Despite recent progress, further studies are needed to elucidate the molecular mechanisms induced by dysfunctional peroxisomes and the role of the dysregulated mitochondria-peroxisome axis in the pathogenesis of renal injury. Antioxid. Redox Signal. 25, 217-231.
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Affiliation(s)
- Radovan Vasko
- Department of Nephrology and Rheumatology, University Medical Center Göttingen , Göttingen, Germany
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31
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Hua R, Kim PK. Multiple paths to peroxisomes: Mechanism of peroxisome maintenance in mammals. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:881-91. [DOI: 10.1016/j.bbamcr.2015.09.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 09/18/2015] [Accepted: 09/21/2015] [Indexed: 12/19/2022]
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Oeljeklaus S, Schummer A, Mastalski T, Platta HW, Warscheid B. Regulation of peroxisome dynamics by phosphorylation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:1027-37. [PMID: 26775584 DOI: 10.1016/j.bbamcr.2015.12.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/22/2015] [Accepted: 12/24/2015] [Indexed: 12/31/2022]
Abstract
Peroxisomes are highly dynamic organelles that can rapidly change in size, abundance, and protein content in response to alterations in nutritional and other environmental conditions. These dynamic changes in peroxisome features, referred to as peroxisome dynamics, rely on the coordinated action of several processes of peroxisome biogenesis. Revealing the regulatory mechanisms of peroxisome dynamics is an emerging theme in cell biology. These mechanisms are inevitably linked to and synchronized with the biogenesis and degradation of peroxisomes. To date, the key players and basic principles of virtually all steps in the peroxisomal life cycle are known, but regulatory mechanisms remained largely elusive. A number of recent studies put the spotlight on reversible protein phosphorylation for the control of peroxisome dynamics and highlighted peroxisomes as hubs for cellular signal integration and regulation. Here, we will present and discuss the results of several studies performed using yeast and mammalian cells that convey a sense of the impact protein phosphorylation may have on the modulation of peroxisome dynamics by regulating peroxisomal matrix and membrane protein import, proliferation, inheritance, and degradation. We further put forward the idea to make use of current data on phosphorylation sites of peroxisomal and peroxisome-associated proteins reported in advanced large-scale phosphoproteomic studies.
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Affiliation(s)
- Silke Oeljeklaus
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, 79104 Freiburg, Germany
| | - Andreas Schummer
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Mastalski
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Harald W Platta
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Bettina Warscheid
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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Jo DS, Bae DJ, Park SJ, Seo HM, Kim HB, Oh JS, Chang JW, Kim SY, Shin JW, Cho DH. Pexophagy is induced by increasing peroxisomal reactive oxygen species in 1'10-phenanthroline-treated cells. Biochem Biophys Res Commun 2015; 467:354-60. [PMID: 26453011 DOI: 10.1016/j.bbrc.2015.09.153] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 09/28/2015] [Indexed: 01/24/2023]
Abstract
Although autophagy regulates the quality and quantity of cellular organelles, the regulatory mechanisms of peroxisomal autophagy remain largely unknown. In this study, we developed a cell-based image screening assay, and identified 1,10-phenanthroline (Phen) as a novel pexophagy inducer from chemical library screening. Treatment with Phen induces selective loss of peroxisomes but not endoplasmic reticulum and Golgi apparatus in hepatocytes. In addition, Phen increases autophagic engulfment of peroxisomes in an ATG5 dependent manner. Interestingly, treatment of Phen excessively produces peroxisomal reactive oxygen species (ROS), and inhibition of the ROS suppresses loss of peroxisome in Phen-treated cells. Taken together, these results suggest that Phen triggers pexophagy by enhancing peroxisomal ROS.
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Affiliation(s)
- Doo Sin Jo
- Graduate School of East-West Medical Science, Kyung Hee University, Yongin, Gyeonggi, South Korea
| | - Dong-Jun Bae
- Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - So Jung Park
- Graduate School of East-West Medical Science, Kyung Hee University, Yongin, Gyeonggi, South Korea
| | - Hae Mi Seo
- Graduate School of East-West Medical Science, Kyung Hee University, Yongin, Gyeonggi, South Korea
| | - Han Byeol Kim
- Graduate School of East-West Medical Science, Kyung Hee University, Yongin, Gyeonggi, South Korea
| | - Jeong Su Oh
- Department of Genetic Engineering, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, South Korea
| | - Jong Wook Chang
- Research Institute for Future Medicine Stem Cell & Regenerative Medicine Center, Samsung Medical Center, Seoul, South Korea
| | - Sang-Yeob Kim
- Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Jung-Won Shin
- Graduate School of East-West Medical Science, Kyung Hee University, Yongin, Gyeonggi, South Korea.
| | - Dong-Hyung Cho
- Graduate School of East-West Medical Science, Kyung Hee University, Yongin, Gyeonggi, South Korea.
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Knoblach B, Rachubinski RA. Motors, anchors, and connectors: orchestrators of organelle inheritance. Annu Rev Cell Dev Biol 2015; 31:55-81. [PMID: 26443192 DOI: 10.1146/annurev-cellbio-100814-125553] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Organelle inheritance is a process whereby organelles are actively distributed between dividing cells at cytokinesis. Much valuable insight into the molecular mechanisms of organelle inheritance has come from the analysis of asymmetrically dividing cells, which transport a portion of their organelles to the bud while retaining another portion in the mother cell. Common principles apply to the inheritance of all organelles, although individual organelles use specific factors for their partitioning. Inheritance factors can be classified as motors, which are required for organelle transport; anchors, which immobilize organelles at distinct cell structures; or connectors, which mediate the attachment of organelles to motors and anchors. Here, we provide an overview of recent advances in the field of organelle inheritance and highlight how motor, anchor, and connector molecules choreograph the segregation of a multicopy organelle, the peroxisome. We also discuss the role of organelle population control in the generation of cellular diversity.
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Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada;
| | - Richard A Rachubinski
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada;
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Colletotrichum orbiculare FAM1 Encodes a Novel Woronin Body-Associated Pex22 Peroxin Required for Appressorium-Mediated Plant Infection. mBio 2015; 6:e01305-15. [PMID: 26374121 PMCID: PMC4600112 DOI: 10.1128/mbio.01305-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
UNLABELLED The cucumber anthracnose fungus Colletotrichum orbiculare forms specialized cells called appressoria for host penetration. We identified a gene, FAM1, encoding a novel peroxin protein that is essential for peroxisome biogenesis and that associates with Woronin bodies (WBs), dense-core vesicles found only in filamentous ascomycete fungi which function to maintain cellular integrity. The fam1 disrupted mutants were unable to grow on medium containing oleic acids as the sole carbon source and were nonpathogenic, being defective in both appressorium melanization and host penetration. Fluorescent proteins carrying peroxisomal targeting signals (PTSs) were not imported into the peroxisomes of fam1 mutants, suggesting that FAM1 is a novel peroxisomal biogenesis gene (peroxin). FAM1 did not show significant homology to any Saccharomyces cerevisiae peroxins but resembled conserved filamentous ascomycete-specific Pex22-like proteins which contain a predicted Pex4-binding site and are potentially involved in recycling PTS receptors from peroxisomes to the cytosol. C. orbiculare FAM1 complemented the peroxisomal matrix protein import defect of the S. cerevisiae pex22 mutant. Confocal microscopy of Fam1-GFP (green fluorescent protein) fusion proteins and immunoelectron microscopy with anti-Fam1 antibodies showed that Fam1 localized to nascent WBs budding from peroxisomes and mature WBs. Association of Fam1 with WBs was confirmed by colocalization with WB matrix protein CoHex1 (C. orbiculare Hex1) and WB membrane protein CoWsc (C. orbiculare Wsc) and by subcellular fractionation and Western blotting with antibodies to Fam1 and CoHex1. In WB-deficient cohex1 mutants, Fam1 was redirected to the peroxisome membrane. Our results show that Fam1 is a WB-associated peroxin required for pathogenesis and raise the possibility that localized receptor recycling occurs in WBs. IMPORTANCE Colletotrichum orbiculare is a fungus causing damaging disease on Cucurbitaceae plants. In this paper, we characterize a novel peroxisome biogenesis gene from this pathogen called FAM1. Although no genes with significant homology are present in Saccharomyces cerevisiae, FAM1 contains a predicted Pex4-binding site typical of Pex22 proteins, which function in the recycling of PTS receptors from peroxisomes to the cytosol. We show that FAM1 complements the defect in peroxisomal matrix protein import of S. cerevisiae pex22 mutants and that fam1 mutants are completely defective in peroxisome function, fatty acid metabolism, and pathogenicity. Remarkably, we found that this novel peroxin is specifically localized on the bounding membrane of Woronin bodies, which are small peroxisome-derived organelles unique to filamentous ascomycete fungi that function in septal pore plugging. Our finding suggests that these fungi have coopted the Woronin body for localized receptor recycling during matrix protein import.
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Platta HW, Brinkmeier R, Reidick C, Galiani S, Clausen MP, Eggeling C. Regulation of peroxisomal matrix protein import by ubiquitination. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:838-49. [PMID: 26367801 DOI: 10.1016/j.bbamcr.2015.09.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/09/2015] [Accepted: 09/10/2015] [Indexed: 02/02/2023]
Abstract
Peroxisomes are organelles that play an important role in many cellular tasks. The functionality of peroxisomes depends on the proper import of their matrix proteins. Peroxisomal matrix proteins are imported posttranslationally in a folded, sometimes even oligomeric state. They harbor a peroxisomal targeting sequence (PTS), which is recognized by dynamic PTS-receptors in the cytosol. The PTS-receptors ferry the cargo to the peroxisomal membrane, where they become part of a transient import pore and then release the cargo into the peroxisomal lumen. Subsequentially, the PTS-receptors are ubiquitinated in order to mark them for the export-machinery, which releases them back to the cytosol. Upon deubiquitination, the PTS-receptors can facilitate further rounds of cargo import. Because the ubiquitination of the receptors is an essential step in the import cycle, it also represents a central regulatory element that governs peroxisomal dynamics. In this review we want to give an introduction to the functional role played by ubiquitination during peroxisomal protein import and highlight the mechanistic concepts that have emerged based on data derived from different species since the discovery of the first ubiquitinated peroxin 15years ago. Moreover, we discuss future tasks and the potential of using advanced technologies for investigating further details of peroxisomal protein transport.
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Affiliation(s)
- Harald W Platta
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany.
| | - Rebecca Brinkmeier
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Christina Reidick
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Silvia Galiani
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - Mathias P Clausen
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom.
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Brown AI, Rutenberg AD. Cluster coarsening on drops exhibits strong and sudden size-selectivity. SOFT MATTER 2015; 11:3786-3793. [PMID: 25846269 DOI: 10.1039/c5sm00284b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Autophagy, an important process for degradation of cellular components, requires the targeting of autophagy receptor proteins to potential substrates. Receptor proteins have been observed to form clusters on membranes. To understand how receptor clusters might affect autophagy selectivity, we model cluster coarsening on a polydisperse collection of spherical drop-like substrates. Our model receptor corresponds to NBR1, which supports peroxisome autophagy. We recover dynamical scaling of cluster sizes, but find that changing the drop size distribution changes the cluster-size scaling distribution. The magnitude of this effect is similar to how changing the spatial-dimension affects scaling in bulk systems. We also observe a sudden onset of size-selection of the remaining drops with clusters, due to clusters evaporating from smaller drops and growing on larger drops. This coarsening-driven size selection provides a physical mechanism for autophagy selectivity, and may explain reports of size selection during peroxisome degradation.
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Affiliation(s)
- Aidan I Brown
- Department of Physics and Atmospheric Science, Dalhousie University, Halifax, NS, CanadaB3H 4R2.
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Young JM, Nelson JW, Cheng J, Zhang W, Mader S, Davis CM, Morrison RS, Alkayed NJ. Peroxisomal biogenesis in ischemic brain. Antioxid Redox Signal 2015; 22:109-20. [PMID: 25226217 PMCID: PMC4281844 DOI: 10.1089/ars.2014.5833] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
AIMS Peroxisomes are highly adaptable and dynamic organelles, adjusting their size, number, and enzyme composition to changing environmental and metabolic demands. We determined whether peroxisomes respond to ischemia, and whether peroxisomal biogenesis is an adaptive response to cerebral ischemia. RESULTS Focal cerebral ischemia induced peroxisomal biogenesis in peri-infarct neurons, which was associated with a corresponding increase in peroxisomal antioxidant enzyme catalase. Peroxisomal biogenesis was also observed in primary cultured cortical neurons subjected to ischemic insult induced by oxygen-glucose deprivation (OGD). A catalase inhibitor increased OGD-induced neuronal death. Moreover, preventing peroxisomal proliferation by knocking down dynamin-related protein 1 (Drp1) exacerbated neuronal death induced by OGD, whereas enhancing peroxisomal biogenesis pharmacologically using a peroxisome proliferator-activated receptor-alpha agonist protected against neuronal death induced by OGD. INNOVATION This is the first documentation of ischemia-induced peroxisomal biogenesis in mammalian brain using a combined in vivo and in vitro approach, electron microscopy, high-resolution laser-scanning confocal microscopy, and super-resolution structured illumination microscopy. CONCLUSION Our findings suggest that neurons respond to ischemic injury by increasing peroxisome biogenesis, which serves a protective function, likely mediated by enhanced antioxidant capacity of neurons.
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Affiliation(s)
- Jennifer M Young
- 1 Department of Anesthesiology & Perioperative Medicine, The Knight Cardiovascular Institute, Oregon Health & Science University , Portland, Oregon
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39
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Avin-Wittenberg T, Fernie AR. At long last: evidence for pexophagy in plants. MOLECULAR PLANT 2014; 7:1257-1260. [PMID: 24705457 DOI: 10.1093/mp/ssu029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Tamar Avin-Wittenberg
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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40
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Hettema EH, Erdmann R, van der Klei I, Veenhuis M. Evolving models for peroxisome biogenesis. Curr Opin Cell Biol 2014; 29:25-30. [PMID: 24681485 PMCID: PMC4148619 DOI: 10.1016/j.ceb.2014.02.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 02/18/2014] [Accepted: 02/21/2014] [Indexed: 12/11/2022]
Abstract
Significant progress has been made towards our understanding of the mechanism of peroxisome formation, in particular concerning sorting of peroxisomal membrane proteins, matrix protein import and organelle multiplication. Here we evaluate the progress made in recent years. We focus mainly on progress made in yeasts. We indicate the gaps in our knowledge and discuss conflicting models.
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Affiliation(s)
- Ewald H Hettema
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
| | - Ralf Erdmann
- System Biochie, Ruhr Universitat Bochum, Universitatstr. 150, D-44780, Bochum, Germany
| | - Ida van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology institute, University of Groningen, 11 103, 9700CC, Groningen, The Netherlands
| | - Marten Veenhuis
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology institute, University of Groningen, 11 103, 9700CC, Groningen, The Netherlands
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41
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Cholesterol biosynthesis and ER stress in peroxisome deficiency. Biochimie 2014; 98:75-85. [DOI: 10.1016/j.biochi.2013.10.019] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 10/22/2013] [Indexed: 12/27/2022]
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Jefferson M, Whelband M, Mohorianu I, Powell PP. The pestivirus N terminal protease N(pro) redistributes to mitochondria and peroxisomes suggesting new sites for regulation of IRF3 by N(pro.). PLoS One 2014; 9:e88838. [PMID: 24551175 PMCID: PMC3925175 DOI: 10.1371/journal.pone.0088838] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 01/14/2014] [Indexed: 01/16/2023] Open
Abstract
The N-terminal protease of pestiviruses, N(pro) is a unique viral protein, both because it is a distinct autoprotease that cleaves itself from the following polyprotein chain, and also because it binds and inactivates IRF3, a central regulator of interferon production. An important question remains the role of N(pro) in the inhibition of apoptosis. In this study, apoptotic signals induced by staurosporine, interferon, double stranded RNA, sodium arsenate and hydrogen peroxide were inhibited by expression of wild type N(pro), but not by mutant protein N(pro) C112R, which we show is less efficient at promoting degradation of IRF3, and led to the conclusion that N(pro) inhibits the stress-induced intrinsic mitochondrial pathway through inhibition of IRF3-dependent Bax activation. Both expression of N(pro) and infection with Bovine Viral Diarrhea Virus (BVDV) prevented Bax redistribution and mitochondrial fragmentation. Given the role played by signaling platforms during IRF3 activation, we have studied the subcellular distribution of N(pro) and we show that, in common with many other viral proteins, N(pro) targets mitochondria to inhibit apoptosis in response to cell stress. N(pro) itself not only relocated to mitochondria but in addition, both N(pro) and IRF3 associated with peroxisomes, with over 85% of N(pro) puncta co-distributing with PMP70, a marker for peroxisomes. In addition, peroxisomes containing N(pro) and IRF3 associated with ubiquitin. IRF3 was degraded, whereas N(pro) accumulated in response to cell stress. These results implicate mitochondria and peroxisomes as new sites for IRF3 regulation by N(pro), and highlight the role of these organelles in the anti-viral pathway.
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Affiliation(s)
- Matthew Jefferson
- Biomedical Research Centre, Norwich Medical School and Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Matthew Whelband
- Biomedical Research Centre, Norwich Medical School and Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Irina Mohorianu
- Biomedical Research Centre, Norwich Medical School and Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Penny P. Powell
- Biomedical Research Centre, Norwich Medical School and Biological Sciences, University of East Anglia, Norwich, United Kingdom
- * E-mail:
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43
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Brown AI, Kim PK, Rutenberg AD. PEX5 and ubiquitin dynamics on mammalian peroxisome membranes. PLoS Comput Biol 2014; 10:e1003426. [PMID: 24453954 PMCID: PMC3894153 DOI: 10.1371/journal.pcbi.1003426] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 11/19/2013] [Indexed: 12/04/2022] Open
Abstract
Peroxisomes are membrane-bound organelles within eukaryotic cells that post-translationally import folded proteins into their matrix. Matrix protein import requires a shuttle receptor protein, usually PEX5, that cycles through docking with the peroxisomal membrane, ubiquitination, and export back into the cytosol followed by deubiquitination. Matrix proteins associate with PEX5 in the cytosol and are translocated into the peroxisome lumen during the PEX5 cycle. This cargo translocation step is not well understood, and its energetics remain controversial. We use stochastic computational models to explore different ways the AAA ATPase driven removal of PEX5 may couple with cargo translocation in peroxisomal importers of mammalian cells. The first model considered is uncoupled, in which translocation is spontaneous, and does not immediately depend on PEX5 removal. The second is directly coupled, in which cargo translocation only occurs when its PEX5 is removed from the peroxisomal membrane. The third, novel, model is cooperatively coupled and requires two PEX5 on a given importomer for cargo translocation — one PEX5 with associated cargo and one with ubiquitin. We measure both the PEX5 and the ubiquitin levels on the peroxisomes as we vary the matrix protein cargo addition rate into the cytosol. We find that both uncoupled and directly coupled translocation behave identically with respect to PEX5 and ubiquitin, and the peroxisomal ubiquitin signal increases as the matrix protein traffic increases. In contrast, cooperatively coupled translocation behaves dramatically differently, with a ubiquitin signal that decreases with increasing matrix protein traffic. Recent work has shown that ubiquitin on mammalian peroxisome membranes can lead to selective degradation by autophagy, or ‘pexophagy.’ Therefore, the high ubiquitin level for low matrix cargo traffic with cooperatively coupled protein translocation could be used as a disuse signal to mediate pexophagy. This mechanism may be one way that cells could regulate peroxisome numbers. Peroxisomes are small organelles that must continually import matrix proteins to contribute to cholesterol and bile acid synthesis, among other important functions. Cargo matrix proteins are shuttled to the peroxisomal membrane, but the only source of energy that has been identified to translocate the cargo into the peroxisome is consumed during the removal of the shuttle protein. Ubiquitin is used to recycle peroxisomal shuttle proteins, but is more generally used in cells to signal degradation of damaged or unneeded cellular components. How shuttle removal and cargo translocation are coupled energetically has been difficult to determine directly, so we investigate how different models of coupling would affect the measurable levels of ubiquitin on mammalian peroxisomes. We find that for the simplest models of coupling, ubiquitin levels decrease as cargo levels decrease. Conversely, for a novel cooperative model of coupling we find that ubiquitin levels increase as cargo levels decrease. This effect could allow the cell to degrade peroxisomes when they are not used, or to avoid degrading peroxisomes as cargo levels increase. Regardless of which model is found to be right, we have shown that ubiquitination levels of peroxisomes should respond to the changing traffic of matrix proteins into peroxisomes.
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Affiliation(s)
- Aidan I. Brown
- Department of Physics and Atmospheric Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Peter K. Kim
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andrew D. Rutenberg
- Department of Physics and Atmospheric Science, Dalhousie University, Halifax, Nova Scotia, Canada
- * E-mail:
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El Magraoui F, Brinkmeier R, Schrötter A, Girzalsky W, Müller T, Marcus K, Meyer HE, Erdmann R, Platta HW. Distinct Ubiquitination Cascades Act on the Peroxisomal Targeting Signal Type 2 Co-receptor Pex18p. Traffic 2013; 14:1290-301. [DOI: 10.1111/tra.12120] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 09/09/2013] [Accepted: 09/11/2013] [Indexed: 01/29/2023]
Affiliation(s)
- Fouzi El Magraoui
- Biochemie Intrazellulärer Transportprozesse; Ruhr-Universität Bochum; Bochum 44780 Germany
- Systembiochemie; Ruhr-Universität Bochum; Bochum 44780 Germany
- Medizinische Proteomik/Bioanalytik, AG Neuro Proteomics; Medizinisches Proteom-Center; Bochum 44801 Germany
| | - Rebecca Brinkmeier
- Biochemie Intrazellulärer Transportprozesse; Ruhr-Universität Bochum; Bochum 44780 Germany
| | - Andreas Schrötter
- Medizinische Proteomik/Bioanalytik, AG Neuro Proteomics; Medizinisches Proteom-Center; Bochum 44801 Germany
| | | | - Thorsten Müller
- Funktionelle Proteomik; Medizinisches Proteom-Center; Bochum 44801 Germany
| | - Katrin Marcus
- Funktionelle Proteomik; Medizinisches Proteom-Center; Bochum 44801 Germany
| | - Helmut E. Meyer
- Medizinische Proteomik/Bioanalytik; Medizinisches Proteom-Center; Bochum 44801 Germany
| | - Ralf Erdmann
- Systembiochemie; Ruhr-Universität Bochum; Bochum 44780 Germany
| | - Harald W. Platta
- Biochemie Intrazellulärer Transportprozesse; Ruhr-Universität Bochum; Bochum 44780 Germany
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45
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Hasan S, Platta HW, Erdmann R. Import of proteins into the peroxisomal matrix. Front Physiol 2013; 4:261. [PMID: 24069002 PMCID: PMC3781343 DOI: 10.3389/fphys.2013.00261] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/03/2013] [Indexed: 12/03/2022] Open
Abstract
Peroxisomes constitute a dynamic compartment in all nucleated cells. They fulfill diverse metabolic tasks in response to environmental changes and cellular demands. This adaptation is implemented by modulation of the enzyme content of the organelles, which is accomplished by dynamically operating peroxisomal protein transport machineries. Soluble import receptors recognize their newly synthesized cargo proteins in the cytosol and ferry them to the peroxisomal membrane. Subsequently, the cargo is translocated into the matrix, where the receptor is ubiquitinated and exported back to the cytosol for further rounds of matrix protein import. This review discusses the recent progress in our understanding of the peroxisomal matrix protein import and its regulation by ubiquitination events as well as the current view on the translocation mechanism of folded proteins into peroxisomes. This article is part of a Special Issue entitled: Origin and spatiotemporal dynamics of the peroxisomal endomembrane system.
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Affiliation(s)
- Sohel Hasan
- Systembiochemie, Medizinische Fakultät, Ruhr-Universität Bochum Bochum, Germany
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46
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Gualdrón-López M, Chevalier N, Van Der Smissen P, Courtoy PJ, Rigden DJ, Michels PAM. Ubiquitination of the glycosomal matrix protein receptor PEX5 in Trypanosoma brucei by PEX4 displays novel features. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:3076-3092. [PMID: 23994617 DOI: 10.1016/j.bbamcr.2013.08.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 08/08/2013] [Accepted: 08/12/2013] [Indexed: 12/12/2022]
Abstract
Trypanosomatids contain peroxisome-like organelles called glycosomes. Peroxisomal biogenesis involves a cytosolic receptor, PEX5, which, after its insertion into the organellar membrane, delivers proteins to the matrix. In yeasts and mammalian cells, transient PEX5 monoubiquitination at the membrane serves as the signal for its retrieval from the organelle for re-use. When its recycling is impaired, PEX5 is polyubiquitinated for proteasomal degradation. Stably monoubiquitinated TbPEX5 was detected in cytosolic fractions of Trypanosoma brucei, indicative for its role as physiological intermediate in receptor recycling. This modification's resistance to dithiothreitol suggests ubiquitin conjugation of a lysine residue. T. brucei PEX4, the functional homologue of the ubiquitin-conjugating (UBC) enzyme responsible for PEX5 monoubiquitination in yeast, was identified. It is associated with the cytosolic face of the glycosomal membrane, probably anchored by an identified putative TbPEX22. The involvement of TbPEX4 in TbPEX5 ubiquitination was demonstrated using procyclic ∆PEX4 trypanosomes. Surprisingly, glycosomal matrix protein import was only mildly affected in this mutant. Since other UBC homologues were upregulated, it might be possible that these have partially rescued PEX4's function in PEX5 ubiquitination. In addition, the altered expression of UBCs, notably of candidates involved in cell-cycle control, could be responsible for observed morphological and motility defects of the ∆PEX4 mutant.
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Affiliation(s)
- Melisa Gualdrón-López
- Research Unit for Tropical Diseases, de Duve Institute, and Laboratory of Biochemistry, Université catholique de Louvain, Avenue Hippocrate 74, B-1200 Brussels, Belgium
| | - Nathalie Chevalier
- Research Unit for Tropical Diseases, de Duve Institute, and Laboratory of Biochemistry, Université catholique de Louvain, Avenue Hippocrate 74, B-1200 Brussels, Belgium
| | - Patrick Van Der Smissen
- Cell Biology Unit, de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, B-1200 Brussels, Belgium
| | - Pierre J Courtoy
- Cell Biology Unit, de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, B-1200 Brussels, Belgium
| | - Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Paul A M Michels
- Research Unit for Tropical Diseases, de Duve Institute, and Laboratory of Biochemistry, Université catholique de Louvain, Avenue Hippocrate 74, B-1200 Brussels, Belgium.
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47
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Crystal structure of peroxisomal targeting signal-2 bound to its receptor complex Pex7p–Pex21p. Nat Struct Mol Biol 2013; 20:987-93. [DOI: 10.1038/nsmb.2618] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 05/13/2013] [Indexed: 12/26/2022]
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48
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Jung S, Smith JJ, von Haller PD, Dilworth DJ, Sitko KA, Miller LR, Saleem RA, Goodlett DR, Aitchison JD. Global analysis of condition-specific subcellular protein distribution and abundance. Mol Cell Proteomics 2013; 12:1421-35. [PMID: 23349476 DOI: 10.1074/mcp.o112.019166] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Cellular control of protein activities by modulation of their abundance or compartmentalization is not easily measured on a large scale. We developed and applied a method to globally interrogate these processes that is widely useful for systems-level analyses of dynamic cellular responses in many cell types. The approach involves subcellular fractionation followed by comprehensive proteomic analysis of the fractions, which is enabled by a data-independent acquisition mass spectrometry approach that samples every available mass to charge channel systematically to maximize sensitivity. Next, various fraction-enrichment ratios are measured for all detected proteins across different environmental conditions and used to group proteins into clusters reflecting changes in compartmentalization and relative conditional abundance. Application of the approach to characterize the response of yeast proteins to fatty acid exposure revealed dynamics of peroxisomes and novel dynamics of MCC/eisosomes, specialized plasma membrane domains comprised of membrane compartment occupied by Can1 (MCC) and eisosome subdomains. It also led to the identification of Fat3, a fatty acid transport protein of the plasma membrane, previously annotated as Ykl187.
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Affiliation(s)
- Sunhee Jung
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195, USA
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49
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Kaur N, Zhao Q, Xie Q, Hu J. Arabidopsis RING peroxins are E3 ubiquitin ligases that interact with two homologous ubiquitin receptor proteins(F). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:108-20. [PMID: 23336935 DOI: 10.1111/jipb.12014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Peroxisomes are essential eukaryotic organelles that mediate various metabolic processes. Peroxisome import depends on a group of peroxisome biogenesis factors called peroxins, many of which are evolutionarily conserved. PEX2, PEX10, and PEX12 are three RING-finger-domain-containing integral membrane peroxins crucial for protein import. In yeast (Saccharomyces cerevisae), RING peroxins act as E3 ligases, facilitating the recycling of the peroxisome import receptor protein PEX5 through ubiquitination. In plants, RING peroxins are essential to plant vitality. To elucidate the mode of action of the plant RING peroxins, we employed in vitro assays to show that the Arabidopsis RING peroxins also have E3 ligase activities. We also identified a PEX2-interacting protein, DSK2b, which is a member of the ubiquitin receptor family known to function as shuttle factors ferrying polyubiquitinated substrates to the proteasome for degradation. DSK2b and its tandem duplicate DSK2a are localized in the cytosol and the nucleus, and both interact with the RING domain of PEX2 and PEX12. DSK2 artificial microRNA lines did not display obvious defects in plant growth or peroxisomal processes, indicating functional redundancies among Arabidopsis ubiquitin receptor proteins. Our results suggest that Arabidopsis RING peroxins can function as E3 ligases and act together with the ubiquitin receptor protein DSK2 in the peroxisomal membrane-associated protein degradation system.
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Affiliation(s)
- Navneet Kaur
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
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50
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Costa A, Drago I, Zottini M, Pizzo P, Pozzan T. Peroxisome Ca(2+) homeostasis in animal and plant cells. Subcell Biochem 2013; 69:111-33. [PMID: 23821146 DOI: 10.1007/978-94-007-6889-5_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Ca(2+) homeostasis in peroxisomes has been an unsolved problem for many years. Recently novel probes to monitor Ca(2+) levels in the lumen of peroxisomes in living cells of both animal and plant cells have been developed. Here we discuss the contrasting results obtained in mammalian cells with chemiluminecsent (aequorin) and fluorescent (cameleon) probes targeted to peroxisomes. We briefly discuss the different characteristics of these probes and the possible pitfalls of the two approaches. We conclude that the contrasting results obtained with the two probes may reflect a heterogeneity among peroxisomes in mammalian cells. We also discuss the results obtained in plant peroxisomes. In particular we demonstrate that Ca(2+) increases in the cytoplasm are mirrored by similar rises of Ca(2+) concentration the lumen of peroxisomes. The increases in peroxisome Ca(2+) level results in the activation of a catalase isoform, CAT3. Other functional roles of peroxisomal Ca(2+) changes in plant physiology are briefly discussed.
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Affiliation(s)
- Alex Costa
- Department of Biosciences, University of Milan, Milan, Italy
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