1
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Plessner M, Thiele L, Hofhuis J, Thoms S. Tissue-specific roles of peroxisomes revealed by expression meta-analysis. Biol Direct 2024; 19:14. [PMID: 38365851 PMCID: PMC10873952 DOI: 10.1186/s13062-024-00458-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/30/2024] [Indexed: 02/18/2024] Open
Abstract
Peroxisomes are primarily studied in the brain, kidney, and liver due to the conspicuous tissue-specific pathology of peroxisomal biogenesis disorders. In contrast, little is known about the role of peroxisomes in other tissues such as the heart. In this meta-analysis, we explore mitochondrial and peroxisomal gene expression on RNA and protein levels in the brain, heart, kidney, and liver, focusing on lipid metabolism. Further, we evaluate a potential developmental and heart region-dependent specificity of our gene set. We find marginal expression of the enzymes for peroxisomal fatty acid oxidation in cardiac tissue in comparison to the liver or cardiac mitochondrial β-oxidation. However, the expression of peroxisome biogenesis proteins in the heart is similar to other tissues despite low levels of peroxisomal fatty acid oxidation. Strikingly, peroxisomal targeting signal type 2-containing factors and plasmalogen biosynthesis appear to play a fundamental role in explaining the essential protective and supporting functions of cardiac peroxisomes.
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Affiliation(s)
- Matthias Plessner
- Department of Biochemistry and Molecular Medicine, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Leonie Thiele
- Department of Biochemistry and Molecular Medicine, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Julia Hofhuis
- Department of Biochemistry and Molecular Medicine, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Sven Thoms
- Department of Biochemistry and Molecular Medicine, Medical School OWL, Bielefeld University, Bielefeld, Germany.
- Department of Child and Adolescent Health, University Medical Center, Göttingen, Germany.
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2
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Swathi D, Ramya L, Archana SS, Krishnappa B, Binsila BK, Selvaraju S. Identification of hub genes and their expression profiling for predicting buffalo (Bubalus bubalis) semen quality and fertility. Sci Rep 2023; 13:22126. [PMID: 38092793 PMCID: PMC10719284 DOI: 10.1038/s41598-023-48925-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023] Open
Abstract
Sperm transcriptomics provide insights into subtle differences in sperm fertilization competence. For predicting the success of complex traits like male fertility, identification of hub genes involved in various sperm functions are essential. The bulls from the transcriptome profiled samples (n = 21), were grouped into good and poor progressive motility (PM), acrosome integrity (AI), functional membrane integrity (FMI) and fertility rate (FR) groups. The up-regulated genes identified in each group were 87, 470, 1715 and 36, respectively. Gene networks were constructed using up- and down-regulated genes from each group. The top clusters from the upregulated gene networks of the PM, AI, FMI and FR groups were involved in tyrosine kinase (FDR = 1.61E-11), apoptosis (FDR = 1.65E-8), translation (FDR = 2.2E-16) and ribosomal pathway (FDR = 1.98E-21), respectively. From the clusters, the hub genes were identified and validated in a fresh set of semen samples (n = 12) using RT-qPCR. Importantly, the genes (fold change) RPL36AL (14.99) in AI, EIF5A (54.32) in FMI, and RPLP0 (8.55) and RPS28 (13.42) in FR were significantly (p < 0.05) up-regulated. The study suggests that the expression levels of MAPK3 (PM), RPL36AL + RPS27A or RPL36AL + EXT2 (AI), RPL36AL or RPS27A (FMI) and RPS18 + RPS28 (FR) are potential markers for diagnosing the semen quality and fertility status of bulls which can be used for the breeding program.
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Affiliation(s)
- Divakar Swathi
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
- Department of Biotechnology, Jain University, Bengaluru, 560001, India
| | - Laxman Ramya
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Santhanahalli Siddalingappa Archana
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Balaganur Krishnappa
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Bala Krishnan Binsila
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Sellappan Selvaraju
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India.
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3
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Fu X, Wan P, Lu L, Wan Y, Liu Z, Hong G, Cao S, Bi X, Zhou J, Qiao R, Guo S, Xiao Y, Wang B, Chang M, Li W, Li P, Zhang A, Sun J, Chai R, Gao J. Peroxisome Deficiency in Cochlear Hair Cells Causes Hearing Loss by Deregulating BK Channels. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023:e2300402. [PMID: 37171794 PMCID: PMC10369297 DOI: 10.1002/advs.202300402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/15/2023] [Indexed: 05/13/2023]
Abstract
The peroxisome is a ubiquitous organelle in rodent cells and plays important roles in a variety of cell types and tissues. It is previously indicated that peroxisomes are associated with auditory function, and patients with peroxisome biogenesis disorders (PBDs) are found to have hearing dysfunction, but the specific role of peroxisomes in hearing remains unclear. In this study, two peroxisome-deficient mouse models (Atoh1-Pex5-/- and Pax2-Pex5-/- ) are established and it is found that peroxisomes mainly function in the hair cells of cochleae. Furthermore, peroxisome deficiency-mediated negative effects on hearing do not involve mitochondrial dysfunction and oxidative damage. Although the mammalian target of rapamycin complex 1 (mTORC1) signaling is shown to function through peroxisomes, no changes are observed in the mTORC1 signaling in Atoh1-Pex5-/- mice when compared to wild-type (WT) mice. However, the expression of large-conductance, voltage-, and Ca2+ -activated K+ (BK) channels is less in Atoh1-Pex5-/- mice as compared to the WT mice, and the administration of activators of BK channels (NS-1619 and NS-11021) restores the auditory function in knockout mice. These results suggest that peroxisomes play an essential role in cochlear hair cells by regulating BK channels. Hence, BK channels appear as the probable target for treating peroxisome-related hearing diseases such as PBDs.
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Affiliation(s)
- Xiaolong Fu
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, 250117, P. R. China
- State Key Laboratory of Digital Medical Engineering, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing, 210096, P. R. China
| | - Peifeng Wan
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, 250117, P. R. China
- School of Life Science, Shandong University, Qingdao, 266237, P. R. China
| | - Ling Lu
- Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical School, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing, 210096, P. R. China
| | - Yingcui Wan
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, 250117, P. R. China
| | - Ziyi Liu
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, 250117, P. R. China
| | - Guodong Hong
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, 250117, P. R. China
| | - Shengda Cao
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, Shandong, 250012, P. R. China
| | - Xiuli Bi
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, 250117, P. R. China
| | - Jing Zhou
- The First Affiliated Hospital of Suzhou University, Suzhou University, Suzhou, P. R. China, 215000
| | - Ruifeng Qiao
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, 250117, P. R. China
| | - Siwei Guo
- School of Life Science, Shandong University, Qingdao, 266237, P. R. China
| | - Yu Xiao
- School of Life Science, Shandong University, Qingdao, 266237, P. R. China
| | - Bingzheng Wang
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, 250117, P. R. China
| | - Miao Chang
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, 250117, P. R. China
| | - Wen Li
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, 250117, P. R. China
| | - Peipei Li
- School of Life Science, Shandong University, Qingdao, 266237, P. R. China
| | - Aizhen Zhang
- School of Life Science, Shandong University, Qingdao, 266237, P. R. China
| | - Jin Sun
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, 250117, P. R. China
| | - Renjie Chai
- State Key Laboratory of Digital Medical Engineering, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing, 210096, P. R. China
- Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, P. R. China
- Department of Otolaryngology Head and Neck Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, P. R. China
- Institute for Stem Cell and Regeneration, Chinese Academy of Science, Beijing, 101408, P. R. China
- Beijing Key Laboratory of Neural Regeneration and Repair, Capital Medical University, Beijing, 100069, P. R. China
| | - Jiangang Gao
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, 250117, P. R. China
- School of Life Science, Shandong University, Qingdao, 266237, P. R. China
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4
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Kocherlakota S, Swinkels D, Van Veldhoven PP, Baes M. Mouse Models to Study Peroxisomal Functions and Disorders: Overview, Caveats, and Recommendations. Methods Mol Biol 2023; 2643:469-500. [PMID: 36952207 DOI: 10.1007/978-1-0716-3048-8_34] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
During the last three decades many mouse lines were created or identified that are deficient in one or more peroxisomal functions. Different methodologies were applied to obtain global, hypomorph, cell type selective, inducible, and knockin mice. Whereas some models closely mimic pathologies in patients, others strongly deviate or no human counterpart has been reported. Often, mice, apparently endowed with a stronger transcriptional adaptation, have to be challenged with dietary additions or restrictions in order to trigger phenotypic changes. Depending on the inactivated peroxisomal protein, several approaches can be taken to validate the loss-of-function. Here, an overview is given of the available mouse models and their most important characteristics.
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Affiliation(s)
- Sai Kocherlakota
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Daniëlle Swinkels
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Paul P Van Veldhoven
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Myriam Baes
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium.
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5
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Kiyozumi D, Ikawa M. Proteolysis in Reproduction: Lessons From Gene-Modified Organism Studies. Front Endocrinol (Lausanne) 2022; 13:876370. [PMID: 35600599 PMCID: PMC9114714 DOI: 10.3389/fendo.2022.876370] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/28/2022] [Indexed: 12/17/2022] Open
Abstract
The physiological roles of proteolysis are not limited to degrading unnecessary proteins. Proteolysis plays pivotal roles in various biological processes through cleaving peptide bonds to activate and inactivate proteins including enzymes, transcription factors, and receptors. As a wide range of cellular processes is regulated by proteolysis, abnormalities or dysregulation of such proteolytic processes therefore often cause diseases. Recent genetic studies have clarified the inclusion of proteases and protease inhibitors in various reproductive processes such as development of gonads, generation and activation of gametes, and physical interaction between gametes in various species including yeast, animals, and plants. Such studies not only clarify proteolysis-related factors but the biological processes regulated by proteolysis for successful reproduction. Here the physiological roles of proteases and proteolysis in reproduction will be reviewed based on findings using gene-modified organisms.
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Affiliation(s)
- Daiji Kiyozumi
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan
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6
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A novel missense variant in ACAA1 contributes to early-onset Alzheimer's disease, impairs lysosomal function, and facilitates amyloid-β pathology and cognitive decline. Signal Transduct Target Ther 2021; 6:325. [PMID: 34465723 PMCID: PMC8408221 DOI: 10.1038/s41392-021-00748-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 02/07/2023] Open
Abstract
Alzheimer's disease (AD) is characterized by progressive synaptic dysfunction, neuronal death, and brain atrophy, with amyloid-β (Aβ) plaque deposits and hyperphosphorylated tau neurofibrillary tangle accumulation in the brain tissue, which all lead to loss of cognitive function. Pathogenic mutations in the well-known AD causal genes including APP, PSEN1, and PSEN2 impair a variety of pathways, including protein processing, axonal transport, and metabolic homeostasis. Here we identified a missense variant rs117916664 (c.896T>C, p.Asn299Ser [p.N299S]) of the acetyl-CoA acyltransferase 1 (ACAA1) gene in a Han Chinese AD family by whole-genome sequencing and validated its association with early-onset familial AD in an independent cohort. Further in vitro and in vivo evidence showed that ACAA1 p.N299S contributes to AD by disturbing its enzymatic activity, impairing lysosomal function, and aggravating the Aβ pathology and neuronal loss, which finally caused cognitive impairment in a murine model. Our findings reveal a fundamental role of peroxisome-mediated lysosomal dysfunction in AD pathogenesis.
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7
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Sperm Lipid Markers of Male Fertility in Mammals. Int J Mol Sci 2021; 22:ijms22168767. [PMID: 34445473 PMCID: PMC8395862 DOI: 10.3390/ijms22168767] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 12/13/2022] Open
Abstract
Sperm plasma membrane lipids are essential for the function and integrity of mammalian spermatozoa. Various lipid types are involved in each key step within the fertilization process in their own yet coordinated way. The balance between lipid metabolism is tightly regulated to ensure physiological cellular processes, especially referring to crucial steps such as sperm motility, capacitation, acrosome reaction or fusion. At the same time, it has been shown that male reproductive function depends on the homeostasis of sperm lipids. Here, we review the effects of phospholipid, neutral lipid and glycolipid homeostasis on sperm fertilization function and male fertility in mammals.
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8
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Lü Z, Gong L, Ren Y, Chen Y, Wang Z, Liu L, Li H, Chen X, Li Z, Luo H, Jiang H, Zeng Y, Wang Y, Wang K, Zhang C, Jiang H, Wan W, Qin Y, Zhang J, Zhu L, Shi W, He S, Mao B, Wang W, Kong X, Li Y. Large-scale sequencing of flatfish genomes provides insights into the polyphyletic origin of their specialized body plan. Nat Genet 2021; 53:742-751. [PMID: 33875864 PMCID: PMC8110480 DOI: 10.1038/s41588-021-00836-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 03/05/2021] [Indexed: 11/09/2022]
Abstract
The evolutionary and genetic origins of the specialized body plan of flatfish are largely unclear. We analyzed the genomes of 11 flatfish species representing 9 of the 14 Pleuronectiforme families and conclude that Pleuronectoidei and Psettodoidei do not form a monophyletic group, suggesting independent origins from different percoid ancestors. Genomic and transcriptomic data indicate that genes related to WNT and retinoic acid pathways, hampered musculature and reduced lipids might have functioned in the evolution of the specialized body plan of Pleuronectoidei. Evolution of Psettodoidei involved similar but not identical genes. Our work provides valuable resources and insights for understanding the genetic origins of the unusual body plan of flatfishes.
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Affiliation(s)
- Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Yandong Ren
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yongjiu Chen
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Zhongkai Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Haorong Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Xianqing Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Zhenzhu Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Hairong Luo
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Hui Jiang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Yan Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yifan Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Chen Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Haifeng Jiang
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Wenting Wan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yanli Qin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Jianshe Zhang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Liang Zhu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wei Shi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Shunping He
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Bingyu Mao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
| | - Xiaoyu Kong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
| | - Yongxin Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
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9
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Anifandis G, Tempest HG, Oliva R, Swanson GM, Simopoulou M, Easley CA, Primig M, Messini CI, Turek PJ, Sutovsky P, Ory SJ, Krawetz SA. COVID-19 and human reproduction: A pandemic that packs a serious punch. Syst Biol Reprod Med 2021; 67:3-23. [PMID: 33719829 DOI: 10.1080/19396368.2020.1855271] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The COVID-19 pandemic has led to a worldwide health emergency that has impacted 188 countries at last count. The rapid community transmission and relatively high mortality rates with COVID-19 in modern times are relatively unique features of this flu pandemic and have resulted in an unparalleled global health crisis. SARS-CoV-2, being a respiratory virus, mainly affects the lungs, but is capable of infecting other vital organs, such as brain, heart and kidney. Emerging evidence suggests that the virus also targets male and female reproductive organs that express its main receptor ACE2, although it is as yet unclear if this has any implications for human fertility. Furthermore, professional bodies have recommended discontinuing fertility services during the pandemic such that reproductive services have also been affected. Although increased safety measures have helped to mitigate the propagation of COVID-19 in a number of countries, it seems that there is no predictable timeline to containment of the virus, a goal likely to remain elusive until an effective vaccine becomes available and widely distributed across the globe. In parallel, research on reproduction has been postponed for obvious reasons, while diagnostic tests that detect the virus or antibodies against it are of vital importance to support public health policies, such as social distancing and our obligation to wear masks in public spaces. This review aims to provide an overview of critical research and ethics issues that have been continuously emerging in the field of reproductive medicine as the COVID-19 pandemic tragically unfolds.Abbreviations: ACE2: angiotensin- converting enzyme 2; ART: Assisted reproductive technology; ASRM: American Society for Reproductive Medicine; CCR9: C-C Motif Chemokine Receptor 9; CDC: Centers for Disease Control and Prevention; COVID-19: Coronavirus disease 2019; Ct: Cycle threshold; CXCR6: C-X-C Motif Chemokine Receptor 6; ELISA: enzyme-linked immunosorbent assay; ESHRE: European Society of Human Reproduction and Embryology; ET: Embryo transfer; FSH: Follicle Stimulating Hormone; FFPE: formalin fixed paraffin embedded; FYCO1: FYVE And Coiled-Coil Domain Autophagy Adaptor 1; IFFS: International Federation of Fertility Societies; IUI: Intrauterine insemination; IVF: In vitro fertilization; LH: Luteinizing Hormone; LZTFL1: Leucine Zipper Transcription Factor Like 1; MAR: medically assisted reproduction services; MERS: Middle East Respiratory syndrome; NGS: Next Generation Sequencing; ORF: Open Reading Frame; PPE: personal protective equipment; RE: RNA Element; REDa: RNA Element Discovery algorithm; RT-PCR: Reverse=trascriptase transcriptase-polymerase chain reaction; SARS: Severe acute respiratory syndrome; SARS-CoV-2: Severe Acute Respiratory Syndrome Coronavirus 2; SLC6A20: Solute Carrier Family 6 Member 20; SMS: Single Molecule Sequencing; T: Testosterone; TMPRSS2: transmembrane serine protease 2; WHO: World Health Organization; XCR1: X-C Motif Chemokine Receptor.
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Affiliation(s)
- George Anifandis
- Department of Obstetrics and Gynecology, School of Health Sciences, Faculty of Medicine, University of Thessaly, Larisa, Greece
| | - Helen G Tempest
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA.,Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Rafael Oliva
- Molecular Biology of Reproduction and Development Research Group, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universitat De Barcelona, and Hospital Clinic from Barcelona, Spain
| | - Grace M Swanson
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA.,Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Mara Simopoulou
- Department of Experimental Physiology, School of Health Sciences, Faculty of Medicine, National and Kapodistrian University of Athens, Athens, Greece, Athens, Greece
| | - Charles A Easley
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, USA.,Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
| | - Michael Primig
- Inserm, EHESP, Irset (Institut De Recherche En Santé, Environnement Et Travail), Rennes, France
| | - Christina I Messini
- Department of Obstetrics and Gynecology, School of Health Sciences, Faculty of Medicine, University of Thessaly, Larisa, Greece
| | - Paul J Turek
- It is a private Clinic, The Turek Clinic, Beverly Hills, CA, USA
| | - Peter Sutovsky
- Division of Animal Sciences and the Department of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, MO, USA
| | - Steve J Ory
- It is a private Clinic, IVF Florida Reproductive Institutes, Margate, FL, USA.,Department of Obstetrics and Gynecology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Stephen A Krawetz
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA.,Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA.,Department of Obstetrics and Gynecology and Center of Molecular Medicine and Genetics, C.S. Mott Center for Human Growth and Development, Wayne State University, Detroit, MI, USA
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10
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Chornyi S, IJlst L, van Roermund CWT, Wanders RJA, Waterham HR. Peroxisomal Metabolite and Cofactor Transport in Humans. Front Cell Dev Biol 2021; 8:613892. [PMID: 33505966 PMCID: PMC7829553 DOI: 10.3389/fcell.2020.613892] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 12/10/2020] [Indexed: 12/20/2022] Open
Abstract
Peroxisomes are membrane-bound organelles involved in many metabolic pathways and essential for human health. They harbor a large number of enzymes involved in the different pathways, thus requiring transport of substrates, products and cofactors involved across the peroxisomal membrane. Although much progress has been made in understanding the permeability properties of peroxisomes, there are still important gaps in our knowledge about the peroxisomal transport of metabolites and cofactors. In this review, we discuss the different modes of transport of metabolites and essential cofactors, including CoA, NAD+, NADP+, FAD, FMN, ATP, heme, pyridoxal phosphate, and thiamine pyrophosphate across the peroxisomal membrane. This transport can be mediated by non-selective pore-forming proteins, selective transport proteins, membrane contact sites between organelles, and co-import of cofactors with proteins. We also discuss modes of transport mediated by shuttle systems described for NAD+/NADH and NADP+/NADPH. We mainly focus on current knowledge on human peroxisomal metabolite and cofactor transport, but also include knowledge from studies in plants, yeast, fruit fly, zebrafish, and mice, which has been exemplary in understanding peroxisomal transport mechanisms in general.
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Affiliation(s)
- Serhii Chornyi
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Lodewijk IJlst
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Carlo W T van Roermund
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
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Harzandi A, Lee S, Bidkhori G, Saha S, Hendry BM, Mardinoglu A, Shoaie S, Sharpe CC. Acute kidney injury leading to CKD is associated with a persistence of metabolic dysfunction and hypertriglyceridemia. iScience 2021; 24:102046. [PMID: 33554059 PMCID: PMC7843454 DOI: 10.1016/j.isci.2021.102046] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/12/2020] [Accepted: 01/06/2021] [Indexed: 12/14/2022] Open
Abstract
Fibrosis is the pathophysiological hallmark of progressive chronic kidney disease (CKD). The kidney is a highly metabolically active organ, and it has been suggested that disruption in its metabolism leads to renal fibrosis. We developed a longitudinal mouse model of acute kidney injury leading to CKD and an in vitro model of epithelial to mesenchymal transition to study changes in metabolism, inflammation, and fibrosis. Using transcriptomics, metabolic modeling, and serum metabolomics, we observed sustained fatty acid metabolic dysfunction in the mouse model from early to late stages of CKD. Increased fatty acid biosynthesis and downregulation of catabolic pathways for triglycerides and diacylglycerides were associated with a marked increase in these lipids in the serum. We therefore suggest that the kidney may be the source of the abnormal lipid profile seen in patients with CKD, which may provide insights into the association between CKD and cardiovascular disease. Following AKI, markers of fibrosis and inflammation go up simultaneously AKI is associated with reduced fatty acid oxidation and oxidative phosphorylation Changes in metabolism persist as chronic kidney disease develops Changes in metabolism are associated with increased serum levels of triglycerides
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Affiliation(s)
- Azadeh Harzandi
- Renal Sciences, Department of Inflammation Biology, School of Immunology & Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, SE5 9NU London, UK
| | - Sunjae Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea, 61005
- Centre for Host–Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT London, UK
| | - Gholamreza Bidkhori
- Centre for Host–Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT London, UK
| | - Sujit Saha
- Renal Sciences, Department of Inflammation Biology, School of Immunology & Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, SE5 9NU London, UK
| | - Bruce M. Hendry
- Renal Sciences, Department of Inflammation Biology, School of Immunology & Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, SE5 9NU London, UK
| | - Adil Mardinoglu
- Centre for Host–Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT London, UK
- Science for Life Laboratory (SciLifeLab), KTH - Royal Institute of Technology, Tomtebodavägen 23, Solna, Stockholm 171 65, Sweden
- Corresponding author
| | - Saeed Shoaie
- Centre for Host–Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT London, UK
- Science for Life Laboratory (SciLifeLab), KTH - Royal Institute of Technology, Tomtebodavägen 23, Solna, Stockholm 171 65, Sweden
- Corresponding author
| | - Claire C. Sharpe
- Renal Sciences, Department of Inflammation Biology, School of Immunology & Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, SE5 9NU London, UK
- Corresponding author
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12
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Mammalian Homologue NME3 of DYNAMO1 Regulates Peroxisome Division. Int J Mol Sci 2020; 21:ijms21218040. [PMID: 33126676 PMCID: PMC7662248 DOI: 10.3390/ijms21218040] [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: 09/08/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 12/21/2022] Open
Abstract
Peroxisomes proliferate by sequential processes comprising elongation, constriction, and scission of peroxisomal membrane. It is known that the constriction step is mediated by a GTPase named dynamin-like protein 1 (DLP1) upon efficient loading of GTP. However, mechanism of fuelling GTP to DLP1 remains unknown in mammals. We earlier show that nucleoside diphosphate (NDP) kinase-like protein, termed dynamin-based ring motive-force organizer 1 (DYNAMO1), generates GTP for DLP1 in a red alga, Cyanidioschyzon merolae. In the present study, we identified that nucleoside diphosphate kinase 3 (NME3), a mammalian homologue of DYNAMO1, localizes to peroxisomes. Elongated peroxisomes were observed in cells with suppressed expression of NME3 and fibroblasts from a patient lacking NME3 due to the homozygous mutation at the initiation codon of NME3. Peroxisomes proliferated by elevation of NME3 upon silencing the expression of ATPase family AAA domain containing 1, ATAD1. In the wild-type cells expressing catalytically-inactive NME3, peroxisomes were elongated. These results suggest that NME3 plays an important role in peroxisome division in a manner dependent on its NDP kinase activity. Moreover, the impairment of peroxisome division reduces the level of ether-linked glycerophospholipids, ethanolamine plasmalogens, implying the physiological importance of regulation of peroxisome morphology.
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Altered mechanisms of genital development identified through integration of DNA methylation and genomic measures in hypospadias. Sci Rep 2020; 10:12715. [PMID: 32728162 PMCID: PMC7391634 DOI: 10.1038/s41598-020-69725-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/19/2020] [Indexed: 12/31/2022] Open
Abstract
Hypospadias is a common birth defect where the urethral opening forms on the ventral side of the penis. We performed integrative methylomic, genomic, and transcriptomic analyses to characterize sites of DNA methylation that influence genital development. In case–control and case-only epigenome-wide association studies (EWAS) of preputial tissue we identified 25 CpGs associated with hypospadias characteristics and used one-sample two stage least squares Mendelian randomization (2SLS MR) to show a causal relationship for 21 of the CpGs. The largest difference was 15.7% lower beta-value at cg14436889 among hypospadias cases than controls (EWAS P = 5.4e−7) and is likely causal (2SLS MR P = 9.8e−15). Integrative annotation using two-sample Mendelian randomization of these methylation regions highlight potentially causal roles of genes involved in germ layer differentiation (WDHD1, DNM1L, TULP3), beta-catenin signaling (PKP2, UBE2R2, TNKS), androgens (CYP4A11, CYP4A22, CYP4B1, CYP4X1, CYP4Z2P, EPHX1, CD33/SIGLEC3, SIGLEC5, SIGLEC7, KLK5, KLK7, KLK10, KLK13, KLK14), and reproductive traits (ACAA1, PLCD1, EFCAB4B, GMCL1, MKRN2, DNM1L, TEAD4, TSPAN9, KLK family). This study identified CpGs that remained differentially methylated after urogenital development and used the most relevant tissue sample available to study hypospadias. We identified multiple methylation sites and candidate genes that can be further evaluated for their roles in regulating urogenital development.
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Chu KY, Mellet N, Thai LM, Meikle PJ, Biden TJ. Short-term inhibition of autophagy benefits pancreatic β-cells by augmenting ether lipids and peroxisomal function, and by countering depletion of n-3 polyunsaturated fatty acids after fat-feeding. Mol Metab 2020; 40:101023. [PMID: 32504884 PMCID: PMC7322075 DOI: 10.1016/j.molmet.2020.101023] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/29/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Investigations of autophagy in β-cells have usually focused on its homeostatic function. More dynamic roles in inhibiting glucose-stimulated insulin secretion (GSIS), potentially involving remodelling of cellular lipids, have been suggested from in vitro studies but not evaluated in vivo. METHODS We employed temporally-regulated deletion of the essential autophagy gene, Atg7, in β-cells. Mice were fed chow or high-fat diets (HFD), in conjunction with deletion of Atg7 for the last 3 weeks (short-term model) or 9 weeks (long-term model). Standard in vivo metabolic phenotyping was undertaken, and 450 lipid species in islets quantified ex vivo using mass spectroscopy (MS). MIN6 cells were also employed for lipidomics and secretory interventions. RESULTS β-cell function was impaired by inhibiting autophagy in the longer-term, but conversely improved by 3-week deletion of Atg7, specifically under HFD conditions. This was accompanied by augmented GSIS ex vivo. Surprisingly, the HFD had minimal effect on sphingolipid and neutral lipid species, but modulated >100 phospholipids and ether lipids, and markedly shifted the profile of polyunsaturated fatty acid (PUFA) sidechains from n3 to n6 forms. These changes were partially countered by Atg7 deletion, consistent with an accompanying upregulation of the PUFA elongase enzyme, Elovl5. Loss of Atg7 separately augmented plasmalogens and alkyl lipids, in association with increased expression of Lonp2, a peroxisomal chaperone/protease that facilitates maturation of ether lipid synthetic enzymes. Depletion of PUFAs and ether lipids was also observed in MIN6 cells chronically exposed to oleate (more so than palmitate). GSIS was inhibited by knocking down Dhrs7b, which encodes an enzyme of peroxisomal ether lipid synthesis. Conversely, impaired GSIS due to oleate pre-treatment was selectively reverted by Dhrs7b overexpression. CONCLUSIONS A detrimental increase in n6:n3 PUFA ratios in ether lipids and phospholipids is revealed as a major response of β-cells to high-fat feeding. This is partially reversed by short-term inhibition of autophagy, which results in compensatory changes in peroxisomal lipid metabolism. The short-term phenotype is linked to improved GSIS, in contrast to the impairment seen with the longer-term inhibition of autophagy. The balance between these positive and negative inputs could help determine whether β-cells adapt or fail in response to obesity.
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Affiliation(s)
- Kwan Yi Chu
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia
| | - Natalie Mellet
- Baker Heart and Diabetes Institute, PO Box 6492, Melbourne, Vic, 3004, Australia
| | - Le May Thai
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, PO Box 6492, Melbourne, Vic, 3004, Australia.
| | - Trevor J Biden
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, The University of New South Wales, Sydney, NSW, Australia.
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15
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Kunze M. The type-2 peroxisomal targeting signal. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1867:118609. [PMID: 31751594 DOI: 10.1016/j.bbamcr.2019.118609] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/08/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022]
Abstract
The type-2 peroxisomal targeting signal (PTS2) is one of two peptide motifs destining soluble proteins for peroxisomes. This signal acts as amphiphilic α-helix exposing the side chains of all conserved residues to the same side. PTS2 motifs are recognized by a bipartite protein complex consisting of the receptor PEX7 and a co-receptor. Cargo-loaded receptor complexes are translocated across the peroxisomal membrane by a transient pore and inside peroxisomes, cargo proteins are released and processed in many, but not all species. The components of the bipartite receptor are re-exported into the cytosol by a ubiquitin-mediated and ATP-driven export mechanism. Structurally, PTS2 motifs resemble other N-terminal targeting signals, whereas the functional relation to the second peroxisomal targeting signal (PTS1) is unclear. Although only a few PTS2-carrying proteins are known in humans, subjects lacking a functional import mechanism for these proteins suffer from the severe inherited disease rhizomelic chondrodysplasia punctata.
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Affiliation(s)
- Markus Kunze
- Medical University of Vienna, Center for Brain Research, Department of Pathobiology of the Nervous System, Spitalgasse 4, 1090 Vienna, Austria.
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16
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Counihan JL, Duckering M, Dalvie E, Ku WM, Bateman LA, Fisher KJ, Nomura DK. Chemoproteomic Profiling of Acetanilide Herbicides Reveals Their Role in Inhibiting Fatty Acid Oxidation. ACS Chem Biol 2017; 12:635-642. [PMID: 28094496 DOI: 10.1021/acschembio.6b01001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Acetanilide herbicides are among the most widely used pesticides in the United States, but their toxicological potential and mechanisms remain poorly understood. Here, we have used chemoproteomic platforms to map proteome-wide cysteine reactivity of acetochlor (AC), the most widely used acetanilide herbicide, in vivo in mice. We show that AC directly reacts with >20 protein targets in vivo in mouse liver, including the catalytic cysteines of several thiolase enzymes involved in mitochondrial and peroxisomal fatty acid oxidation. We show that the fatty acids that are not oxidized, due to impaired fatty acid oxidation, are instead diverted into other lipid pathways, resulting in heightened free fatty acids, triglycerides, cholesteryl esters, and other lipid species in the liver. Our findings show the utility of chemoproteomic approaches for identifying novel mechanisms of toxicity associated with environmental chemicals like acetanilide herbicides.
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Affiliation(s)
- Jessica L. Counihan
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Megan Duckering
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Esha Dalvie
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Wan-min Ku
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Leslie A. Bateman
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Karl J. Fisher
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
| | - Daniel K. Nomura
- Departments of Chemistry,
Molecular and Cell Biology, and Nutritional Sciences and Toxicology, 127 Morgan Hall, University of California, Berkeley, Berkeley, California 94720, United States
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17
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Ford B, Bateman LA, Gutierrez-Palominos L, Park R, Nomura DK. Mapping Proteome-wide Targets of Glyphosate in Mice. Cell Chem Biol 2017; 24:133-140. [PMID: 28132892 DOI: 10.1016/j.chembiol.2016.12.013] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/14/2016] [Accepted: 12/21/2016] [Indexed: 12/30/2022]
Abstract
Glyphosate, the active ingredient in the herbicide Roundup, is one of the most widely used pesticides in agriculture and home garden use. Whether glyphosate causes any mammalian toxicity remains highly controversial. While many studies have associated glyphosate with numerous adverse health effects, the mechanisms underlying glyphosate toxicity in mammals remain poorly understood. Here, we used activity-based protein profiling to map glyphosate targets in mice. We show that glyphosate at high doses can be metabolized in vivo to reactive metabolites such as glyoxylate and react with cysteines across many proteins in mouse liver. We show that glyoxylate inhibits liver fatty acid oxidation enzymes and glyphosate treatment in mice increases the levels of triglycerides and cholesteryl esters, likely resulting from diversion of fatty acids away from oxidation and toward other lipid pathways. Our study highlights the utility of using chemoproteomics to identify novel toxicological mechanisms of environmental chemicals such as glyphosate.
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Affiliation(s)
- Breanna Ford
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Leslie A Bateman
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Leilani Gutierrez-Palominos
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA
| | - Robin Park
- Integrated Proteomics Applications, Inc., 12707 High Bluff Drive Suite 200, San Diego, CA 92130, USA
| | - Daniel K Nomura
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, 127 Morgan Hall, Berkeley, CA 94720, USA.
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18
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Furusawa Y, Kubo T, Fukazawa T. Phyhd1, an XPhyH-like homologue, is induced in mouse T cells upon T cell stimulation. Biochem Biophys Res Commun 2016; 472:551-6. [PMID: 26970303 DOI: 10.1016/j.bbrc.2016.03.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 03/09/2016] [Indexed: 11/28/2022]
Abstract
We previously identified XPhyH-like as a gene whose expression is enhanced in Xenopus blood cells during the refractory period, in which Xenopus tadpoles transiently lose their tail regenerative ability. Although we hypothesized that some autoreactive immune cells attack tail blastemal cells during the refractory period and XPhyH-like expressing immune cells were involved in the process, the nature of cells expressing XPhyH-like remain unknown, partly due to the lack of leukocyte markers available in Xenopus. In the present study, we used mice to analyze the expression pattern of XPhyH-like homologues. When we used quantitative reverse transcription-polymerase chain reaction (RT--PCR) to analyze the expression of mouse Phyhd1, an XPhyH-like orthologue, and Phyh, a Phyhd1 paralogue, both Phyhd1 and Phyh showed similar tissue-specific expression patterns. The expression pattern in leukocytes, however, differed between Phyhd1 and Phyh; Phyhd1 was considerably expressed in T cells and B cells. Moreover, the expression of Phyhd1 in T cells was up-regulated for approximately 3- to 7-times by T cell stimulation 3-4 days after the stimulation, unlike Phyh. Our findings suggest that Phyhd1 and Phyh have distinct roles in mouse leukocytes and Phyhd1 is related to T cell differentiation and/or function of effector T cells.
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Affiliation(s)
- Yuri Furusawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Takeo Kubo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Taro Fukazawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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Baes M, Van Veldhoven PP. Hepatic dysfunction in peroxisomal disorders. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:956-70. [PMID: 26453805 DOI: 10.1016/j.bbamcr.2015.09.035] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/25/2015] [Accepted: 09/28/2015] [Indexed: 12/18/2022]
Abstract
The peroxisomal compartment in hepatocytes hosts several essential metabolic conversions. These are defective in peroxisomal disorders that are either caused by failure to import the enzymes in the organelle or by mutations in the enzymes or in transporters needed to transfer the substrates across the peroxisomal membrane. Hepatic pathology is one of the cardinal features in disorders of peroxisome biogenesis and peroxisomal β-oxidation although it only rarely determines the clinical fate. In mouse models of these diseases liver pathologies also occur, although these are not always concordant with the human phenotype which might be due to differences in diet, expression of enzymes and backup mechanisms. Besides the morphological changes, we overview the impact of peroxisome malfunction on other cellular compartments including mitochondria and the ER. We further focus on the metabolic pathways that are affected such as bile acid formation, and dicarboxylic acid and branched chain fatty acid degradation. It appears that the association between deregulated metabolites and pathological events remains unclear.
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Affiliation(s)
- Myriam Baes
- Laboratory for Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, B-3000 Leuven, Belgium.
| | - Paul P Van Veldhoven
- Laboratory for Lipid Biochemistry and Protein Interactions, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium.
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20
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Kunze M, Berger J. The similarity between N-terminal targeting signals for protein import into different organelles and its evolutionary relevance. Front Physiol 2015; 6:259. [PMID: 26441678 PMCID: PMC4585086 DOI: 10.3389/fphys.2015.00259] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/04/2015] [Indexed: 12/04/2022] Open
Abstract
The proper distribution of proteins between the cytosol and various membrane-bound compartments is crucial for the functionality of eukaryotic cells. This requires the cooperation between protein transport machineries that translocate diverse proteins from the cytosol into these compartments and targeting signal(s) encoded within the primary sequence of these proteins that define their cellular destination. The mechanisms exerting protein translocation differ remarkably between the compartments, but the predominant targeting signals for mitochondria, chloroplasts and the ER share the N-terminal position, an α-helical structural element and the removal from the core protein by intraorganellar cleavage. Interestingly, similar properties have been described for the peroxisomal targeting signal type 2 mediating the import of a fraction of soluble peroxisomal proteins, whereas other peroxisomal matrix proteins encode the type 1 targeting signal residing at the extreme C-terminus. The structural similarity of N-terminal targeting signals poses a challenge to the specificity of protein transport, but allows the generation of ambiguous targeting signals that mediate dual targeting of proteins into different compartments. Dual targeting might represent an advantage for adaptation processes that involve a redistribution of proteins, because it circumvents the hierarchy of targeting signals. Thus, the co-existence of two equally functional import pathways into peroxisomes might reflect a balance between evolutionary constant and flexible transport routes.
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Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna Vienna, Austria
| | - Johannes Berger
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna Vienna, Austria
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21
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Selkälä EM, Nair RR, Schmitz W, Kvist AP, Baes M, Hiltunen JK, Autio KJ. Phytol is lethal for Amacr-deficient mice. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1851:1394-405. [PMID: 26248199 DOI: 10.1016/j.bbalip.2015.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 07/08/2015] [Accepted: 07/31/2015] [Indexed: 01/22/2023]
Abstract
α-Methylacyl-CoA racemase (Amacr) catalyzes the racemization of the 25-methyl group in C27-intermediates in bile acid synthesis and in methyl-branched fatty acids such as pristanic acid, a metabolite derived from phytol. Consequently, patients with Amacr deficiency accumulate C27-bile acid intermediates, pristanic and phytanic acid and display sensorimotor neuropathy, seizures and relapsing encephalopathy. In contrast to humans, Amacr-deficient mice are clinically symptomless on a standard laboratory diet, but failed to thrive when fed phytol-enriched chow. In this study, the effect and the mechanisms behind the development of the phytol-feeding associated disease state in Amacr-deficient mice were investigated. All Amacr-/- mice died within 36weeks on a phytol diet, while wild-type mice survived. Liver failure was the main cause of death accompanied by kidney and brain abnormalities. Histological analysis of liver showed inflammation, fibrotic and necrotic changes, Kupffer cell proliferation and fatty changes in hepatocytes, and serum analysis confirmed the hepatic disease. Pristanic and phytanic acids accumulated in livers of Amacr-/- mice after a phytol diet. Microarray analysis also revealed changes in the expression levels of numerous genes in wild-type mouse livers after two weeks of the phytol diet compared to a control diet. This indicates that detoxification of phytol metabolites in liver is accompanied by activation of multiple pathways at the molecular level and Amacr-/- mice are not able to respond adequately. Phytol causes primary failure in liver leading to death of Amacr-/- mice thus emphasizing the indispensable role of Amacr in detoxification of α-methyl-branched fatty acids.
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Affiliation(s)
- Eija M Selkälä
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FI-90014, Finland; Biocenter Oulu, University of Oulu, Finland
| | - Remya R Nair
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FI-90014, Finland; Biocenter Oulu, University of Oulu, Finland
| | - Werner Schmitz
- Theodor-Boveri-Institut für Biowissenschaften, Lehrstuhl für Biochemie und Molekularbiologie der Universität Würzburg, Am Hubland, 97974 Würzburg, Germany
| | - Ari-Pekka Kvist
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FI-90014, Finland; Biocenter Oulu, University of Oulu, Finland
| | - Myriam Baes
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, University of Leuven, Herestraat 49 O&N 2, 3000 Leuven, Belgium
| | - J Kalervo Hiltunen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FI-90014, Finland; Biocenter Oulu, University of Oulu, Finland
| | - Kaija J Autio
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FI-90014, Finland; Biocenter Oulu, University of Oulu, Finland.
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Revisiting the intraperoxisomal pathway of mammalian PEX7. Sci Rep 2015; 5:11806. [PMID: 26138649 PMCID: PMC4490337 DOI: 10.1038/srep11806] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 06/08/2015] [Indexed: 02/07/2023] Open
Abstract
Newly synthesized peroxisomal proteins containing a cleavable type 2 targeting signal (PTS2) are transported to the peroxisome by a cytosolic PEX5-PEX7 complex. There, the trimeric complex becomes inserted into the peroxisomal membrane docking/translocation machinery (DTM), a step that leads to the translocation of the cargo into the organelle matrix. Previous work suggests that PEX5 is retained at the DTM during all the steps occurring at the peroxisome but whether the same applies to PEX7 was unknown. By subjecting different pre-assembled trimeric PEX5-PEX7-PTS2 complexes to in vitro co-import/export assays we found that the export competence of peroxisomal PEX7 is largely determined by the PEX5 molecule that transported it to the peroxisome. This finding suggests that PEX7 is also retained at the DTM during the peroxisomal steps and implies that cargo proteins are released into the organelle matrix by DTM-embedded PEX7. The release step does not depend on PTS2 cleavage. Rather, our data suggest that insertion of the trimeric PEX5-PEX7-PTS2 protein complex into the DTM is probably accompanied by conformational alterations in PEX5 to allow release of the PTS2 protein into the organelle matrix.
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23
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Wanders RJA, Ferdinandusse S, Ebberink MS, Waterham HR. Phytanoyl-CoA Hydroxylase: A 2-Oxoglutarate-Dependent Dioxygenase Crucial for Fatty Acid Alpha-Oxidation in Humans. 2-OXOGLUTARATE-DEPENDENT OXYGENASES 2015. [DOI: 10.1039/9781782621959-00338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Phytanoyl-CoA hydroxylase belongs to the family of 2-oxoglutarate-dependent dioxygenases and plays a crucial role in the α-oxidation of fatty acids. The complete α-oxidation pathway involves five different enzymes localized in peroxisomes. Thus far, phytanoyl-CoA hydroxylase deficiency has remained the only genetically determined inborn error of metabolism affecting the α-oxidation pathway. In this chapter we describe the current state of knowledge on fatty acid α-oxidation with special emphasis on phytanoyl-CoA hydroxylase and its deficiency in Refsum disease.
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Affiliation(s)
- Ronald J. A. Wanders
- Laboratory Genetic Metabolic Diseases, Departments of Paediatrics, Emma Children’s Hospital, and Clinical Chemistry, Academic Medical Center, University of Amsterdam Meibergdreef 9 1105 AZ Amsterdam the Netherlands
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Departments of Paediatrics, Emma Children’s Hospital, and Clinical Chemistry, Academic Medical Center, University of Amsterdam Meibergdreef 9 1105 AZ Amsterdam the Netherlands
| | - Merel S. Ebberink
- Laboratory Genetic Metabolic Diseases, Departments of Paediatrics, Emma Children’s Hospital, and Clinical Chemistry, Academic Medical Center, University of Amsterdam Meibergdreef 9 1105 AZ Amsterdam the Netherlands
| | - Hans R. Waterham
- Laboratory Genetic Metabolic Diseases, Departments of Paediatrics, Emma Children’s Hospital, and Clinical Chemistry, Academic Medical Center, University of Amsterdam Meibergdreef 9 1105 AZ Amsterdam the Netherlands
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24
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Moreira GCM, Godoy TF, Boschiero C, Gheyas A, Gasparin G, Andrade SCS, Paduan M, Montenegro H, Burt DW, Ledur MC, Coutinho LL. Variant discovery in a QTL region on chromosome 3 associated with fatness in chickens. Anim Genet 2015; 46:141-7. [PMID: 25643900 DOI: 10.1111/age.12263] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2014] [Indexed: 12/17/2022]
Abstract
Abdominal fat content is an economically important trait in commercially bred chickens. Although many quantitative trait loci (QTL) related to fat deposition have been detected, the resolution for these regions is low and functional variants are still unknown. The current study was conducted aiming at increasing resolution for a region previously shown to have a QTL associated with fat deposition, to detect novel variants from this region and to annotate those variants to delineate potentially functional ones as candidates for future studies. To achieve this, 18 chickens from a parental generation used in a reciprocal cross between broiler and layer lines were sequenced using the Illumina next-generation platform with an initial coverage of 18X/chicken. The discovery of genetic variants was performed in a QTL region located on chromosome 3 between microsatellite markers LEI0161 and ADL0371 (33,595,706-42,632,651 bp). A total of 136,054 unique SNPs and 15,496 unique INDELs were detected in this region, and after quality filtering, 123,985 SNPs and 11,298 INDELs were retained. Of these variants, 386 SNPs and 15 INDELs were located in coding regions of genes related to important metabolic pathways. Loss-of-function variants were identified in several genes, and six of those, namely LOC771163, EGLN1, GNPAT, FAM120B, THBS2 and GGPS1, were related to fat deposition. Therefore, these loss-of-function variants are candidate mutations for conducting further studies on this important trait in chickens.
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Affiliation(s)
- G C M Moreira
- Departamento de Zootecnia, USP/ESALQ, Piracicaba, SP, 13418-900, Brazil
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25
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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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26
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Nordgren M, Wang B, Apanasets O, Fransen M. Peroxisome degradation in mammals: mechanisms of action, recent advances, and perspectives. Front Physiol 2013; 4:145. [PMID: 23785334 PMCID: PMC3682127 DOI: 10.3389/fphys.2013.00145] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 05/30/2013] [Indexed: 12/18/2022] Open
Abstract
Peroxisomes are remarkably dynamic organelles that participate in a diverse array of cellular processes, including the metabolism of lipids and reactive oxygen species. In order to regulate peroxisome function in response to changing nutritional and environmental stimuli, new organelles need to be formed and superfluous and dysfunctional organelles have to be selectively removed. Disturbances in any of these processes have been associated with the etiology and progression of various congenital neurodegenerative and age-related human disorders. The aim of this review is to critically explore our current knowledge of how peroxisomes are degraded in mammalian cells and how defects in this process may contribute to human disease. Some of the key issues highlighted include the current concepts of peroxisome removal, the peroxisome quality control mechanisms, the initial triggers for peroxisome degradation, the factors for dysfunctional peroxisome recognition, and the regulation of peroxisome homeostasis. We also dissect the functional and mechanistic relationship between different forms of selective organelle degradation and consider how lysosomal dysfunction may lead to defects in peroxisome turnover. In addition, we draw lessons from studies on other organisms and extrapolate this knowledge to mammals. Finally, we discuss the potential pathological implications of dysfunctional peroxisome degradation for human health.
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Affiliation(s)
- Marcus Nordgren
- Laboratory of Lipid Biochemistry and Protein Interactions, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven Leuven, Vlaams-Brabant, Belgium
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