1
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Prashar A, Bussi C, Fearns A, Capurro MI, Gao X, Sesaki H, Gutierrez MG, Jones NL. Lysosomes drive the piecemeal removal of mitochondrial inner membrane. Nature 2024:10.1038/s41586-024-07835-w. [PMID: 39169179 DOI: 10.1038/s41586-024-07835-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 07/16/2024] [Indexed: 08/23/2024]
Abstract
Mitochondrial membranes define distinct structural and functional compartments. Cristae of the inner mitochondrial membrane (IMM) function as independent bioenergetic units that undergo rapid and transient remodelling, but the significance of this compartmentalized organization is unknown1. Using super-resolution microscopy, here we show that cytosolic IMM vesicles, devoid of outer mitochondrial membrane or mitochondrial matrix, are formed during resting state. These vesicles derived from the IMM (VDIMs) are formed by IMM herniation through pores formed by voltage-dependent anion channel 1 in the outer mitochondrial membrane. Live-cell imaging showed that lysosomes in proximity to mitochondria engulfed the herniating IMM and, aided by the endosomal sorting complex required for transport machinery, led to the formation of VDIMs in a microautophagy-like process, sparing the remainder of the organelle. VDIM formation was enhanced in mitochondria undergoing oxidative stress, suggesting their potential role in maintenance of mitochondrial function. Furthermore, the formation of VDIMs required calcium release by the reactive oxygen species-activated, lysosomal calcium channel, transient receptor potential mucolipin 1, showing an interorganelle communication pathway for maintenance of mitochondrial homeostasis. Thus, IMM compartmentalization could allow for the selective removal of damaged IMM sections via VDIMs, which should protect mitochondria from localized injury. Our findings show a new pathway of intramitochondrial quality control.
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Affiliation(s)
- Akriti Prashar
- Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- NHLBI, NIH, Bethesda, MD, USA
| | - Claudio Bussi
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
- School of Biological Sciences, Nanyang Technical University, Singapore, Singapore
| | - Antony Fearns
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Mariana I Capurro
- Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Xiaodong Gao
- Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Hiromi Sesaki
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Maximiliano G Gutierrez
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Nicola L Jones
- Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Departments of Paediatrics and Physiology, University of Toronto, Toronto, Ontario, Canada.
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2
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Ma W, Lu Y, Jin X, Lin N, Zhang L, Song Y. Targeting selective autophagy and beyond: From underlying mechanisms to potential therapies. J Adv Res 2024:S2090-1232(24)00199-1. [PMID: 38750694 DOI: 10.1016/j.jare.2024.05.009] [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: 03/07/2024] [Revised: 04/26/2024] [Accepted: 05/08/2024] [Indexed: 05/21/2024] Open
Abstract
BACKGROUND Autophagy is an evolutionarily conserved turnover process for intracellular substances in eukaryotes, relying on lysosomal (in animals) or vacuolar (in yeast and plants) mechanisms. In the past two decades, emerging evidence suggests that, under specific conditions, autophagy can target particular macromolecules or organelles for degradation, a process termed selective autophagy. Recently, accumulating studies have demonstrated that the abnormality of selective autophagy is closely associated with the occurrence and progression of many human diseases, including neurodegenerative diseases, cancers, metabolic diseases, and cardiovascular diseases. AIM OF REVIEW This review aims at systematically and comprehensively introducing selective autophagy and its role in various diseases, while unravelling the molecular mechanisms of selective autophagy. By providing a theoretical basis for the development of related small-molecule drugs as well as treating related human diseases, this review seeks to contribute to the understanding of selective autophagy and its therapeutic potential. KEY SCIENTIFIC CONCEPTS OF REVIEW In this review, we systematically introduce and dissect the major categories of selective autophagy that have been discovered. We also focus on recent advances in understanding the molecular mechanisms underlying both classical and non-classical selective autophagy. Moreover, the current situation of small-molecule drugs targeting different types of selective autophagy is further summarized, providing valuable insights into the discovery of more candidate small-molecule drugs targeting selective autophagy in the future. On the other hand, we also reveal clinically relevant implementations that are potentially related to selective autophagy, such as predictive approaches and treatments tailored to individual patients.
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Affiliation(s)
- Wei Ma
- Department of Breast Surgery, Department of Ultrasound, Department of Hematology and Department of Radiation Oncology, The First Hospital of China Medical University, Shenyang 110001, China
| | - Yingying Lu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Xin Jin
- Department of Breast Surgery, Department of Ultrasound, Department of Hematology and Department of Radiation Oncology, The First Hospital of China Medical University, Shenyang 110001, China
| | - Na Lin
- Department of Breast Surgery, Department of Ultrasound, Department of Hematology and Department of Radiation Oncology, The First Hospital of China Medical University, Shenyang 110001, China.
| | - Lan Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
| | - Yaowen Song
- Department of Breast Surgery, Department of Ultrasound, Department of Hematology and Department of Radiation Oncology, The First Hospital of China Medical University, Shenyang 110001, China.
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3
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Duan Y, Yao RQ, Ling H, Zheng LY, Fan Q, Li Q, Wang L, Zhou QY, Wu LM, Dai XG, Yao YM. Organellophagy regulates cell death:A potential therapeutic target for inflammatory diseases. J Adv Res 2024:S2090-1232(24)00203-0. [PMID: 38740259 DOI: 10.1016/j.jare.2024.05.012] [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: 03/11/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Dysregulated alterations in organelle structure and function have a significant connection with cell death, as well as the occurrence and development of inflammatory diseases. Maintaining cell viability and inhibiting the release of inflammatory cytokines are essential measures to treat inflammatory diseases. Recently, many studies have showed that autophagy selectively targets dysfunctional organelles, thereby sustaining the functional stability of organelles, alleviating the release of multiple cytokines, and maintaining organismal homeostasis. Organellophagy dysfunction is critically engaged in different kinds of cell death and inflammatory diseases. AIM OF REVIEW We summarized the current knowledge of organellophagy (e.g., mitophagy, reticulophagy, golgiphagy, lysophagy, pexophagy, nucleophagy, and ribophagy) and the underlying mechanisms by which organellophagy regulates cell death. KEY SCIENTIFIC CONCEPTS OF REVIEW We outlined the potential role of organellophagy in the modulation of cell fate during the inflammatory response to develop an intervention strategy for the organelle quality control in inflammatory diseases.
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Affiliation(s)
- Yu Duan
- Department of Critical Care Medicine, Affiliated Chenzhou Hospital (the First People's Hospital of Chenzhou), Southern Medical University, Chenzhou 423000, China; Translational Medicine Research Center, Medical Innovation Research Division and Fourth Medical Center of the Chinese PLA General Hospital, Beijing 100853, China
| | - Ren-Qi Yao
- Translational Medicine Research Center, Medical Innovation Research Division and Fourth Medical Center of the Chinese PLA General Hospital, Beijing 100853, China; Department of General Surgery, the First Medical Center of the Chinese PLA General Hospital, Beijing 100853, China.
| | - Hua Ling
- Department of Critical Care Medicine, Affiliated Chenzhou Hospital (the First People's Hospital of Chenzhou), Southern Medical University, Chenzhou 423000, China
| | - Li-Yu Zheng
- Translational Medicine Research Center, Medical Innovation Research Division and Fourth Medical Center of the Chinese PLA General Hospital, Beijing 100853, China
| | - Qi Fan
- Translational Medicine Research Center, Medical Innovation Research Division and Fourth Medical Center of the Chinese PLA General Hospital, Beijing 100853, China
| | - Qiong Li
- Department of Critical Care Medicine, Affiliated Chenzhou Hospital (the First People's Hospital of Chenzhou), Southern Medical University, Chenzhou 423000, China
| | - Lu Wang
- Department of Critical Care Medicine, the First Medical Center of the Chinese PLA General Hospital, Beijing 100853, China
| | - Qi-Yuan Zhou
- Department of Emergency, the Second Hospital of Hebei Medical University, Shijiazhuang 050000, China
| | - Le-Min Wu
- Department of Critical Care Medicine, Affiliated Chenzhou Hospital (the First People's Hospital of Chenzhou), Southern Medical University, Chenzhou 423000, China
| | - Xin-Gui Dai
- Department of Critical Care Medicine, Affiliated Chenzhou Hospital (the First People's Hospital of Chenzhou), Southern Medical University, Chenzhou 423000, China.
| | - Yong-Ming Yao
- Translational Medicine Research Center, Medical Innovation Research Division and Fourth Medical Center of the Chinese PLA General Hospital, Beijing 100853, China.
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4
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Bajdzienko J, Bremm A. Mammalian pexophagy at a glance. J Cell Sci 2024; 137:jcs259775. [PMID: 38752931 PMCID: PMC11166455 DOI: 10.1242/jcs.259775] [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] [Indexed: 05/21/2024] Open
Abstract
Peroxisomes are highly plastic organelles that are involved in several metabolic processes, including fatty acid oxidation, ether lipid synthesis and redox homeostasis. Their abundance and activity are dynamically regulated in response to nutrient availability and cellular stress. Damaged or superfluous peroxisomes are removed mainly by pexophagy, the selective autophagy of peroxisomes induced by ubiquitylation of peroxisomal membrane proteins or ubiquitin-independent processes. Dysregulated pexophagy impairs peroxisome homeostasis and has been linked to the development of various human diseases. Despite many recent insights into mammalian pexophagy, our understanding of this process is still limited compared to our understanding of pexophagy in yeast. In this Cell Science at a Glance article and the accompanying poster, we summarize current knowledge on the control of mammalian pexophagy and highlight which aspects require further attention. We also discuss the role of ubiquitylation in pexophagy and describe the ubiquitin machinery involved in regulating signals for the recruitment of phagophores to peroxisomes.
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Affiliation(s)
- Justyna Bajdzienko
- Goethe University Frankfurt,Medical Faculty,Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Anja Bremm
- Goethe University Frankfurt,Medical Faculty,Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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5
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Francisco T, Pedrosa AG, Rodrigues TA, Abalkhail T, Li H, Ferreira MJ, van der Heden van Noort GJ, Fransen M, Hettema EH, Azevedo JE. Noncanonical and reversible cysteine ubiquitination prevents the overubiquitination of PEX5 at the peroxisomal membrane. PLoS Biol 2024; 22:e3002567. [PMID: 38470934 PMCID: PMC10959387 DOI: 10.1371/journal.pbio.3002567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 03/22/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
PEX5, the peroxisomal protein shuttling receptor, binds newly synthesized proteins in the cytosol and transports them to the organelle. During its stay at the peroxisomal protein translocon, PEX5 is monoubiquitinated at its cysteine 11 residue, a mandatory modification for its subsequent ATP-dependent extraction back into the cytosol. The reason why a cysteine and not a lysine residue is the ubiquitin acceptor is unknown. Using an established rat liver-based cell-free in vitro system, we found that, in contrast to wild-type PEX5, a PEX5 protein possessing a lysine at position 11 is polyubiquitinated at the peroxisomal membrane, a modification that negatively interferes with the extraction process. Wild-type PEX5 cannot retain a polyubiquitin chain because ubiquitination at cysteine 11 is a reversible reaction, with the E2-mediated deubiquitination step presenting faster kinetics than PEX5 polyubiquitination. We propose that the reversible nonconventional ubiquitination of PEX5 ensures that neither the peroxisomal protein translocon becomes obstructed with polyubiquitinated PEX5 nor is PEX5 targeted for proteasomal degradation.
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Affiliation(s)
- Tânia Francisco
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Ana G. Pedrosa
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Tony A. Rodrigues
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Tarad Abalkhail
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Hongli Li
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Maria J. Ferreira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | | | - Marc Fransen
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Ewald H. Hettema
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Jorge E. Azevedo
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
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6
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Jin S, Li Y, Xia T, Liu Y, Zhang S, Hu H, Chang Q, Yan M. Mechanisms and therapeutic implications of selective autophagy in nonalcoholic fatty liver disease. J Adv Res 2024:S2090-1232(24)00041-9. [PMID: 38295876 DOI: 10.1016/j.jare.2024.01.027] [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: 12/03/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Nonalcoholic fatty liver disease (NAFLD) has become the most common chronic liver disease worldwide, whereas there is no approved drug therapy due to its complexity. Studies are emerging to discuss the role of selective autophagy in the pathogenesis of NAFLD, because the specificity among the features of selective autophagy makes it a crucial process in mitigating hepatocyte damage caused by aberrant accumulation of dysfunctional organelles, for which no other pathway can compensate. AIM OF REVIEW This review aims to summarize the types, functions, and dynamics of selective autophagy that are of particular importance in the initiation and progression of NAFLD. And on this basis, the review outlines the therapeutic strategies against NAFLD, in particular the medications and potential natural products that can modulate selective autophagy in the pathogenesis of this disease. KEY SCIENTIFIC CONCEPTS OF REVIEW The critical roles of lipophagy and mitophagy in the pathogenesis of NAFLD are well established, while reticulophagy and pexophagy are still being identified in this disease due to the insufficient understanding of their molecular details. As gradual blockage of autophagic flux reveals the complexity of NAFLD, studies unraveling the underlying mechanisms have made it possible to successfully treat NAFLD with multiple pharmacological compounds that target associated pathways. Overall, it is convinced that the continued research into selective autophagy occurring in NAFLD will further enhance the understanding of the pathogenesis and uncover novel therapeutic targets.
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Affiliation(s)
- Suwei Jin
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, China
| | - Yujia Li
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Tianji Xia
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, China
| | - Yongguang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, China
| | - Shanshan Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, China
| | - Hongbo Hu
- College of Food Science and Nutritional Engineering, China Agricultural University, China.
| | - Qi Chang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, China.
| | - Mingzhu Yan
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, China.
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7
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Liu J, Wu Y, Meng S, Xu P, Li S, Li Y, Hu X, Ouyang L, Wang G. Selective autophagy in cancer: mechanisms, therapeutic implications, and future perspectives. Mol Cancer 2024; 23:22. [PMID: 38262996 PMCID: PMC10807193 DOI: 10.1186/s12943-024-01934-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/05/2024] [Indexed: 01/25/2024] Open
Abstract
Eukaryotic cells engage in autophagy, an internal process of self-degradation through lysosomes. Autophagy can be classified as selective or non-selective depending on the way it chooses to degrade substrates. During the process of selective autophagy, damaged and/or redundant organelles like mitochondria, peroxisomes, ribosomes, endoplasmic reticulum (ER), lysosomes, nuclei, proteasomes, and lipid droplets are selectively recycled. Specific cargo is delivered to autophagosomes by specific receptors, isolated and engulfed. Selective autophagy dysfunction is closely linked with cancers, neurodegenerative diseases, metabolic disorders, heart failure, etc. Through reviewing latest research, this review summarized molecular markers and important signaling pathways for selective autophagy, and its significant role in cancers. Moreover, we conducted a comprehensive analysis of small-molecule compounds targeting selective autophagy for their potential application in anti-tumor therapy, elucidating the underlying mechanisms involved. This review aims to supply important scientific references and development directions for the biological mechanisms and drug discovery of anti-tumor targeting selective autophagy in the future.
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Affiliation(s)
- Jiaxi Liu
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Yongya Wu
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Sha Meng
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Ping Xu
- Emergency Department, Zigong Fourth People's Hospital, Zigong, 643000, China
| | - Shutong Li
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Yong Li
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Xiuying Hu
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China.
| | - Liang Ouyang
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China.
| | - Guan Wang
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China.
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8
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Kim YH, Park NY, Jo DS, Bae JE, Kim JB, Park K, Jeong K, Kim P, Yeom E, Cho DH. Inhibition of VHL by VH298 Accelerates Pexophagy by Activation of HIF-1α in HeLa Cells. Molecules 2024; 29:482. [PMID: 38257395 PMCID: PMC10819186 DOI: 10.3390/molecules29020482] [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: 12/15/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
Autophagy is a pivotal biological process responsible for maintaining the homeostasis of intracellular organelles. Yet the molecular intricacies of peroxisomal autophagy (pexophagy) remain largely elusive. From a ubiquitin-related chemical library for screening, we identified several inhibitors of the Von Hippel-Lindau (VHL) E3 ligase, including VH298, thereby serving as potent inducers of pexophagy. In this study, we observed that VH298 stimulates peroxisomal degradation by ATG5 dependently and escalates the ubiquitination of the peroxisomal membrane protein ABCD3. Interestingly, the ablation of NBR1 is similar to the curtailed peroxisomal degradation in VH298-treated cells. We also found that the pexophagy induced by VH298 is impeded upon the suppression of gene expression by the translation inhibitor cycloheximide. Beyond VHL inhibition, we discovered that roxadustat, a direct inhibitor of HIF-α prolyl hydroxylase, is also a potent inducer of pexophagy. Furthermore, we found that VH298-mediated pexophagy is blocked by silencing HIF-1α. In conclusion, our findings suggest that VH298 promotes pexophagy by modulating VHL-mediated HIF-α transcriptional activity.
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Affiliation(s)
- Yong Hwan Kim
- School of Life Sciences, BK21 FOUR KNU Creative Bio Research Group, Kyungpook National University, Daegu 41566, Republic of Korea; (Y.H.K.)
| | - Na Yeon Park
- School of Life Sciences, BK21 FOUR KNU Creative Bio Research Group, Kyungpook National University, Daegu 41566, Republic of Korea; (Y.H.K.)
| | - Doo Sin Jo
- ORGASIS Corp., Suwon 16229, Republic of Korea
| | - Ji-Eun Bae
- KNU LAMP Research Center, KNU Institute of Basic Sciences, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Joon Bum Kim
- School of Life Sciences, BK21 FOUR KNU Creative Bio Research Group, Kyungpook National University, Daegu 41566, Republic of Korea; (Y.H.K.)
| | - Kyuhee Park
- Bio Industry Department, Gyeonggido Business & Science Accelerator, Suwon 16229, Republic of Korea
| | - Kwiwan Jeong
- Bio Industry Department, Gyeonggido Business & Science Accelerator, Suwon 16229, Republic of Korea
| | - Pansoo Kim
- ORGASIS Corp., Suwon 16229, Republic of Korea
| | - Eunbyul Yeom
- School of Life Sciences, BK21 FOUR KNU Creative Bio Research Group, Kyungpook National University, Daegu 41566, Republic of Korea; (Y.H.K.)
- KNU LAMP Research Center, KNU Institute of Basic Sciences, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Dong-Hyung Cho
- School of Life Sciences, BK21 FOUR KNU Creative Bio Research Group, Kyungpook National University, Daegu 41566, Republic of Korea; (Y.H.K.)
- ORGASIS Corp., Suwon 16229, Republic of Korea
- Organelle Institute, Kyungpook National University, Daegu 41566, Republic of Korea
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9
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Germain K, So RWL, DiGiovanni LF, Watts JC, Bandsma RHJ, Kim PK. Upregulated pexophagy limits the capacity of selective autophagy. Nat Commun 2024; 15:375. [PMID: 38195640 PMCID: PMC10776696 DOI: 10.1038/s41467-023-44005-4] [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: 05/23/2023] [Accepted: 11/27/2023] [Indexed: 01/11/2024] Open
Abstract
Selective autophagy is an essential process to maintain cellular homeostasis through the constant recycling of damaged or superfluous components. Over a dozen selective autophagy pathways mediate the degradation of diverse cellular substrates, but whether these pathways can influence one another remains unknown. We address this question using pexophagy, the autophagic degradation of peroxisomes, as a model. We show in cells that upregulated pexophagy impairs the selective autophagy of both mitochondria and protein aggregates by exhausting the autophagy initiation factor, ULK1. We confirm this finding in cell models of the pexophagy-mediated form of Zellweger Spectrum Disorder, a disease characterized by peroxisome dysfunction. Further, we extend the generalizability of limited selective autophagy by determining that increased protein aggregate degradation reciprocally reduces pexophagy using cell models of Parkinson's Disease and Huntington's Disease. Our findings suggest that the degradative capacity of selective autophagy can become limited by an increase in one substrate.
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Affiliation(s)
- Kyla Germain
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Raphaella W L So
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, Toronto, ON, M5T 0S8, Canada
| | - Laura F DiGiovanni
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Joel C Watts
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, Toronto, ON, M5T 0S8, Canada
| | - Robert H J Bandsma
- Translational Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1A8, Canada.
| | - Peter K Kim
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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10
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Rüttermann M, Koci M, Lill P, Geladas ED, Kaschani F, Klink BU, Erdmann R, Gatsogiannis C. Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a substrate. Nat Commun 2023; 14:5942. [PMID: 37741838 PMCID: PMC10518020 DOI: 10.1038/s41467-023-41640-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 09/12/2023] [Indexed: 09/25/2023] Open
Abstract
The double-ring AAA+ ATPase Pex1/Pex6 is required for peroxisomal receptor recycling and is essential for peroxisome formation. Pex1/Pex6 mutations cause severe peroxisome associated developmental disorders. Despite its pathophysiological importance, mechanistic details of the heterohexamer are not yet available. Here, we report cryoEM structures of Pex1/Pex6 from Saccharomyces cerevisiae, with an endogenous protein substrate trapped in the central pore of the catalytically active second ring (D2). Pairs of Pex1/Pex6(D2) subdomains engage the substrate via a staircase of pore-1 loops with distinct properties. The first ring (D1) is catalytically inactive but undergoes significant conformational changes resulting in alternate widening and narrowing of its pore. These events are fueled by ATP hydrolysis in the D2 ring and disengagement of a "twin-seam" Pex1/Pex6(D2) heterodimer from the staircase. Mechanical forces are propagated in a unique manner along Pex1/Pex6 interfaces that are not available in homo-oligomeric AAA-ATPases. Our structural analysis reveals the mechanisms of how Pex1 and Pex6 coordinate to achieve substrate translocation.
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Affiliation(s)
- Maximilian Rüttermann
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany
| | - Michelle Koci
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Pascal Lill
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Ermis Dionysios Geladas
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany
| | - Farnusch Kaschani
- Analytics Core Facility Essen, Center of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Björn Udo Klink
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany
| | - Ralf Erdmann
- Institute for Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Christos Gatsogiannis
- Institute for Medical Physics and Biophysics, University Münster, Münster, Germany.
- Center for Soft Nanoscience (SoN), University Münster, Münster, Germany.
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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11
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Yamashita A, Ignatenko O, Nguyen M, Lambert R, Watt K, Daneault C, Robillard-Frayne I, Topisirovic I, Rosiers CD, McBride HM. Depletion of LONP2 unmasks differential requirements for peroxisomal function between cell types and in cholesterol metabolism. Biol Direct 2023; 18:60. [PMID: 37736739 PMCID: PMC10515011 DOI: 10.1186/s13062-023-00416-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
Peroxisomes play a central role in tuning metabolic and signaling programs in a tissue- and cell-type-specific manner. However, the mechanisms by which the status of peroxisomes is communicated and integrated into cellular signaling pathways are not yet understood. Herein, we report the cellular responses to peroxisomal proteotoxic stress upon silencing the peroxisomal protease/chaperone LONP2. Depletion of LONP2 triggered the accumulation of its substrate TYSND1 protease, while the overall expression of peroxisomal proteins, as well as TYSND1-dependent ACOX1 processing appeared normal, reflecting early stages of peroxisomal proteotoxic stress. Consequently, the alteration of peroxisome size and numbers, and luminal protein import failure was coupled with induction of cell-specific cellular stress responses. Specific to COS-7 cells was a strong activation of the integrated stress response (ISR) and upregulation of ribosomal biogenesis gene expression levels. Common changes between COS-7 and U2OS cell lines included repression of the retinoic acid signaling pathway and upregulation of sphingolipids. Cholesterol accumulated in the endomembrane compartments in both cell lines, consistent with evidence that peroxisomes are required for cholesterol flux out of late endosomes. These unexpected consequences of peroxisomal stress provide an important insight into our understanding of the tissue-specific responses seen in peroxisomal disorders.
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Affiliation(s)
- Akihiro Yamashita
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada
| | - Olesia Ignatenko
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Mai Nguyen
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Raphaëlle Lambert
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Kathleen Watt
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | | | | | - Ivan Topisirovic
- Lady Davis Institute, McGill University, Montreal, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, QC, Canada
- Department of Biochemistry, McGill University, Montréal, QC, Canada
- Division of Experimental Medicine, McGill University, Montréal, QC, Canada
| | | | - Heidi M McBride
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada.
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12
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Cen X, Li Z, Chen X. Ubiquitination in the regulation of autophagy. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1348-1357. [PMID: 37587758 PMCID: PMC10520486 DOI: 10.3724/abbs.2023149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/01/2023] [Indexed: 08/18/2023] Open
Abstract
Autophagy, an efficient and effective approach to clear rapidly damaged organelles, macromolecules, and other harmful cellular components, enables the recycling of nutrient materials and supply of nutrients to maintain cellular homeostasis. Ubiquitination plays an important regulatory role in autophagy. This paper summarizes the most recent progress in ubiquitin modification in various stages of autophagy, including initiation, elongation, and termination. Moreover, this paper shows that ubiquitination is an important way through which selective autophagy achieves substrate specificity. Furthermore, we note the distinction between monoubiquitination and polyubiquitination in the regulation of autophagy. Compared with monoubiquitination, polyubiquitination is a more common strategy to regulate the activity of the autophagy molecular machinery. In addition, the role of ubiquitination in the closure and fusion of autophagosomes warrants further study. This article not only clarifies the regulatory mechanism of autophagy but also contributes to a deeper understanding of the importance of ubiquitination modification.
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Affiliation(s)
- Xueyan Cen
- Hubei Key laboratory of Edible Wild Plants Conservation & UtilizationHubei Engineering Research Center of Special Wild Vegetables Breeding and Comprehensive Utilization TechnologySchool of Life ScienceHubei Normal UniversityHuangshi435002China
| | - Ziling Li
- Hubei Key laboratory of Edible Wild Plants Conservation & UtilizationHubei Engineering Research Center of Special Wild Vegetables Breeding and Comprehensive Utilization TechnologySchool of Life ScienceHubei Normal UniversityHuangshi435002China
| | - Xinpeng Chen
- Hubei Key laboratory of Edible Wild Plants Conservation & UtilizationHubei Engineering Research Center of Special Wild Vegetables Breeding and Comprehensive Utilization TechnologySchool of Life ScienceHubei Normal UniversityHuangshi435002China
- National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
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13
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Ning B, Hang S, Zhang W, Mao C, Li D. An update on the bridging factors connecting autophagy and Nrf2 antioxidant pathway. Front Cell Dev Biol 2023; 11:1232241. [PMID: 37621776 PMCID: PMC10445655 DOI: 10.3389/fcell.2023.1232241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Macroautophagy/autophagy is a lysosome-dependent catabolic pathway for the degradation of intracellular proteins and organelles. Autophagy dysfunction is related to many diseases, including lysosomal storage diseases, cancer, neurodegenerative diseases, cardiomyopathy, and chronic metabolic diseases, in which increased reactive oxygen species (ROS) levels are also observed. ROS can randomly oxidize proteins, lipids, and DNA, causing oxidative stress and damage. Cells have developed various antioxidant pathways to reduce excessive ROS and maintain redox homeostasis. Treatment targeting only one aspect of diseases with autophagy dysfunction and oxidative stress shows very limited effects. Herein, identifying the bridging factors that can regulate both autophagy and antioxidant pathways is beneficial for dual-target therapies. This review intends to provide insights into the current identified bridging factors that connect autophagy and Nrf2 antioxidant pathway, as well as their tight interconnection with each other. These factors could be potential dual-purpose targets for the treatment of diseases implicated in both autophagy dysfunction and oxidative stress.
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Affiliation(s)
- Baike Ning
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Shuqi Hang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Wenhe Zhang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Caiwen Mao
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Dan Li
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
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14
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Wu CC, Chen WC, Hsiao WP, Huang KF, Liao YS, Lin HB, Wu YJ, Kao CH, Chen SL. Reciprocal Regulation of Peroxisome Biogenesis and Myogenic Factors Is Critical for Myogenesis. Int J Mol Sci 2023; 24:12262. [PMID: 37569637 PMCID: PMC10419124 DOI: 10.3390/ijms241512262] [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: 06/26/2023] [Revised: 07/25/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Mitochondria (MITO) and peroxisomes (PEXO) are the major organelles involved in the oxidative metabolism of cells, but detailed examination of their dynamics and functional adaptations during skeletal muscle (SKM) development (myogenesis) is still lacking. In this study, we found that during myogenesis, MITO DNA, ROS level, and redox ratio increased in myotubes, but the membrane potential (Δψm) and ATP content reduced, implying that the MITO efficiency might reduce during myogenesis. The PEXO number and density both increased during myogenesis, which probably resulted from the accumulation and increased biogenesis of PEXO. The expression of PEXO biogenesis factors was induced during myogenesis in vitro and in utero, and their promoters were also activated by MyoD. Knockdown of the biogenesis factors Pex3 repressed not only the PEXO density and functions but also the levels of MITO genes and functions, suggesting a close coupling between PEXO biogenesis and MITO functions. Surprisingly, Pex3 knockdown by the CRISPRi system repressed myogenic differentiation, indicating critical involvement of PEXO biogenesis in myogenesis. Taken together, these observations suggest that the dynamics and functions of both MITO and PEXO are coupled with each other and with the metabolic changes that occur during myogenesis, and these metabolic couplings are critical to myogenesis.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Shen-Liang Chen
- Department of Life Sciences, College of Health Sciences and Technology, National Central University, Taoyuan 320317, Taiwan; (C.-C.W.); (W.-C.C.); (W.-P.H.); (K.-F.H.); (Y.-S.L.); (H.-B.L.); (Y.-J.W.); (C.-H.K.)
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15
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Chi L, Lee D, Leung S, Hu G, Wen B, Delgado-Olguin P, Vissa M, Li R, Brumell JH, Kim PK, Bandsma RHJ. Loss of functional peroxisomes leads to increased mitochondrial biogenesis and reduced autophagy that preserve mitochondrial function. Cell Mol Life Sci 2023; 80:183. [PMID: 37338571 DOI: 10.1007/s00018-023-04827-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 06/21/2023]
Abstract
Peroxisomes are essential for mitochondrial health, as the absence of peroxisomes leads to altered mitochondria. However, it is unclear whether the changes in mitochondria are a function of preserving cellular function or a response to cellular damage caused by the absence of peroxisomes. To address this, we developed conditional hepatocyte-specific Pex16 deficient (Pex16 KO) mice that develop peroxisome loss and subjected them to a low-protein diet to induce metabolic stress. Loss of PEX16 in hepatocytes led to increased biogenesis of small mitochondria and reduced autophagy flux but with preserved capacity for respiration and ATP capacity. Metabolic stress induced by low protein feeding led to mitochondrial dysfunction in Pex16 KO mice and impaired biogenesis. Activation of PPARα partially corrected these mitochondrial disturbances, despite the absence of peroxisomes. The findings of this study demonstrate that the absence of peroxisomes in hepatocytes results in a concerted effort to preserve mitochondrial function, including increased mitochondrial biogenesis, altered morphology, and modified autophagy activity. Our study underscores the relationship between peroxisomes and mitochondria in regulating the hepatic metabolic responses to nutritional stressors.
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Affiliation(s)
- Lijun Chi
- Translational Medicine Program, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
| | - Dorothy Lee
- Translational Medicine Program, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
- Department of Physiology, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Sharon Leung
- Cell Biology Program, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
| | - Guanlan Hu
- Translational Medicine Program, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
- Department of Nutritional Sciences, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Bijun Wen
- Translational Medicine Program, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
- Department of Nutritional Sciences, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Paul Delgado-Olguin
- Translational Medicine Program, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Heart and Stroke Richard Lewar Centre of Excellence, Toronto, ON, M5S 3H2, Canada
| | - Miluska Vissa
- Cell Biology Program, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
| | - Ren Li
- Cell Biology Program, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
| | - John H Brumell
- Cell Biology Program, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Peter K Kim
- Cell Biology Program, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON, M5G 0A4, Canada.
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A1, Canada.
| | - Robert H J Bandsma
- Translational Medicine Program, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, Toronto, ON, M5G 0A4, Canada.
- Department of Nutritional Sciences, University of Toronto, Toronto, ON, M5S 1A1, Canada.
- Centre for Global Child Health, The Hospital of Sick Children, Toronto, ON, M5G 0A4, Canada.
- Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
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16
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Ke PY. Crosstalk between Autophagy and RLR Signaling. Cells 2023; 12:cells12060956. [PMID: 36980296 PMCID: PMC10047499 DOI: 10.3390/cells12060956] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Autophagy plays a homeostatic role in regulating cellular metabolism by degrading unwanted intracellular materials and acts as a host defense mechanism by eliminating infecting pathogens, such as viruses. Upon viral infection, host cells often activate retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) signaling to induce the transcription of type I interferons, thus establishing the first line of the innate antiviral response. In recent years, numerous studies have shown that virus-mediated autophagy activation may benefit viral replication through different actions on host cellular processes, including the modulation of RLR-mediated innate immunity. Here, an overview of the functional molecules and regulatory mechanism of the RLR antiviral immune response as well as autophagy is presented. Moreover, a summary of the current knowledge on the biological role of autophagy in regulating RLR antiviral signaling is provided. The molecular mechanisms underlying the crosstalk between autophagy and RLR innate immunity are also discussed.
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Affiliation(s)
- Po-Yuan Ke
- Department of Biochemistry & Molecular Biology, Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan
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17
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Chen S, Diao J, Yue Z, Wei R. Identification and validation of ferroptosis-related genes and immune cell infiltration in thyroid associated ophthalmopathy. Front Genet 2023; 14:1118391. [PMID: 37021001 PMCID: PMC10067720 DOI: 10.3389/fgene.2023.1118391] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/13/2023] [Indexed: 03/22/2023] Open
Abstract
Thyroid associated ophthalmopathy (TAO) is an orbital autoimmune inflammatory disease that is commonly associated with thyroid dysfunction. Although the etiology of TAO is unclear, ROS accumulation and oxidative stress have been closely linked to the pathogenesis of TAO. Ferroptosis is an iron-dependent programmed cell death characterized by intracellular labile iron levels, excessive accumulation of reactive oxygen species (ROS) and lipid peroxidation. Currently, there are few reports regarding the role of ferroptosis in TAO. This article aimed to identify ferroptosis-related genes (FRGs) with diagnostic and therapeutic potential in TAO and explore their relationship with immune cells and lncRNAs. GSE58331 was downloaded from Gene Expression Omnibus (GEO) database. A total of 162 DEGs were identified between 27 TAO samples and 22 health samples from GSE58331, among which six FRGs (CYBB, CTSB, SLC38A1, TLR4, PEX3, and ABCC1) were obtained. The AUC of SLC38A1, TLR4, PEX3 in lacrimal gland tissues was greater than 80 which suggested high diagnostic value in TAO. The result of immune cell infiltrate analysis indicated increased infiltration of monocytes (p < 0.001), macrophages M0(p = 0.039), mast cells activated (p = 0.008), and neutrophils (p = 0.045) in orbital tissues from TAO patients. Meanwhile, mast cells resting (p = 0.043) and macrophages M2 (p = 0.02) showed reduced infiltration in TAO samples. There were no gender differences in immune cell infiltration in the TAO patients. Two differentially expressed lncRNAs, LINC01140 and ZFHX4-AS1, in TAO groups were identified as ferroptosis-related lncRNAs. CYBB-LINC01140-TLR4, CYBB- LINC01140- SLC38A1, TLR4- LINC01140- SLC38A1, and CTSB- ZFHX4-AS1- CYBB may be potential RNA regulatory pathways in TAO. Targeted drugs and transcription factors for differential expressed FRGs were also screened out in our study. In vitro, experiments revealed that CTSB, PEX3, ABCC1 and ZFHX4-AS1(lncRNA) were differentially expressed in orbital fibroblasts (OFs) between TAO groups and healthy controls at the transcriptional level.
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18
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Li H, Lismont C, Costa CF, Hussein MAF, Baes M, Fransen M. Enhanced Levels of Peroxisome-Derived H2O2 Do Not Induce Pexophagy but Impair Autophagic Flux in HEK-293 and HeLa Cells. Antioxidants (Basel) 2023; 12:antiox12030613. [PMID: 36978861 PMCID: PMC10045779 DOI: 10.3390/antiox12030613] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
Peroxisomes are functionally specialized organelles that harbor multiple hydrogen peroxide (H2O2)-producing and -degrading enzymes. Given that this oxidant functions as a major redox signaling agent, peroxisomes have the intrinsic ability to mediate and modulate H2O2-driven processes, including autophagy. However, it remains unclear whether changes in peroxisomal H2O2 (po-H2O2) emission impact the autophagic process and to which extent peroxisomes with a disturbed H2O2 metabolism are selectively eliminated through a process called “pexophagy”. To address these issues, we generated and validated HEK-293 and HeLa pexophagy reporter cell lines in which the production of po-H2O2 can be modulated. We demonstrate that (i) po-H2O2 can oxidatively modify multiple selective autophagy receptors and core autophagy proteins, (ii) neither modest nor robust levels of po-H2O2 emission act as a prime determinant of pexophagy, and (iii) high levels of po-H2O2 impair autophagic flux by oxidative inhibition of enzymes involved in LC3II formation. Unexpectedly, our analyses also revealed that the autophagy receptor optineurin can be recruited to peroxisomes, thereby triggering pexophagy. In summary, these findings lend support to the idea that, during cellular and organismal aging, peroxisomes with enhanced H2O2 release can escape pexophagy and downregulate autophagic activity, thereby perpetuating the accumulation of damaged and toxic cellular debris.
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Affiliation(s)
- Hongli Li
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Celien Lismont
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Cláudio F. Costa
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Mohamed A. F. Hussein
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Department of Biochemistry, Faculty of Pharmacy, Assiut University, Asyut 71515, Egypt
| | - Myriam Baes
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Marc Fransen
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Correspondence: ; Tel.: +32-16-330114
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19
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Horcas-Nieto JM, Versloot CJ, Langelaar-Makkinje M, Gerding A, Blokzijl T, Koster MH, Baanstra M, Martini IA, Coppes RP, Bourdon C, van Ijzendoorn SCD, Kim P, Bandsma RHJ, Bakker BM. Organoids as a model to study intestinal and liver dysfunction in severe malnutrition. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166635. [PMID: 36581145 DOI: 10.1016/j.bbadis.2022.166635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/02/2022] [Accepted: 12/20/2022] [Indexed: 12/27/2022]
Affiliation(s)
- José M Horcas-Nieto
- Laboratory of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Christian J Versloot
- Laboratory of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Miriam Langelaar-Makkinje
- Laboratory of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Albert Gerding
- Laboratory of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, the Netherlands; Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tjasso Blokzijl
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mirjam H Koster
- Laboratory of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Mirjam Baanstra
- Department of Biomedical Sciences of Cell & Systems, Section Molecular Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ingrid A Martini
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Robert P Coppes
- Department of Biomedical Sciences of Cell & Systems, Section Molecular Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Céline Bourdon
- Translational Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sven C D van Ijzendoorn
- Department of Biomedical Sciences of Cell & Systems, Section Molecular Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Peter Kim
- Translational Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Robert H J Bandsma
- Laboratory of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, the Netherlands; Translational Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, Canada; Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Division of Gastroenterology, Hepatology, and Nutrition, The Hospital for Sick Children, Toronto, ON, Canada.
| | - Barbara M Bakker
- Laboratory of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, University of Groningen, University Medical Center Groningen, the Netherlands.
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20
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Vargas JNS, Hamasaki M, Kawabata T, Youle RJ, Yoshimori T. The mechanisms and roles of selective autophagy in mammals. Nat Rev Mol Cell Biol 2023; 24:167-185. [PMID: 36302887 DOI: 10.1038/s41580-022-00542-2] [Citation(s) in RCA: 228] [Impact Index Per Article: 228.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2022] [Indexed: 11/09/2022]
Abstract
Autophagy is a process that targets various intracellular elements for degradation. Autophagy can be non-selective - associated with the indiscriminate engulfment of cytosolic components - occurring in response to nutrient starvation and is commonly referred to as bulk autophagy. By contrast, selective autophagy degrades specific targets, such as damaged organelles (mitophagy, lysophagy, ER-phagy, ribophagy), aggregated proteins (aggrephagy) or invading bacteria (xenophagy), thereby being importantly involved in cellular quality control. Hence, not surprisingly, aberrant selective autophagy has been associated with various human pathologies, prominently including neurodegeneration and infection. In recent years, considerable progress has been made in understanding mechanisms governing selective cargo engulfment in mammals, including the identification of ubiquitin-dependent selective autophagy receptors such as p62, NBR1, OPTN and NDP52, which can bind cargo and ubiquitin simultaneously to initiate pathways leading to autophagy initiation and membrane recruitment. This progress opens the prospects for enhancing selective autophagy pathways to boost cellular quality control capabilities and alleviate pathology.
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Affiliation(s)
- Jose Norberto S Vargas
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, UK
- UK Dementia Research Institute, University College London, London, UK
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Maho Hamasaki
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan.
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
| | - Tsuyoshi Kawabata
- Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Richard J Youle
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan.
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
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21
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Akhter D, Zhang Y, Hu J, Pan R. Protein ubiquitination in plant peroxisomes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:371-380. [PMID: 35975710 DOI: 10.1111/jipb.13346] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Protein ubiquitination regulates diverse cellular processes in eukaryotic organisms, from growth and development to stress response. Proteins subjected to ubiquitination can be found in virtually all subcellular locations and organelles, including peroxisomes, single-membrane and highly dynamic organelles ubiquitous in eukaryotes. Peroxisomes contain metabolic functions essential to plants and animals such as lipid catabolism, detoxification of reactive oxygen species (ROS), biosynthesis of vital hormones and cofactors, and photorespiration. Plant peroxisomes possess a complex proteome with functions varying among different tissue types and developmental stages, and during plant response to distinct environmental cues. However, how these diverse functions are regulated at the post-translational level is poorly understood, especially in plants. In this review, we summarized current knowledge of the involvement of protein ubiquitination in peroxisome protein import, remodeling, pexophagy, and metabolism, focusing on plants, and referencing discoveries from other eukaryotic systems when relevant. Based on previous ubiquitinomics studies, we compiled a list of 56 ubiquitinated Arabidopsis peroxisomal proteins whose functions are associated with all the major plant peroxisomal metabolic pathways. This discovery suggests a broad impact of protein ubiquitination on plant peroxisome functions, therefore substantiating the need to investigate this significant regulatory mechanism in peroxisomes at more depths.
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Affiliation(s)
- Delara Akhter
- State Key Laboratory of Rice Biology, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058/311200, China
- Zhejiang Laboratory, Hangzhou, 311121, China
- Department of Genetics and Plant Breeding, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Yuchan Zhang
- State Key Laboratory of Rice Biology, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058/311200, China
- Zhejiang Laboratory, Hangzhou, 311121, China
| | - Jianping Hu
- Department of Energy Plant Research Laboratory and Plant Biology Department, Michigan State University, East Lansing,, Michigan, USA
- Department of Plant Biology, Michigan State University, East Lansing,, Michigan, USA
| | - Ronghui Pan
- State Key Laboratory of Rice Biology, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058/311200, China
- Zhejiang Laboratory, Hangzhou, 311121, China
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22
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Demers ND, Riccio V, Jo DS, Bhandari S, Law KB, Liao W, Kim C, McQuibban GA, Choe SK, Cho DH, Kim PK. PEX13 prevents pexophagy by regulating ubiquitinated PEX5 and peroxisomal ROS. Autophagy 2023:1-22. [PMID: 36541703 DOI: 10.1080/15548627.2022.2160566] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Peroxisomes are rapidly degraded during amino acid and oxygen deprivation by a type of selective autophagy called pexophagy. However, how damaged peroxisomes are detected and removed from the cell is poorly understood. Recent studies suggest that the peroxisomal matrix protein import machinery may serve double duty as a quality control machinery, where they are directly involved in activating pexophagy. Here, we explored whether any matrix import factors are required to prevent pexophagy, such that their loss designates peroxisomes for degradation. Using gene editing and quantitative fluorescence microscopy on culture cells and a zebrafish model system, we found that PEX13, a component of the peroxisomal matrix import system, is required to prevent the degradation of otherwise healthy peroxisomes. The loss of PEX13 caused an accumulation of ubiquitinated PEX5 on peroxisomes and an increase in peroxisome-dependent reactive oxygen species that coalesce to induce pexophagy. We also found that PEX13 protein level is downregulated to aid in the induction of pexophagy during amino acid starvation. Together, our study points to PEX13 as a novel pexophagy regulator that is modulated to maintain peroxisome homeostasis.Abbreviations: AAA ATPases: ATPases associated with diverse cellular activities; ABCD3: ATP binding cassette subfamily D member; 3ACOX1: acyl-CoA oxidase; 1ACTA1: actin alpha 1, skeletal muscle; ACTB: actin beta; ATG5: autophagy related 5; ATG7: autophagy related 7; ATG12: autophagy related 12; ATG16L1: autophagy related 16 like 1; CAT: catalase; CQ: chloroquine; Dpf: days post fertilization: FBS: fetal bovine serum; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; H2O2: hydrogen peroxide; HA - human influenza hemagglutinin; HBSS: Hanks' Balanced Salt Solution; HCQ; hydroxychloroquine; KANL: lysine alanine asparagine leucine; KO: knockout; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; MEF: mouse embryonic fibroblast; MTOR: mechanistic target of rapamycin kinase; MTORC1: mechanistic target of rapamycin kinase complex 1; MTORC2: mechanistic target of rapamycin kinase complex 2; MYC: MYC proto-oncogene, bHLH transcription factor; MZ: maternal and zygotic; NAC: N-acetyl cysteine; NBR1 - NBR1 autophagy cargo receptor; PBD: peroxisome biogenesis disorder; PBS: phosphate-buffered saline; PEX: peroxisomal biogenesis factor; PTS1: peroxisome targeting sequence 1; RFP: red fluorescent protein; ROS: reactive oxygen speciess; iRNA: short interfering RNA; SKL: serine lysine leucine; SLC25A17/PMP34: solute carrier family 25 member 17; Ub: ubiquitin; USP30: ubiquitin specific peptidase 30.
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Affiliation(s)
- Nicholas D Demers
- Cell Biology Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Victoria Riccio
- Cell Biology Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Doo Sin Jo
- School of Life Sciences, BK21 Four Knu Creative BioResearch Group Kyungpook National University, Republic of Korea
| | - Sushil Bhandari
- Department of Microbiology, Wonkwang University School of Medicine, Iksan, Republic of Korea
| | - Kelsey B Law
- Cell Biology Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Weifang Liao
- Department of Microbiology, Wonkwang University School of Medicine, Iksan, Republic of Korea
| | - Choy Kim
- Department of Microbiology, Wonkwang University School of Medicine, Iksan, Republic of Korea
| | - G Angus McQuibban
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Seong-Kyu Choe
- Department of Microbiology, Wonkwang University School of Medicine, Iksan, Republic of Korea
| | - Dong-Hyung Cho
- School of Life Sciences, BK21 Four Knu Creative BioResearch Group Kyungpook National University, Republic of Korea
| | - Peter K Kim
- Cell Biology Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada.,Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, South Korea
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23
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Wanders RJA, Baes M, Ribeiro D, Ferdinandusse S, Waterham HR. The physiological functions of human peroxisomes. Physiol Rev 2023; 103:957-1024. [PMID: 35951481 DOI: 10.1152/physrev.00051.2021] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Peroxisomes are subcellular organelles that play a central role in human physiology by catalyzing a range of unique metabolic functions. The importance of peroxisomes for human health is exemplified by the existence of a group of usually severe diseases caused by an impairment in one or more peroxisomal functions. Among others these include the Zellweger spectrum disorders, X-linked adrenoleukodystrophy, and Refsum disease. To fulfill their role in metabolism, peroxisomes require continued interaction with other subcellular organelles including lipid droplets, lysosomes, the endoplasmic reticulum, and mitochondria. In recent years it has become clear that the metabolic alliance between peroxisomes and other organelles requires the active participation of tethering proteins to bring the organelles physically closer together, thereby achieving efficient transfer of metabolites. This review intends to describe the current state of knowledge about the metabolic role of peroxisomes in humans, with particular emphasis on the metabolic partnership between peroxisomes and other organelles and the consequences of genetic defects in these processes. We also describe the biogenesis of peroxisomes and the consequences of the multiple genetic defects therein. In addition, we discuss the functional role of peroxisomes in different organs and tissues and include relevant information derived from model systems, notably peroxisomal mouse models. Finally, we pay particular attention to a hitherto underrated role of peroxisomes in viral infections.
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Affiliation(s)
- Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, Amsterdam, The Netherlands
| | - Myriam Baes
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Daniela Ribeiro
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, Amsterdam, The Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, Amsterdam, The Netherlands
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24
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Nagashima S, Ito N, Shiiba I, Shimura H, Yanagi S. Ubiquitin-mediated mitochondrial regulation by MITOL/MARCHF5 at a glance. J Biochem 2022; 173:1-11. [PMID: 36346121 DOI: 10.1093/jb/mvac092] [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: 07/30/2022] [Revised: 10/03/2022] [Accepted: 10/27/2022] [Indexed: 11/10/2022] Open
Abstract
Mitochondria are involved in various cellular processes, such as energy production, inflammatory responses and cell death. Mitochondrial dysfunction is associated with many age-related diseases, including neurological disorders and heart failure. Mitochondrial quality is strictly maintained by mitochondrial dynamics linked to an adequate supply of phospholipids and other substances from the endoplasmic reticulum (ER). The outer mitochondrial membrane-localized E3 ubiquitin ligase MITOL/MARCHF5 is responsible for mitochondrial quality control through the regulation of mitochondrial dynamics, formation of mitochondria-ER contacts and mitophagy. MITOL deficiency has been shown to impair mitochondrial function, cause an excessive inflammatory response and increase vulnerability to stress, resulting in the exacerbation of the disease. In this study, we overview the ubiquitin-mediated regulation of mitochondrial function by MITOL and the relationship between MITOL and diseases.
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Affiliation(s)
- Shun Nagashima
- Laboratory of Regenerative Medicine, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Naoki Ito
- Laboratory of Molecular Biochemistry, Department of Life Science, Faculty of Science, Gakushuin University, Toshima, Tokyo 171-8588, Japan
| | - Isshin Shiiba
- Laboratory of Molecular Biochemistry, Department of Life Science, Faculty of Science, Gakushuin University, Toshima, Tokyo 171-8588, Japan
| | - Hiroki Shimura
- Laboratory of Regenerative Medicine, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Shigeru Yanagi
- Laboratory of Molecular Biochemistry, Department of Life Science, Faculty of Science, Gakushuin University, Toshima, Tokyo 171-8588, Japan
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25
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Wilhelm LP, Zapata-Muñoz J, Villarejo-Zori B, Pellegrin S, Freire CM, Toye AM, Boya P, Ganley IG. BNIP3L/NIX regulates both mitophagy and pexophagy. EMBO J 2022; 41:e111115. [PMID: 36215693 PMCID: PMC9753467 DOI: 10.15252/embj.2022111115] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 01/15/2023] Open
Abstract
Mitochondria and peroxisomes are closely related metabolic organelles, both in terms of origin and in terms of function. Mitochondria and peroxisomes can also be turned over by autophagy, in processes termed mitophagy and pexophagy, respectively. However, despite their close relationship, it is not known if both organelles are turned over under similar conditions, and if so, how this might be coordinated molecularly. Here, we find that multiple selective autophagy pathways are activated upon iron chelation and show that mitophagy and pexophagy occur in a BNIP3L/NIX-dependent manner. We reveal that the outer mitochondrial membrane-anchored NIX protein, previously described as a mitophagy receptor, also independently localises to peroxisomes and drives pexophagy. We show this process happens in vivo, with mouse tissue that lacks NIX having a higher peroxisomal content. We further show that pexophagy is stimulated under the same physiological conditions that activate mitophagy, including cardiomyocyte and erythrocyte differentiation. Taken together, our work uncovers a dual role for NIX, not only in mitophagy but also in pexophagy, thus illustrating the interconnection between selective autophagy pathways.
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Affiliation(s)
- Léa P Wilhelm
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Juan Zapata-Muñoz
- Department of Cellular and Molecular Biology, Margarita Salas Center for Biological Research, CSIC, Madrid, Spain
| | - Beatriz Villarejo-Zori
- Department of Cellular and Molecular Biology, Margarita Salas Center for Biological Research, CSIC, Madrid, Spain
| | - Stephanie Pellegrin
- School of Biochemistry, Biomedical Sciences Building, University Walk, Bristol, UK.,National Institute for Health Research (NIHR) Blood and Transplant Research Unit in Red Blood Cell Products, University of Bristol, Bristol, UK
| | | | - Ashley M Toye
- School of Biochemistry, Biomedical Sciences Building, University Walk, Bristol, UK.,National Institute for Health Research (NIHR) Blood and Transplant Research Unit in Red Blood Cell Products, University of Bristol, Bristol, UK
| | - Patricia Boya
- Department of Cellular and Molecular Biology, Margarita Salas Center for Biological Research, CSIC, Madrid, Spain
| | - Ian G Ganley
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
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26
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Liang JR, Corn JE. A CRISPR view on autophagy. Trends Cell Biol 2022; 32:1008-1022. [PMID: 35581059 DOI: 10.1016/j.tcb.2022.04.006] [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: 02/23/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/21/2023]
Abstract
Autophagy is a fundamental pathway for the degradation of cytoplasmic content in response to pleiotropic extracellular and intracellular stimuli. Recent advances in the autophagy field have demonstrated that different organelles can also be specifically targeted for autophagy with broad implications on cellular and organismal health. This opens new dimensions in the autophagy field and more unanswered questions on the rationale and underlying mechanisms to degrade different organelles. Functional genomics via clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9-based screening has gained popularity in the autophagy field to understand the common and unique factors that are implicated in the signaling, recognition, and execution of different cargo-specific autophagies. We focus on recent applications of CRISPR-based screens in the autophagy field, their discoveries, and the future directions of autophagy screens.
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Affiliation(s)
- Jin Rui Liang
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093, Zürich, Switzerland; Medical Research Council, Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
| | - Jacob E Corn
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093, Zürich, Switzerland.
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27
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Inhibition of mTOR improves malnutrition induced hepatic metabolic dysfunction. Sci Rep 2022; 12:19948. [PMID: 36402829 PMCID: PMC9675758 DOI: 10.1038/s41598-022-24428-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 11/15/2022] [Indexed: 11/21/2022] Open
Abstract
Severe malnutrition accounts for half-a-million deaths annually in children under the age of five. Despite improved WHO guidelines, inpatient mortality remains high and is associated with metabolic dysfunction. Previous studies suggest a correlation between hepatic metabolic dysfunction and impaired autophagy. We aimed to determine the role of mTORC1 inhibition in a murine model of malnutrition-induced hepatic dysfunction. Wild type weanling C57/B6 mice were fed a 18 or 1% protein diet for two weeks. A third low-protein group received daily rapamycin injections, an mTORC1 inhibitor. Hepatic metabolic function was assessed by histology, immunofluorescence, gene expression, metabolomics and protein levels. Low protein-fed mice manifested characteristics of severe malnutrition, including weight loss, hypoalbuminemia, hypoglycemia, hepatic steatosis and cholestasis. Low protein-fed mice had fewer mitochondria and showed signs of impaired mitochondrial function. Rapamycin prevented hepatic steatosis, restored ATP levels and fasted plasma glucose levels compared to untreated mice. This correlated with increased content of LC3-II, and decreased content mitochondrial damage marker, PINK1. We demonstrate that hepatic steatosis and disturbed mitochondrial function in a murine model of severe malnutrition can be partially prevented through inhibition of mTORC1. These findings suggest that stimulation of autophagy could be a novel approach to improve metabolic function in severely malnourished children.
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28
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Rasmussen NL, Kournoutis A, Lamark T, Johansen T. NBR1: The archetypal selective autophagy receptor. J Cell Biol 2022; 221:213552. [PMID: 36255390 PMCID: PMC9582228 DOI: 10.1083/jcb.202208092] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/03/2022] [Accepted: 10/03/2022] [Indexed: 11/24/2022] Open
Abstract
NBR1 was discovered as an autophagy receptor not long after the first described vertebrate autophagy receptor p62/SQSTM1. Since then, p62 has currently been mentioned in >10,000 papers on PubMed, while NBR1 is mentioned in <350 papers. Nonetheless, evolutionary analysis reveals that NBR1, and likely also selective autophagy, was present already in the last eukaryotic common ancestor (LECA), while p62 appears first in the early Metazoan lineage. Furthermore, yeast-selective autophagy receptors Atg19 and Atg34 represent NBR1 homologs. NBR1 is the main autophagy receptor in plants that do not contain p62, while most animal taxa contain both NBR1 and p62. Mechanistic studies are starting to shed light on the collaboration between mammalian NBR1 and p62 in the autophagic degradation of protein aggregates (aggrephagy). Several domains of NBR1 are involved in cargo recognition, and the list of known substrates for NBR1-mediated selective autophagy is increasing. Lastly, roles of NBR1 in human diseases such as proteinopathies and cancer are emerging.
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Affiliation(s)
- Nikoline Lander Rasmussen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Athanasios Kournoutis
- Autophagy Research Group, Department of Medical Biology, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Trond Lamark
- Autophagy Research Group, Department of Medical Biology, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Terje Johansen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
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29
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Kim YH, Jo DS, Park NY, Bae JE, Kim JB, Lee HJ, Kim SH, Kim SH, Lee S, Son M, Park K, Jeong K, Yeom E, Cho DH. Inhibition of BRD4 Promotes Pexophagy by Increasing ROS and ATM Activation. Cells 2022; 11:cells11182839. [PMID: 36139416 PMCID: PMC9497081 DOI: 10.3390/cells11182839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/09/2022] [Accepted: 09/10/2022] [Indexed: 01/18/2023] Open
Abstract
Although autophagy regulates the quality and quantity of cellular compartments, the regulatory mechanisms underlying peroxisomal autophagy (pexophagy) remain largely unknown. In this study, we identified several BRD4 inhibitors, including molibresib, a novel pexophagy inducer, via chemical library screening. Treatment with molibresib promotes loss of peroxisomes selectively, but not mitochondria, ER, or Golgi apparatus in HeLa cells. Consistently, depletion of BRD4 expression also induced pexophagy in RPE cells. In addition, the inhibition of BRD4 by molibresib increased autophagic degradation of peroxisome ATG7-dependency. We further found that molibresib produced reactive oxygen species (ROS), which potentiates ATM activation. Inhibition of ROS or ATM suppressed the loss of peroxisomes in molibresib-treated cells. Taken together, our data suggest that inhibition of BRD4 promotes pexophagy by increasing ROS and ATM activation.
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Affiliation(s)
- Yong Hwan Kim
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Doo Sin Jo
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Na Yeon Park
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Ji-Eun Bae
- Brain Science and Engineering Institute, Kyungpook National University, Daegu 41566, Korea
| | - Joon Bum Kim
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Ha Jung Lee
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - So Hyun Kim
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Seong Hyun Kim
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Sunwoo Lee
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Mikyung Son
- Orgasis Corp., Suwon 16229, Gyeonggi-do, Korea
| | - Kyuhee Park
- Bio-Center, Gyeonggido Business & Science Accelerator, Suwon 16229, Gyeonggi-do, Korea
| | - Kwiwan Jeong
- Bio-Center, Gyeonggido Business & Science Accelerator, Suwon 16229, Gyeonggi-do, Korea
| | - Eunbyul Yeom
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Dong-Hyung Cho
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Korea
- Orgasis Corp., Suwon 16229, Gyeonggi-do, Korea
- Correspondence: ; Tel.: +82-53-950-5382
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30
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Muhammad D, Smith KA, Bartel B. Plant peroxisome proteostasis-establishing, renovating, and dismantling the peroxisomal proteome. Essays Biochem 2022; 66:229-242. [PMID: 35538741 PMCID: PMC9375579 DOI: 10.1042/ebc20210059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/28/2022]
Abstract
Plant peroxisomes host critical metabolic reactions and insulate the rest of the cell from reactive byproducts. The specialization of peroxisomal reactions is rooted in how the organelle modulates its proteome to be suitable for the tissue, environment, and developmental stage of the organism. The story of plant peroxisomal proteostasis begins with transcriptional regulation of peroxisomal protein genes and the synthesis, trafficking, import, and folding of peroxisomal proteins. The saga continues with assembly and disaggregation by chaperones and degradation via proteases or the proteasome. The story concludes with organelle recycling via autophagy. Some of these processes as well as the proteins that facilitate them are peroxisome-specific, while others are shared among organelles. Our understanding of translational regulation of plant peroxisomal protein transcripts and proteins necessary for pexophagy remain based in findings from other models. Recent strides to elucidate transcriptional control, membrane dynamics, protein trafficking, and conditions that induce peroxisome turnover have expanded our knowledge of plant peroxisomal proteostasis. Here we review our current understanding of the processes and proteins necessary for plant peroxisome proteostasis-the emergence, maintenance, and clearance of the peroxisomal proteome.
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Affiliation(s)
| | - Kathryn A Smith
- Department of BioSciences, Rice University, Houston, TX 77005, U.S.A
| | - Bonnie Bartel
- Department of BioSciences, Rice University, Houston, TX 77005, U.S.A
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31
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Insights into the Structure and Function of the Pex1/Pex6 AAA-ATPase in Peroxisome Homeostasis. Cells 2022; 11:cells11132067. [PMID: 35805150 PMCID: PMC9265785 DOI: 10.3390/cells11132067] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/25/2022] [Accepted: 06/26/2022] [Indexed: 02/01/2023] Open
Abstract
The AAA-ATPases Pex1 and Pex6 are required for the formation and maintenance of peroxisomes, membrane-bound organelles that harbor enzymes for specialized metabolism. Together, Pex1 and Pex6 form a heterohexameric AAA-ATPase capable of unfolding substrate proteins via processive threading through a central pore. Here, we review the proposed roles for Pex1/Pex6 in peroxisome biogenesis and degradation, discussing how the unfolding of potential substrates contributes to peroxisome homeostasis. We also consider how advances in cryo-EM, computational structure prediction, and mechanisms of related ATPases are improving our understanding of how Pex1/Pex6 converts ATP hydrolysis into mechanical force. Since mutations in PEX1 and PEX6 cause the majority of known cases of peroxisome biogenesis disorders such as Zellweger syndrome, insights into Pex1/Pex6 structure and function are important for understanding peroxisomes in human health and disease.
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Luong AM, Koestel J, Bhati KK, Batoko H. Cargo receptors and adaptors for selective autophagy in plant cells. FEBS Lett 2022; 596:2104-2132. [PMID: 35638898 DOI: 10.1002/1873-3468.14412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/08/2022] [Accepted: 05/23/2022] [Indexed: 11/06/2022]
Abstract
Plant selective (macro)autophagy is a highly regulated process whereby eukaryotic cells spatiotemporally degrade some of their constituents that have become superfluous or harmful. The identification and characterization of the factors determining this selectivity make it possible to integrate selective (macro)autophagy into plant cell physiology and homeostasis. The specific cargo receptors and/or scaffold proteins involved in this pathway are generally not structurally conserved, as are the biochemical mechanisms underlying recognition and integration of a given cargo into the autophagosome in different cell types. This review discusses the few specific cargo receptors described in plant cells to highlight key features of selective autophagy in the plant kingdom and its integration with plant physiology, so as to identify evolutionary convergence and knowledge gaps to be filled by future research.
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Affiliation(s)
- Ai My Luong
- Louvain Institute of Biomolecular Science and Technology, University of Louvain Croix du Sud 4, L7.07.14, 1348, Louvain-la-Neuve, Belgium
| | - Jérôme Koestel
- Louvain Institute of Biomolecular Science and Technology, University of Louvain Croix du Sud 4, L7.07.14, 1348, Louvain-la-Neuve, Belgium
| | - Kaushal Kumar Bhati
- Louvain Institute of Biomolecular Science and Technology, University of Louvain Croix du Sud 4, L7.07.14, 1348, Louvain-la-Neuve, Belgium
| | - Henri Batoko
- Louvain Institute of Biomolecular Science and Technology, University of Louvain Croix du Sud 4, L7.07.14, 1348, Louvain-la-Neuve, Belgium
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Wang F, Gao Y, Zhou L, Chen J, Xie Z, Ye Z, Wang Y. USP30: Structure, Emerging Physiological Role, and Target Inhibition. Front Pharmacol 2022; 13:851654. [PMID: 35308234 PMCID: PMC8927814 DOI: 10.3389/fphar.2022.851654] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/04/2022] [Indexed: 12/22/2022] Open
Abstract
Ubiquitin-specific protease 30 (USP30) is a deubiquitinating enzyme (DUB) belonging to the USP subfamily, which was found localized in the mitochondrial outer membrane and peroxisomes owing to its unique transmembrane domain. Structural study revealed that USP30 employed a unique catalytic triad and molecular architecture to preferentially cleave the Lys6 linked ubiquitin chains. USP30 plays an essential role in several cellular events, such as the PINK1/Parkin-mediated mitophagy, pexophagy, BAX/BAK-dependent apoptosis, and IKKβ–USP30–ACLY-regulated lipogenesis/tumorigenesis, and is tightly regulated by post-translational modification including phosphorylation and mono-ubiquitination. Dysregulation of USP30 is associated with a range of physiological disorders, such as neurodegenerative disease, hepatocellular carcinoma, pulmonary disorders, and peroxisome biogenesis disorders. Nowadays, scientists and many biopharmaceutical companies are making much effort to explore USP30 inhibitors including natural compounds, phenylalanine derivatives, N-cyano pyrrolidines, benzosulphonamide, and other compounds. For the treatment of pulmonary disorders, the study in Mission Therapeutics of USP30 inhibitor is already in the pre-clinical stage. In this review, we will summarize the current knowledge of the structure, regulation, emerging physiological role, and target inhibition of USP30, hoping to prompt further investigation and understanding of it.
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Rusilowicz-Jones EV, Barone FG, Lopes FM, Stephen E, Mortiboys H, Urbé S, Clague MJ. Benchmarking a highly selective USP30 inhibitor for enhancement of mitophagy and pexophagy. Life Sci Alliance 2022; 5:e202101287. [PMID: 34844982 PMCID: PMC8645336 DOI: 10.26508/lsa.202101287] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 12/21/2022] Open
Abstract
The deubiquitylase USP30 is an actionable target considered for treatment of conditions associated with defects in the PINK1-PRKN pathway leading to mitophagy. We provide a detailed cell biological characterization of a benzosulphonamide molecule, compound 39, that has previously been reported to inhibit USP30 in an in vitro enzymatic assay. The current compound offers increased selectivity over previously described inhibitors. It enhances mitophagy and generates a signature response for USP30 inhibition after mitochondrial depolarization. This includes enhancement of TOMM20 and SYNJ2BP ubiquitylation and phosphoubiquitin accumulation, alongside increased mitophagy. In dopaminergic neurons, generated from Parkinson disease patients carrying loss of function PRKN mutations, compound 39 could significantly restore mitophagy to a level approaching control values. USP30 is located on both mitochondria and peroxisomes and has also been linked to the PINK1-independent pexophagy pathway. Using a fluorescence reporter of pexophagy expressed in U2OS cells, we observe increased pexophagy upon application of compound 39 that recapitulates the previously described effect for USP30 depletion. This provides the first pharmacological intervention with a synthetic molecule to enhance peroxisome turnover.
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Affiliation(s)
- Emma V Rusilowicz-Jones
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Francesco G Barone
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Fernanda Martins Lopes
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Elezabeth Stephen
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Heather Mortiboys
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Sylvie Urbé
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Michael J Clague
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
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Qiu S, Wu Z, Chen Z, Abbew AW, Li J, Ge S. Microalgal Activity and Nutrient Uptake from Wastewater Enhanced by Nanoscale Zerovalent Iron: Performance and Molecular Mechanism. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:585-594. [PMID: 34933554 DOI: 10.1021/acs.est.1c05503] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Microalgae-based bioremediation presents an alternative to traditional biological wastewater treatment. However, its efficiency is still challenging due to low microalgal activities and growth rate in wastewater. Iron plays an important role in microbial metabolism and is effective to stimulate microbial growth. In this study, a novel approach was proposed to simultaneously promote microalgal activity and nutrient uptake from wastewater using nanoscale zerovalent iron (nZVI), and the underlying molecular mechanism was explored. Compared to the control, 0.05 mg/L of nZVI significantly enhanced biomass production by 113.3% as well as NH4+-N and PO43--P uptake rates by 32.2% and 75.0%, respectively. These observations were attributed to the enhanced metabolic pathways and intracellular regulations. Specifically, nZVI alleviated the cellular oxidative stress via decreased peroxisome biogenesis as indicated by reduced reactive oxygen species, enzymes, and genes involved. nZVI promoted ammonium assimilation, phosphate metabolism, carbon fixation, and energy generation. Moreover, nZVI regulated the biosynthesis and conversions of intracellular biocomposition, leading to increased carotenoid, carbohydrate, and lipid productions and decreased protein and fatty acid yields. The above metabolisms were supported by the regulations of differentially expressed genes involved. This study provided an nZVI-based approach and molecular mechanism for enhancing microalgal activities and nutrient uptake from wastewater.
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Affiliation(s)
- Shuang Qiu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Zhengshuai Wu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Zhipeng Chen
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Abdul-Wahab Abbew
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Jinxiang Li
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Shijian Ge
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
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Zheng J, Chen X, Liu Q, Zhong G, Zhuang M. Ubiquitin ligase MARCH5 localizes to peroxisomes to regulate pexophagy. J Cell Biol 2022; 221:212749. [PMID: 34747980 PMCID: PMC8579195 DOI: 10.1083/jcb.202103156] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 09/04/2021] [Accepted: 10/21/2021] [Indexed: 11/22/2022] Open
Abstract
Mitochondria and peroxisomes are independent but functionally closely related organelles. A few proteins have been characterized as dual-organelle locating proteins with distinct or similar roles on mitochondria and peroxisomes. MARCH5 is a mitochondria-associated ubiquitin ligase best known for its regulatory role in mitochondria quality control, fission, and fusion. Here, we used a proximity tagging system, PUP-IT, and identified new interacting proteins of MARCH5. Our data uncover that MARCH5 is a dual-organelle locating protein that interacts with several peroxisomal proteins. PEX19 binds the transmembrane region on MARCH5 and targets it to peroxisomes. On peroxisomes, MARCH5 binds and mediates the ubiquitination of PMP70. Furthermore, we find PMP70 ubiquitination and pexophagy induced by mTOR inhibition are blocked in the absence of MARCH5. Our study suggests novel roles of MARCH5 on peroxisomes.
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Affiliation(s)
- Jun Zheng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xi Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Qiang Liu
- Key Laboratory of Women's Reproductive Health Research of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, China
| | - Guisheng Zhong
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Min Zhuang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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37
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Platta HW, Erdmann R. The ides of MARCH5: The E3 ligase essential for peroxisome degradation by pexophagy. J Cell Biol 2022; 221:e202111008. [PMID: 34889952 PMCID: PMC8669516 DOI: 10.1083/jcb.202111008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A recent study by Zheng et al. (2021. J. Cell Biol.https://doi.org/10.1083/jcb.202103156) identifies the ubiquitin-protein ligase (E3) MARCH5 as a dual-organelle localized protein that not only targets to mitochondria but also to peroxisomes in a PEX19-mediated manner. Moreover, the authors demonstrate that the Torin1-dependent induction of pexophagy is executed by the MARCH5-catalyzed ubiquitination of the peroxisomal membrane protein PMP70.
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Affiliation(s)
- Harald W. Platta
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, Bochum, Germany
| | - Ralf Erdmann
- Systembiochemie, Ruhr-Universität Bochum, Bochum, Germany
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38
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Byrnes K, Blessinger S, Bailey NT, Scaife R, Liu G, Khambu B. Therapeutic regulation of autophagy in hepatic metabolism. Acta Pharm Sin B 2022; 12:33-49. [PMID: 35127371 PMCID: PMC8799888 DOI: 10.1016/j.apsb.2021.07.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/04/2021] [Accepted: 07/09/2021] [Indexed: 02/07/2023] Open
Abstract
Metabolic homeostasis requires dynamic catabolic and anabolic processes. Autophagy, an intracellular lysosomal degradative pathway, can rewire cellular metabolism linking catabolic to anabolic processes and thus sustain homeostasis. This is especially relevant in the liver, a key metabolic organ that governs body energy metabolism. Autophagy's role in hepatic energy regulation has just begun to emerge and autophagy seems to have a much broader impact than what has been appreciated in the field. Though classically known for selective or bulk degradation of cellular components or energy-dense macromolecules, emerging evidence indicates autophagy selectively regulates various signaling proteins to directly impact the expression levels of metabolic enzymes or their upstream regulators. Hence, we review three specific mechanisms by which autophagy can regulate metabolism: A) nutrient regeneration, B) quality control of organelles, and C) signaling protein regulation. The plasticity of the autophagic function is unraveling a new therapeutic approach. Thus, we will also discuss the potential translation of promising preclinical data on autophagy modulation into therapeutic strategies that can be used in the clinic to treat common metabolic disorders.
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Key Words
- AIM, Atf8 interacting motif
- ATGL, adipose triglyceride lipase
- ATL3, Atlastin GTPase 3
- ATM, ATM serine/threonine kinase
- Autophagy
- BA, bile acid
- BCL2L13, BCL2 like 13
- BNIP3, BCL2 interacting protein 3
- BNIP3L, BCL2 interacting protein 3 like
- CAR, constitutive androstane receptor
- CCPG1, cell cycle progression 1
- CLN3, lysosomal/endosomal transmembrane protein
- CMA, chaperonin mediated autophagy
- CREB, cAMP response element binding protein
- CRY1, cryptochrome 1
- CYP27A1, sterol 27-hydroxylase
- CYP7A1, cholesterol 7α-hydroxylase
- Cryptochrome 1
- DFCP1, double FYVE-containing protein 1
- FAM134B, family with sequence similarity 134, member B
- FFA, free fatty acid
- FOXO1, Forkhead box O1
- FUNDC1, FUN14 domain containing 1
- FXR, farnesoid X receptor
- Farnesoid X receptor
- GABARAPL1, GABA type A receptor associated protein like 1
- GIM, GABARAP-interacting motif
- LAAT-1, lysosomal amino acid transporter 1 homologue
- LALP70, lysosomal apyrase-like protein of 70 kDa
- LAMP1, lysosomal-associated membrane protein-1
- LAMP2, lysosomal-associated membrane protein-2
- LD, lipid droplet
- LIMP1, lysosomal integral membrane protein-1
- LIMP3, lysosomal integral membrane protein-3
- LIR, LC3 interacting region
- LXRa, liver X receptor a
- LYAAT-1, lysosomal amino acid transporter 1
- Liver metabolism
- Lysosome
- MCOLN1, mucolipin 1
- MFSD1, major facilitator superfamily domain containing 1
- NAFLD, non-alcoholic fatty liver disease
- NBR1, BRCA1 gene 1 protein
- NCoR1, nuclear receptor co-repressor 1
- NDP52, calcium-binding and coiled-coil domain-containing protein 2
- NPC-1, Niemann-Pick disease, type C1
- Nutrient regeneration
- OPTN, optineurin
- PEX5, peroxisomal biogenesis factor 5
- PI3K, phosphatidylinositol-4,5-bisphosphate 3-kinase
- PINK1, phosphatase and tensin homolog (PTEN)-induced kinase 1
- PKA, protein kinase A
- PKB, protein kinase B
- PLIN2, perilipin 2
- PLIN3, perilipin 3
- PP2A, protein phosphatase 2a
- PPARα, peroxisomal proliferator-activated receptor-alpha
- PQLC2, PQ-loop protein
- PXR, pregnane X receptor
- Quality control
- RETREG1, reticulophagy regulator 1
- ROS, reactive oxygen species
- RTN3, reticulon 3
- RTNL3, a long isoform of RTN3
- S1PR2, sphingosine-1-phosphate receptor 2
- S6K, P70-S6 kinase
- S6RP, S6 ribosomal protein
- SCARB2, scavenger receptor class B member 2
- SEC62, SEC62 homolog, preprotein translocation factor
- SIRT1, sirtuin 1
- SLC36A1, solute carrier family 36 member 1
- SLC38A7, solute carrier family 38 member 7
- SLC38A9, sodium-coupled neutral amino acid transporter 9
- SNAT7, sodium-coupled neutral amino acid transporter 7
- SPIN, spindling
- SQSTM1, sequestosome 1
- STBD1, starch-binding domain-containing protein 1
- Signaling proteins
- TBK1, serine/threonine-protein kinase
- TEX264, testis expressed 264, ER-phagy receptor
- TFEB/TFE3, transcription factor EB
- TGR5, takeda G protein receptor 5
- TRAC-1, thyroid-hormone-and retinoic acid-receptor associated co-repressor 1
- TRPML1, transient receptor potential mucolipin 1
- ULK1, Unc-51 like autophagy activating kinase 1
- UPR, unfolded protein response
- V-ATPase, vacuolar-ATPase
- VDR, vitamin D3 receptor
- VLDL, very-low-density lipoprotein
- WIPI1, WD repeat domain phosphoinositide-interacting protein 1
- mTORC1, mammalian target of rapamycin complex 1
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Li H, Lismont C, Revenco I, Hussein MAF, Costa CF, Fransen M. The Peroxisome-Autophagy Redox Connection: A Double-Edged Sword? Front Cell Dev Biol 2021; 9:814047. [PMID: 34977048 PMCID: PMC8717923 DOI: 10.3389/fcell.2021.814047] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/02/2021] [Indexed: 01/18/2023] Open
Abstract
Peroxisomes harbor numerous enzymes that can produce or degrade hydrogen peroxide (H2O2). Depending on its local concentration and environment, this oxidant can function as a redox signaling molecule or cause stochastic oxidative damage. Currently, it is well-accepted that dysfunctional peroxisomes are selectively removed by the autophagy-lysosome pathway. This process, known as "pexophagy," may serve a protective role in curbing peroxisome-derived oxidative stress. Peroxisomes also have the intrinsic ability to mediate and modulate H2O2-driven processes, including (selective) autophagy. However, the molecular mechanisms underlying these phenomena are multifaceted and have only recently begun to receive the attention they deserve. This review provides a comprehensive overview of what is known about the bidirectional relationship between peroxisomal H2O2 metabolism and (selective) autophagy. After introducing the general concepts of (selective) autophagy, we critically examine the emerging roles of H2O2 as one of the key modulators of the lysosome-dependent catabolic program. In addition, we explore possible relationships among peroxisome functioning, cellular H2O2 levels, and autophagic signaling in health and disease. Finally, we highlight the most important challenges that need to be tackled to understand how alterations in peroxisomal H2O2 metabolism contribute to autophagy-related disorders.
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Affiliation(s)
- Hongli Li
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Celien Lismont
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Iulia Revenco
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Mohamed A. F. Hussein
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
- Department of Biochemistry, Faculty of Pharmacy, Assiut University, Asyut, Egypt
| | - Cláudio F. Costa
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Marc Fransen
- Laboratory of Peroxisome Biology and Intracellular Communication, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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Liu Y, Yu X, Huang A, Zhang X, Wang Y, Geng W, Xu R, Li S, He H, Zheng B, Chen G, Xu Y. INTS7-ABCD3 Interaction Stimulates the Proliferation and Osteoblastic Differentiation of Mouse Bone Marrow Mesenchymal Stem Cells by Suppressing Oxidative Stress. Front Physiol 2021; 12:758607. [PMID: 34880777 PMCID: PMC8647813 DOI: 10.3389/fphys.2021.758607] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022] Open
Abstract
Increased adipocyte and decreased osteoblast differentiation, combined with the ectopic proliferation of bone marrow mesenchymal stem cells (BM-MSCs), represent the primary causes of osteoporosis. The dysregulation of numerous intracellular bioactive factors is responsible for the aberrant differentiation and growth of BM-MSCs. In this study, we focused on a new stimulative factor, integrator complex subunit 7 (INTS7), and its cooperative protein ATP-binding cassette subfamily D member 3 (ABCD3)/high-density lipoprotein-binding protein (HDLBP) in mouse BM-MSCs. We aimed to uncover the effects of the INTS7–ABCD3/HDLBP interaction on BM-MSC biological behaviors and the potential mechanism underlying these effects. Functional in vitro experiments showed that the suppression of the INTS7–ABCD3 interaction rather than HDLBP could impair BM-MSC proliferation and induce cell apoptosis. Moreover, Alizarin Red S and Oil Red O staining, respectively, revealed that INTS7 and ABCD3 knockdown but not HDLBP knockdown could decrease osteoblastic differentiation and accelerate the adipogenic differentiation of BM-MSCs. Mechanistically, reactive oxygen species (ROS) and histone γ-H2AX quantities significantly increased, whereas the levels of antioxidants declined due to INTS7 and ABCD3 inhibition in BM-MSCs. These findings indicated that the suppression of oxidative stress could be involved in the INTS7/ABCD3 co-regulatory mechanisms for BM-MSC proliferation and differentiation, identifying new potential candidates for osteoporosis therapy.
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Affiliation(s)
- Yubo Liu
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China.,Department of Orthopaedics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Xiao Yu
- Department of Orthopaedics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Anquan Huang
- Department of Orthopaedics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Xiangxin Zhang
- Department of Orthopaedics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Yijun Wang
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Wei Geng
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Renjie Xu
- Department of Orthopaedics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Suoyuan Li
- Department of Orthopaedics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Hui He
- Department of Orthopaedics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Bo Zheng
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, China.,State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Guangxiang Chen
- Department of Orthopaedics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Yaozeng Xu
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
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41
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Ke PY. Autophagy and antiviral defense. IUBMB Life 2021; 74:317-338. [PMID: 34859938 DOI: 10.1002/iub.2582] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/04/2021] [Accepted: 11/15/2021] [Indexed: 12/14/2022]
Abstract
Targeting intracellular components for lysosomal degradation by autophagy not only maintains cellular homeostasis but also counteracts the effects of external stimuli, including invading pathogens. Among various kinds of pathogens, viruses have been extensively shown to induce autophagy to benefit viral growth in infected cells and to modulate host defense responses, such as innate antiviral immunity. Recently, numerous lines of evidence have implied that virus-induced autophagy triggers multilayer mechanisms to regulate the innate antiviral response of host cells, thus promoting a balance in virus-host cell interactions. In this review, the detailed mechanisms underlying autophagy and the innate antiviral immune response are first described. Then, I summarize the current information regarding the diverse functional role(s) of autophagy in the control of antiviral defenses against different types of viral infections. Moreover, the physiological significance of autophagy-regulated antiviral responses on the viral life cycle and the potential autophagy alterations induced by virus-associated antiviral signaling is further discussed.
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Affiliation(s)
- Po-Yuan Ke
- Department of Biochemistry & Molecular Biology and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC.,Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan, ROC
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42
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Paul B, Henne WM. How cells flex their PEX to fine-tune lipolysis in NAFLD. Nat Metab 2021; 3:1591-1593. [PMID: 34903885 DOI: 10.1038/s42255-021-00490-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Blessy Paul
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - W Mike Henne
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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43
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Ding L, Sun W, Balaz M, He A, Klug M, Wieland S, Caiazzo R, Raverdy V, Pattou F, Lefebvre P, Lodhi IJ, Staels B, Heim M, Wolfrum C. Peroxisomal β-oxidation acts as a sensor for intracellular fatty acids and regulates lipolysis. Nat Metab 2021; 3:1648-1661. [PMID: 34903883 PMCID: PMC8688145 DOI: 10.1038/s42255-021-00489-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/06/2021] [Indexed: 01/07/2023]
Abstract
To liberate fatty acids (FAs) from intracellular stores, lipolysis is regulated by the activity of the lipases adipose triglyceride lipase (ATGL), hormone-sensitive lipase and monoacylglycerol lipase. Excessive FA release as a result of uncontrolled lipolysis results in lipotoxicity, which can in turn promote the progression of metabolic disorders. However, whether cells can directly sense FAs to maintain cellular lipid homeostasis is unknown. Here we report a sensing mechanism for cellular FAs based on peroxisomal degradation of FAs and coupled with reactive oxygen species (ROS) production, which in turn regulates FA release by modulating lipolysis. Changes in ROS levels are sensed by PEX2, which modulates ATGL levels through post-translational ubiquitination. We demonstrate the importance of this pathway for non-alcoholic fatty liver disease progression using genetic and pharmacological approaches to alter ROS levels in vivo, which can be utilized to increase hepatic ATGL levels and ameliorate hepatic steatosis. The discovery of this peroxisomal β-oxidation-mediated feedback mechanism, which is conserved in multiple organs, couples the functions of peroxisomes and lipid droplets and might serve as a new way to manipulate lipolysis to treat metabolic disorders.
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Affiliation(s)
- Lianggong Ding
- Institute of Food, Nutrition and Health, ETH Zürich, Schwerzenbach, Switzerland
| | - Wenfei Sun
- Institute of Food, Nutrition and Health, ETH Zürich, Schwerzenbach, Switzerland
| | - Miroslav Balaz
- Institute of Food, Nutrition and Health, ETH Zürich, Schwerzenbach, Switzerland
- Institute of Experimental Endocrinology, Biomedical Research Center at the Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Animal Physiology and Ethology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Anyuan He
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- School of Life Sciences, Anhui Medical University, Hefei, China
| | - Manuel Klug
- Institute of Food, Nutrition and Health, ETH Zürich, Schwerzenbach, Switzerland
| | - Stefan Wieland
- Hepatology, Department of Biomedicine, University Hospital and University of Basel, Basel, Switzerland
| | - Robert Caiazzo
- University Lille, CHU Lille, Institut Pasteur Lille, Inserm, UMR1190 Translational Research in Diabetes, Lille, France
| | - Violeta Raverdy
- University Lille, CHU Lille, Institut Pasteur Lille, Inserm, UMR1190 Translational Research in Diabetes, Lille, France
| | - Francois Pattou
- University Lille, CHU Lille, Institut Pasteur Lille, Inserm, UMR1190 Translational Research in Diabetes, Lille, France
| | - Philippe Lefebvre
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille, France
| | - Irfan J Lodhi
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bart Staels
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille, France
| | - Markus Heim
- Hepatology, Department of Biomedicine, University Hospital and University of Basel, Basel, Switzerland
- Division of Gastroenterology and Hepatology, Clarunis, University Center for Gastrointestinal and Liver Diseases, Basel, Switzerland
| | - Christian Wolfrum
- Institute of Food, Nutrition and Health, ETH Zürich, Schwerzenbach, Switzerland.
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Rehman NU, Zeng P, Mo Z, Guo S, Liu Y, Huang Y, Xie Q. Conserved and Diversified Mechanism of Autophagy between Plants and Animals upon Various Stresses. Antioxidants (Basel) 2021; 10:1736. [PMID: 34829607 PMCID: PMC8615172 DOI: 10.3390/antiox10111736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 01/01/2023] Open
Abstract
Autophagy is a highly conserved degradation mechanism in eukaryotes, executing the breakdown of unwanted cell components and subsequent recycling of cellular material for stress relief through vacuole-dependence in plants and yeast while it is lysosome-dependent in animal manner. Upon stress, different types of autophagy are stimulated to operate certain biological processes by employing specific selective autophagy receptors (SARs), which hijack the cargo proteins or organelles to the autophagy machinery for subsequent destruction in the vacuole/lysosome. Despite recent advances in autophagy, the conserved and diversified mechanism of autophagy in response to various stresses between plants and animals still remain a mystery. In this review, we intend to summarize and discuss the characterization of the SARs and their corresponding processes, expectantly advancing the scope and perspective of the evolutionary fate of autophagy between plants and animals.
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Affiliation(s)
- Naveed Ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (N.U.R.); (P.Z.); (Z.M.); (S.G.)
| | - Peichun Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (N.U.R.); (P.Z.); (Z.M.); (S.G.)
| | - Zulong Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (N.U.R.); (P.Z.); (Z.M.); (S.G.)
| | - Shaoying Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (N.U.R.); (P.Z.); (Z.M.); (S.G.)
| | - Yunfeng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences and Technology, Guangxi University, Nanning 530004, China;
| | - Yifeng Huang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou 310001, China
| | - Qingjun Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (N.U.R.); (P.Z.); (Z.M.); (S.G.)
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45
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Molecular mechanisms of mammalian autophagy. Biochem J 2021; 478:3395-3421. [PMID: 34554214 DOI: 10.1042/bcj20210314] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/19/2021] [Accepted: 07/28/2021] [Indexed: 02/06/2023]
Abstract
The ubiquitin-proteasome pathway (UPP) and autophagy play integral roles in cellular homeostasis. As part of their normal life cycle, most proteins undergo ubiquitination for some form of redistribution, localization and/or functional modulation. However, ubiquitination is also important to the UPP and several autophagic processes. The UPP is initiated after specific lysine residues of short-lived, damaged or misfolded proteins are conjugated to ubiquitin, which targets these proteins to proteasomes. Autophagy is the endosomal/lysosomal-dependent degradation of organelles, invading microbes, zymogen granules and macromolecules such as protein, carbohydrates and lipids. Autophagy can be broadly separated into three distinct subtypes termed microautophagy, chaperone-mediated autophagy and macroautophagy. Although autophagy was once thought of as non-selective bulk degradation, advancements in the field have led to the discovery of several selective forms of autophagy. Here, we focus on the mechanisms of primary and selective mammalian autophagy pathways and highlight the current knowledge gaps in these molecular pathways.
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Papandreou ME, Tavernarakis N. Selective Autophagy as a Potential Therapeutic Target in Age-Associated Pathologies. Metabolites 2021; 11:metabo11090588. [PMID: 34564405 PMCID: PMC8472713 DOI: 10.3390/metabo11090588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/12/2021] [Accepted: 08/27/2021] [Indexed: 11/16/2022] Open
Abstract
Progressive accumulation of damaged cellular constituents contributes to age-related diseases. Autophagy is the main catabolic process, which recycles cellular material in a multitude of tissues and organs. Autophagy is activated upon nutrient deprivation, and oncogenic, heat or oxidative stress-induced stimuli to selectively degrade cell constituents and compartments. Specificity and accuracy of the autophagic process is maintained via the precision of interaction of autophagy receptors or adaptors and substrates by the intricate, stepwise orchestration of specialized integrating stimuli. Polymorphisms in genes regulating selective autophagy have been linked to aging and age-associated disorders. The involvement of autophagy perturbations in aging and disease indicates that pharmacological agents balancing autophagic flux may be beneficial, in these contexts. Here, we introduce the modes and mechanisms of selective autophagy, and survey recent experimental evidence of dysfunctional autophagy triggering severe pathology. We further highlight identified pharmacological targets that hold potential for developing therapeutic interventions to alleviate cellular autophagic cargo burden and associated pathologies.
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Affiliation(s)
- Margarita-Elena Papandreou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece;
- Department of Basic Sciences, Faculty of Medicine, University of Crete, 70013 Heraklion, Greece
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece;
- Department of Basic Sciences, Faculty of Medicine, University of Crete, 70013 Heraklion, Greece
- Correspondence:
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Adolphe F, Ferlicot S, Verkarre V, Posseme K, Couvé S, Garnier P, Droin N, Deloger M, Job B, Giraud S, Paillerets BBD, Gardie B, Richard S, Renaud F, Gad S. Germline mutation in the NBR1 gene involved in autophagy detected in a family with renal tumors. Cancer Genet 2021; 258-259:51-56. [PMID: 34488032 DOI: 10.1016/j.cancergen.2021.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 06/10/2021] [Accepted: 07/26/2021] [Indexed: 01/09/2023]
Abstract
Hereditary Renal Cell Carcinomas (RCC) are caused by mutations in predisposing genes, the major ones including VHL, FLCN, FH and MET. However, many families with inherited RCC have no germline mutation in these genes. Using Whole Exome Sequencing on germline DNA from a family presenting three different histological renal tumors (an angiomyolipoma, a clear-cell RCC and an oncocytic papillary RCC), we identified a frameshift mutation in the Neighbor of BRCA1 gene 1 (NBR1), segregating with the tumors. NBR1 encodes a cargo receptor protein involved in autophagy. Genetic and functional analyses suggested a pathogenic impact of the mutation. Indeed, functional study performed in renal cell lines showed that the mutation alters NBR1 interactions with some of its partners (such as p62/SQSTM1), leading to a dominant negative effect. This results in an altered autophagic process and an increased proliferative capacity in renal cell lines. Our study suggests that NBR1 may be a new predisposing gene for RCC, however its characterization needs to be further investigated in order to confirm its role in renal carcinogenesis.
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Affiliation(s)
- Florine Adolphe
- EPHE, PSL Université, Paris, France; CNRS UMR 9019, Gustave Roussy, Université Paris-Saclay, UMR 9019 CNRS, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Sophie Ferlicot
- CNRS UMR 9019, Gustave Roussy, Université Paris-Saclay, UMR 9019 CNRS, 114 rue Edouard Vaillant, Villejuif 94800, France; Département de Pathologie, AP-HP, Université Paris-Saclay, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France; Réseau National de Référence pour Cancers Rares de l'Adulte PREDIR labellisé par l'INCa, Hôpital de Bicêtre, AP-HP, et Service d'Urologie, Le Kremlin-Bicêtre, France
| | - Virginie Verkarre
- Réseau National de Référence pour Cancers Rares de l'Adulte PREDIR labellisé par l'INCa, Hôpital de Bicêtre, AP-HP, et Service d'Urologie, Le Kremlin-Bicêtre, France; Service d'Anatomie et de Cytologie Pathologiques, Hôpital Européen Georges Pompidou, AP-HP centre, Université de Paris, Paris, France; Université de Paris, PARCC, INSERM, Equipe Labellisée par la Ligue contre le Cancer, F-75015 Paris, France
| | - Katia Posseme
- Département de Pathologie, AP-HP, Université Paris-Saclay, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - Sophie Couvé
- EPHE, PSL Université, Paris, France; CNRS UMR 9019, Gustave Roussy, Université Paris-Saclay, UMR 9019 CNRS, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Pauline Garnier
- EPHE, PSL Université, Paris, France; CNRS UMR 9019, Gustave Roussy, Université Paris-Saclay, UMR 9019 CNRS, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Nathalie Droin
- Plateforme de Génomique, Gustave Roussy, Villejuif, France
| | - Marc Deloger
- Plateforme de Bioinformatique, Gustave Roussy, Villejuif, France
| | - Bastien Job
- Plateforme de Bioinformatique, Gustave Roussy, Villejuif, France
| | - Sophie Giraud
- Réseau National de Référence pour Cancers Rares de l'Adulte PREDIR labellisé par l'INCa, Hôpital de Bicêtre, AP-HP, et Service d'Urologie, Le Kremlin-Bicêtre, France; Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Brigitte Bressac-de Paillerets
- Réseau National de Référence pour Cancers Rares de l'Adulte PREDIR labellisé par l'INCa, Hôpital de Bicêtre, AP-HP, et Service d'Urologie, Le Kremlin-Bicêtre, France; Département de Biopathologie, Service de Génétique, Gustave Roussy, Villejuif, France
| | - Betty Gardie
- EPHE, PSL Université, Paris, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, Nantes, France
| | - Stéphane Richard
- EPHE, PSL Université, Paris, France; CNRS UMR 9019, Gustave Roussy, Université Paris-Saclay, UMR 9019 CNRS, 114 rue Edouard Vaillant, Villejuif 94800, France; Réseau National de Référence pour Cancers Rares de l'Adulte PREDIR labellisé par l'INCa, Hôpital de Bicêtre, AP-HP, et Service d'Urologie, Le Kremlin-Bicêtre, France
| | - Flore Renaud
- EPHE, PSL Université, Paris, France; CNRS UMR 9019, Gustave Roussy, Université Paris-Saclay, UMR 9019 CNRS, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Sophie Gad
- EPHE, PSL Université, Paris, France; CNRS UMR 9019, Gustave Roussy, Université Paris-Saclay, UMR 9019 CNRS, 114 rue Edouard Vaillant, Villejuif 94800, France.
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48
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Chen H, Bühler K, Zhu Y, Nie X, Liu W. Proteomics analysis reveals the effect of 1α,25(OH) 2VD 3-glycosides on development of early testes in piglets. Sci Rep 2021; 11:11341. [PMID: 34059707 PMCID: PMC8167176 DOI: 10.1038/s41598-021-90676-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/07/2021] [Indexed: 12/31/2022] Open
Abstract
1α,25(OH)2VD3 is the most active form of VD3 in animals. It plays an important role in regulating mineral metabolism but also in reproduction. Testes are the main reproductive organs of male mammals. Our research aims to reveal the effect of 1α,25(OH)2VD3-glycosides on development of early testes in piglets. 140 weaned 21-day old piglets were selected. The piglets were randomly divided into four groups and were fed a commercial diet supplemented with 0, 1, 2 and 4 μg/kg of 1α,25(OH)2VD3, provided as 1α,25(OH)2VD3-glycosides. Sixty days after the start of the experiment, at piglet age 82 days, testes were harvested. The morphology and histology of early testicular development were assessed. In addition, the proteomic TMT/iTRAQ labelling technique was used to analyse the protein profile of the testes in each group. Western blotting was applied to verify the target of differentially abundant proteins (DAPs). The analysis of morphology and histology of testes showed that a certain concentration of 1α,25(OH)2VD3-glycosides had a positive and significant effect on testicular development. And the results of proteomics analysis showed that of the identified 132,715 peptides, 122,755 were unique peptides. 7852 proteins, of which 6573 proteins contain quantitative information. Screening for DAPs focused on proteins closely related to the regulation of testicular development such as steroid hormone synthesis, steroid biosynthesis, peroxisome and fatty acid metabolism pathways. These results indicated that 1α,25(OH)2VD3 is involved in the regulation of early testicular development in piglets. At the same time, these findings provide valuable information for the proteins involved in the regulation of testicular development, and help to better understand the mechanisms of 1α,25(OH)2VD3 in regulating the development of piglets’ testes.
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Affiliation(s)
- Haodong Chen
- College of Animal Science and Technology, Huazhong Agricultural University, Hongshan District, No.1 Shizishan Road, Wuhan, 430070, China.,National Engineering and Technology Research Center for Livestock, Wuhan, 430070, China.,The Breeding Swine Quality Supervision and Testing Center, Ministry of Agriculture, Wuhan, 430070, China
| | - Kathrin Bühler
- Herbonis Animal Health GmbH, Rheinstrasse 30, CH-4302, Augst BL, Switzerland
| | - Yan Zhu
- College of Animal Science and Technology, Huazhong Agricultural University, Hongshan District, No.1 Shizishan Road, Wuhan, 430070, China
| | - Xiongwei Nie
- College of Animal Science and Technology, Huazhong Agricultural University, Hongshan District, No.1 Shizishan Road, Wuhan, 430070, China
| | - Wanghong Liu
- College of Animal Science and Technology, Huazhong Agricultural University, Hongshan District, No.1 Shizishan Road, Wuhan, 430070, China. .,National Engineering and Technology Research Center for Livestock, Wuhan, 430070, China. .,The Breeding Swine Quality Supervision and Testing Center, Ministry of Agriculture, Wuhan, 430070, China.
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49
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Mechanisms and Functions of Pexophagy in Mammalian Cells. Cells 2021; 10:cells10051094. [PMID: 34063724 PMCID: PMC8147788 DOI: 10.3390/cells10051094] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/28/2021] [Accepted: 05/01/2021] [Indexed: 12/17/2022] Open
Abstract
Peroxisomes play essential roles in diverse cellular metabolism functions, and their dynamic homeostasis is maintained through the coordination of peroxisome biogenesis and turnover. Pexophagy, selective autophagic degradation of peroxisomes, is a major mechanism for removing damaged and/or superfluous peroxisomes. Dysregulation of pexophagy impairs the physiological functions of peroxisomes and contributes to the progression of many human diseases. However, the mechanisms and functions of pexophagy in mammalian cells remain largely unknown compared to those in yeast. This review focuses on mammalian pexophagy and aims to advance the understanding of the roles of pexophagy in human health and diseases. Increasing evidence shows that ubiquitination can serve as a signal for pexophagy, and ubiquitin-binding receptors, substrates, and E3 ligases/deubiquitinases involved in pexophagy have been described. Alternatively, pexophagy can be achieved in a ubiquitin-independent manner. We discuss the mechanisms of these ubiquitin-dependent and ubiquitin-independent pexophagy pathways and summarize several inducible conditions currently used to study pexophagy. We highlight several roles of pexophagy in human health and how its dysregulation may contribute to diseases.
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50
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Miller DR, Thorburn A. Autophagy and organelle homeostasis in cancer. Dev Cell 2021; 56:906-918. [PMID: 33689692 PMCID: PMC8026727 DOI: 10.1016/j.devcel.2021.02.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/11/2021] [Accepted: 02/09/2021] [Indexed: 12/16/2022]
Abstract
Beginning with the earliest studies of autophagy in cancer, there have been indications that autophagy can both promote and inhibit cancer growth and progression; autophagy regulation of organelle homeostasis is similarly complicated. In this review we discuss pro- and antitumor effects of organelle-targeted autophagy and how this contributes to several hallmarks of cancer, such as evading cell death, genomic instability, and altered metabolism. Typically, the removal of damaged or dysfunctional organelles prevents tumor development but can also aid in proliferation or drug resistance in established tumors. By better understanding how organelle-specific autophagy takes place and can be manipulated, it may be possible to go beyond the brute-force approach of trying to manipulate all autophagy in order to improve therapeutic targeting of this process in cancer.
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Affiliation(s)
- Dannah R Miller
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Andrew Thorburn
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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