1
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Proikas-Cezanne T, Haas ML, Pastor-Maldonado CJ, Schüssele DS. Human WIPI β-propeller function in autophagy and neurodegeneration. FEBS Lett 2024; 598:127-139. [PMID: 38058212 DOI: 10.1002/1873-3468.14782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/10/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023]
Abstract
The four human WIPI β-propellers, WIPI1 through WIPI4, belong to the ancient PROPPIN family and fulfill scaffold functions in the control of autophagy. In this context, WIPI β-propellers function as PI3P effectors during autophagosome formation and loss of WIPI function negatively impacts autophagy and contributes to neurodegeneration. Of particular interest are mutations in WDR45, the human gene that encodes WIPI4. Sporadic WDR45 mutations are the cause of a rare human neurodegenerative disease called BPAN, hallmarked by high brain iron accumulation. Here, we discuss the current understanding of the functions of human WIPI β-propellers and address unanswered questions with a particular focus on the role of WIPI4 in autophagy and BPAN.
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Affiliation(s)
- Tassula Proikas-Cezanne
- Interfaculty Institute of Cell Biology, Department of Biology, Faculty of Science, Eberhard Karls University Tübingen, Germany
| | - Maximilian L Haas
- Interfaculty Institute of Cell Biology, Department of Biology, Faculty of Science, Eberhard Karls University Tübingen, Germany
| | - Carmen J Pastor-Maldonado
- Interfaculty Institute of Cell Biology, Department of Biology, Faculty of Science, Eberhard Karls University Tübingen, Germany
| | - David S Schüssele
- Interfaculty Institute of Cell Biology, Department of Biology, Faculty of Science, Eberhard Karls University Tübingen, Germany
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2
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Char R, Liu Z, Jacqueline C, Davieau M, Delgado MG, Soufflet C, Fallet M, Chasson L, Chapuy R, Camosseto V, Strock E, Rua R, Almeida CR, Su B, Lennon-Duménil AM, Nal B, Roquilly A, Liang Y, Méresse S, Gatti E, Pierre P. RUFY3 regulates endolysosomes perinuclear positioning, antigen presentation and migration in activated phagocytes. Nat Commun 2023; 14:4290. [PMID: 37463962 PMCID: PMC10354229 DOI: 10.1038/s41467-023-40062-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
Endo-lysosomes transport along microtubules and clustering in the perinuclear area are two necessary steps for microbes to activate specialized phagocyte functions. We report that RUN and FYVE domain-containing protein 3 (RUFY3) exists as two alternative isoforms distinguishable by the presence of a C-terminal FYVE domain and by their affinity for phosphatidylinositol 3-phosphate on endosomal membranes. The FYVE domain-bearing isoform (iRUFY3) is preferentially expressed in primary immune cells and up-regulated upon activation by microbes and Interferons. iRUFY3 is necessary for ARL8b + /LAMP1+ endo-lysosomes positioning in the pericentriolar organelles cloud of LPS-activated macrophages. We show that iRUFY3 controls macrophages migration, MHC II presentation and responses to Interferon-γ, while being important for intracellular Salmonella replication. Specific inactivation of rufy3 in phagocytes leads to aggravated pathologies in mouse upon LPS injection or bacterial pneumonia. This study highlights the role of iRUFY3 in controlling endo-lysosomal dynamics, which contributes to phagocyte activation and immune response regulation.
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Affiliation(s)
- Rémy Char
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Zhuangzhuang Liu
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, PR China
| | - Cédric Jacqueline
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR1064, F-44000, Nantes, France
| | - Marion Davieau
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR1064, F-44000, Nantes, France
| | - Maria-Graciela Delgado
- INSERM U932, Institut Curie, ANR-10-IDEX-0001-02 PSL* and ANR-11-LABX-0043, Paris, France
| | - Clara Soufflet
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Mathieu Fallet
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Lionel Chasson
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Raphael Chapuy
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Voahirana Camosseto
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Eva Strock
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Rejane Rua
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Catarina R Almeida
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Bing Su
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, PR China
| | | | - Beatrice Nal
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Antoine Roquilly
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR1064, F-44000, Nantes, France
| | - Yinming Liang
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, PR China
| | - Stéphane Méresse
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France
| | - Evelina Gatti
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France.
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal.
| | - Philippe Pierre
- Aix Marseille Université, CNRS, INSERM, CIML, 13288, Marseille, cedex 9, France.
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, 3810-193, Aveiro, Portugal.
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, PR China.
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3
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Tang T, Hasan M, Capelluto DGS. Phafins Are More Than Phosphoinositide-Binding Proteins. Int J Mol Sci 2023; 24:ijms24098096. [PMID: 37175801 PMCID: PMC10178739 DOI: 10.3390/ijms24098096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Phafins are PH (Pleckstrin Homology) and FYVE (Fab1, YOTB, Vac1, and EEA1) domain-containing proteins. The Phafin protein family is classified into two groups based on their sequence homology and functional similarity: Phafin1 and Phafin2. This protein family is unique because both the PH and FYVE domains bind to phosphatidylinositol 3-phosphate [PtdIns(3)P], a phosphoinositide primarily found in endosomal and lysosomal membranes. Phafin proteins act as PtdIns(3)P effectors in apoptosis, endocytic cargo trafficking, and autophagy. Additionally, Phafin2 is recruited to macropinocytic compartments through coincidence detection of PtdIns(3)P and PtdIns(4)P. Membrane-associated Phafins serve as adaptor proteins that recruit other binding partners. In addition to the phosphoinositide-binding domains, Phafin proteins present a poly aspartic acid motif that regulates membrane binding specificity. In this review, we summarize the involvement of Phafins in several cellular pathways and their potential physiological functions while highlighting the similarities and differences between Phafin1 and Phafin2. Besides, we discuss research perspectives for Phafins.
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Affiliation(s)
- Tuoxian Tang
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mahmudul Hasan
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Fralin Life Sciences Institute and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
| | - Daniel G S Capelluto
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Fralin Life Sciences Institute and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA 24061, USA
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4
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Enrich C, Lu A, Tebar F, Rentero C, Grewal T. Ca 2+ and Annexins - Emerging Players for Sensing and Transferring Cholesterol and Phosphoinositides via Membrane Contact Sites. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1422:393-438. [PMID: 36988890 DOI: 10.1007/978-3-031-21547-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Maintaining lipid composition diversity in membranes from different organelles is critical for numerous cellular processes. However, many lipids are synthesized in the endoplasmic reticulum (ER) and require delivery to other organelles. In this scenario, formation of membrane contact sites (MCS) between neighbouring organelles has emerged as a novel non-vesicular lipid transport mechanism. Dissecting the molecular composition of MCS identified phosphoinositides (PIs), cholesterol, scaffolding/tethering proteins as well as Ca2+ and Ca2+-binding proteins contributing to MCS functioning. Compelling evidence now exists for the shuttling of PIs and cholesterol across MCS, affecting their concentrations in distinct membrane domains and diverse roles in membrane trafficking. Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) at the plasma membrane (PM) not only controls endo-/exocytic membrane dynamics but is also critical in autophagy. Cholesterol is highly concentrated at the PM and enriched in recycling endosomes and Golgi membranes. MCS-mediated cholesterol transfer is intensely researched, identifying MCS dysfunction or altered MCS partnerships to correlate with de-regulated cellular cholesterol homeostasis and pathologies. Annexins, a conserved family of Ca2+-dependent phospholipid binding proteins, contribute to tethering and untethering events at MCS. In this chapter, we will discuss how Ca2+ homeostasis and annexins in the endocytic compartment affect the sensing and transfer of cholesterol and PIs across MCS.
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Affiliation(s)
- Carlos Enrich
- Departament de Biomedicina, Unitat de Biologia Cel⋅lular, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
- Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain.
| | - Albert Lu
- Departament de Biomedicina, Unitat de Biologia Cel⋅lular, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Francesc Tebar
- Departament de Biomedicina, Unitat de Biologia Cel⋅lular, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Carles Rentero
- Departament de Biomedicina, Unitat de Biologia Cel⋅lular, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Thomas Grewal
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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5
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The intracellular Ca 2+ channel TRPML3 is a PI3P effector that regulates autophagosome biogenesis. Proc Natl Acad Sci U S A 2022; 119:e2200085119. [PMID: 36252030 PMCID: PMC9618060 DOI: 10.1073/pnas.2200085119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Autophagy is a multiple fusion event, initiating with autophagosome formation and culminating with fusion with endo-lysosomes in a Ca2+-dependent manner. The source of Ca2+ and the molecular mechanism by which Ca2+ is provided for this process are not known. The intracellular Ca2+ permeable channel transient receptor potential mucolipin 3 (TRPML3) localizes in the autophagosome and interacts with the mammalian autophagy-related protein 8 (ATG8) homolog GATE16. Here, we show that lipid-regulated TRPML3 is the Ca2+ release channel in the phagophore that provides the Ca2+ necessary for autophagy progress. We generated a TRPML3-GCaMP6 fusion protein as a targeted reporter of TRPML3 compartment localization and channel function. Notably, TRPML3-GCaMP6 localized in the phagophores, the level of which increased in response to nutrient starvation. Importantly, phosphatidylinositol-3-phosphate (PI3P), an essential lipid for autophagosome formation, is a selective regulator of TRPML3. TRPML3 interacted with PI3P, which is a direct activator of TRPML3 current and Ca2+ release from the phagophore, to promote and increase autophagy. Inhibition of TRPML3 suppressed autophagy even in the presence of excess PI3P, while activation of TRPML3 reversed the autophagy inhibition caused by blocking PI3P. Moreover, disruption of the TRPML3-PI3P interaction abolished both TRPML3 activation by PI3P and the increase in autophagy. Taken together, these results reveal that TRPML3 is a downstream effector of PI3P and a key regulator of autophagy. Activation of TRPML3 by PI3P is the critical step providing Ca2+ from the phagophore for the fusion process, which is essential for autophagosome biogenesis.
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6
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Visintin R, Ray SK. Specific microRNAs for Modulation of Autophagy in Spinal Cord Injury. Brain Sci 2022; 12:brainsci12020247. [PMID: 35204010 PMCID: PMC8870708 DOI: 10.3390/brainsci12020247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/02/2022] [Accepted: 02/06/2022] [Indexed: 02/05/2023] Open
Abstract
The treatment of spinal cord injury (SCI) is currently a major challenge, with a severe lack of effective therapies for yielding meaningful improvements in function. Therefore, there is a great opportunity for the development of novel treatment strategies for SCI. The modulation of autophagy, a process by which a cell degrades and recycles unnecessary or harmful components (protein aggregates, organelles, etc.) to maintain cellular homeostasis and respond to a changing microenvironment, is thought to have potential for treating many neurodegenerative conditions, including SCI. The discovery of microRNAs (miRNAs), which are short ribonucleotide transcripts for targeting of specific messenger RNAs (mRNAs) for silencing, shows prevention of the translation of mRNAs to the corresponding proteins affecting various cellular processes, including autophagy. The number of known miRNAs and their targets continues to grow rapidly. This review article aims to explore the relationship between autophagy and SCI, specifically with the intent of identifying specific miRNAs that can be useful to modulate autophagy for neuroprotection and the improvement of functional recovery in SCI.
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Affiliation(s)
- Rhett Visintin
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA;
| | - Swapan K. Ray
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC 29209, USA
- Correspondence: ; Tel.: +1-803-216-3420; Fax: +1-803-216-3428
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7
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Orii M, Tsuji T, Ogasawara Y, Fujimoto T. Transmembrane phospholipid translocation mediated by Atg9 is involved in autophagosome formation. J Cell Biol 2021; 220:211678. [PMID: 33439214 PMCID: PMC7809878 DOI: 10.1083/jcb.202009194] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 12/15/2022] Open
Abstract
The mechanism of isolation membrane formation in autophagy is receiving intensive study. We recently found that Atg9 translocates phospholipids across liposomal membranes and proposed that this functionality plays an essential role in the expansion of isolation membranes. The distribution of phosphatidylinositol 3-phosphate in both leaflets of yeast autophagosomal membranes supports this proposal, but if Atg9-mediated lipid transport is crucial, symmetrical distribution in autophagosomes should be found broadly for other phospholipids. To test this idea, we analyzed the distributions of phosphatidylcholine, phosphatidylserine, and phosphatidylinositol 4-phosphate by freeze-fracture electron microscopy. We found that all these phospholipids are distributed with comparable densities in the two leaflets of autophagosomes and autophagic bodies. Moreover, de novo–synthesized phosphatidylcholine is incorporated into autophagosomes preferentially and shows symmetrical distribution in autophagosomes within 30 min after synthesis, whereas this symmetrical distribution is compromised in yeast expressing an Atg9 mutant. These results indicate that transbilayer phospholipid movement that is mediated by Atg9 is involved in the biogenesis of autophagosomes.
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Affiliation(s)
- Minami Orii
- Department of Anatomy and Molecular Cell Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takuma Tsuji
- Laboratory of Molecular Cell Biology, Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yuta Ogasawara
- Laboratory of Molecular Cell Biology, Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Toyoshi Fujimoto
- Laboratory of Molecular Cell Biology, Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
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8
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Liu C, Zeng Y, Li H, Yang C, Shen W, Xu M, Xiao Z, Chen T, Li B, Cao W, Jiang L, Otegui MS, Gao C. A plant-unique ESCRT component, FYVE4, regulates multivesicular endosome biogenesis and plant growth. THE NEW PHYTOLOGIST 2021; 231:193-209. [PMID: 33772801 DOI: 10.1111/nph.17358] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
During evolution, land plants generated unique proteins that participate in endosomal sorting and multivesicular endosome (MVE) biogenesis, many of them with specific phosphoinositide-binding capabilities. Nonetheless, the function of most plant phosphoinositide-binding proteins in endosomal trafficking remains elusive. Here, we analysed several Arabidopsis mutants lacking predicted phosphoinositide-binding proteins and first identified fyve4-1 as a mutant with a hypersensitive response to high-boron conditions and defects in degradative vacuolar sorting of membrane proteins such as the borate exporter BOR1-GFP. FYVE4 encodes a plant-unique, FYVE domain-containing protein that interacts with SNF7, a core component of ESCRT-III (Endosomal Sorting Complex Required for Transport III). FYVE4 affects the membrane association of the late-acting ESCRT components SNF7 and VPS4, and modulates the formation of intraluminal vesicles (ILVs) inside MVEs. The critical function of FYVE4 in the ESCRT pathway was further demonstrated by the strong genetic interactions with SNF7B and LIP5. Although the fyve4-1, snf7b and lip5 single mutants were viable, the fyve4-1 snf7b and fyve4-1 lip5 double mutants were seedling lethal, with strong defects in MVE biogenesis and vacuolar sorting of ubiquitinated membrane proteins. Taken together, we identified FYVE4 as a novel plant endosomal regulator, which functions in ESCRTing pathway to regulate MVE biogenesis.
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Affiliation(s)
- Chuanliang Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yonglun Zeng
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Hongbo Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Chao Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Wenjin Shen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Min Xu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Zhidan Xiao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Tongsheng Chen
- MOE Key Laboratory & Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Baiying Li
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Wenhan Cao
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Liwen Jiang
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Marisa S Otegui
- Department of Botany, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
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Valečka J, Camosseto V, McEwan DG, Terawaki S, Liu Z, Strock E, Almeida CR, Su B, Dikic I, Liang Y, Gatti E, Pierre P. RUFY4 exists as two translationally regulated isoforms, that localize to the mitochondrion in activated macrophages. ROYAL SOCIETY OPEN SCIENCE 2021; 8:202333. [PMID: 34295519 PMCID: PMC8278043 DOI: 10.1098/rsos.202333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 06/22/2021] [Indexed: 05/11/2023]
Abstract
We report here that RUFY4, a newly characterized member of the 'RUN and FYVE domain-containing' family of proteins previously associated with autophagy enhancement, is highly expressed in alveolar macrophages (AM). We show that RUFY4 interacts with mitochondria upon stimulation by microbial-associated molecular patterns of AM and dendritic cells. RUFY4 interaction with mitochondria and other organelles is dependent on a previously uncharacterized OmpH domain located immediately upstream of its C-terminal FYVE domain. Further, we demonstrate that rufy4 messenger RNA can be translated from an alternative translation initiation codon, giving rise to a N-terminally truncated form of the molecule lacking most of its RUN domain and with enhanced potential for its interaction with mitochondria. Our observations point towards a role of RUFY4 in selective mitochondria clearance in activated phagocytes.
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Affiliation(s)
- Jan Valečka
- Aix Marseille Université, CNRS, INSERM, CIML, 13288 Marseille cedex 9, France
| | - Voahirana Camosseto
- Aix Marseille Université, CNRS, INSERM, CIML, 13288 Marseille cedex 9, France
| | - David G. McEwan
- Tumour Cell Death Laboratory, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Seigo Terawaki
- Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Zhuangzhuang Liu
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, People's Republic of China
| | - Eva Strock
- Aix Marseille Université, CNRS, INSERM, CIML, 13288 Marseille cedex 9, France
| | - Catarina R. Almeida
- Institute for Research in Biomedicine (iBiMED) and Ilidio Pinho Foundation, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Bing Su
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt (Main), Germany
| | - Yinming Liang
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, People's Republic of China
| | - Evelina Gatti
- Aix Marseille Université, CNRS, INSERM, CIML, 13288 Marseille cedex 9, France
- Institute for Research in Biomedicine (iBiMED) and Ilidio Pinho Foundation, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Philippe Pierre
- Aix Marseille Université, CNRS, INSERM, CIML, 13288 Marseille cedex 9, France
- Institute for Research in Biomedicine (iBiMED) and Ilidio Pinho Foundation, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China
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10
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Li L, Tong M, Fu Y, Chen F, Zhang S, Chen H, Ma X, Li D, Liu X, Zhong Q. Lipids and membrane-associated proteins in autophagy. Protein Cell 2021; 12:520-544. [PMID: 33151516 PMCID: PMC8225772 DOI: 10.1007/s13238-020-00793-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/07/2020] [Indexed: 12/19/2022] Open
Abstract
Autophagy is essential for the maintenance of cellular homeostasis and its dysfunction has been linked to various diseases. Autophagy is a membrane driven process and tightly regulated by membrane-associated proteins. Here, we summarized membrane lipid composition, and membrane-associated proteins relevant to autophagy from a spatiotemporal perspective. In particular, we focused on three important membrane remodeling processes in autophagy, lipid transfer for phagophore elongation, membrane scission for phagophore closure, and autophagosome-lysosome membrane fusion. We discussed the significance of the discoveries in this field and possible avenues to follow for future studies. Finally, we summarized the membrane-associated biochemical techniques and assays used to study membrane properties, with a discussion of their applications in autophagy.
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Affiliation(s)
- Linsen Li
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Mindan Tong
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yuhui Fu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Fang Chen
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Shen Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hanmo Chen
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xi Ma
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Defa Li
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Xiaoxia Liu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Qing Zhong
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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11
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Peña-Oyarzun D, Rodriguez-Peña M, Burgos-Bravo F, Vergara A, Kretschmar C, Sotomayor-Flores C, Ramirez-Sarmiento CA, De Smedt H, Reyes M, Perez W, Torres VA, Morselli E, Altamirano F, Wilson CAM, Hill JA, Lavandero S, Criollo A. PKD2/polycystin-2 induces autophagy by forming a complex with BECN1. Autophagy 2021; 17:1714-1728. [PMID: 32543276 PMCID: PMC8354594 DOI: 10.1080/15548627.2020.1782035] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 05/29/2020] [Accepted: 06/03/2020] [Indexed: 12/15/2022] Open
Abstract
Macroautophagy/autophagy is an intracellular process involved in the breakdown of macromolecules and organelles. Recent studies have shown that PKD2/PC2/TRPP2 (polycystin 2, transient receptor potential cation channel), a nonselective cation channel permeable to Ca2+ that belongs to the family of transient receptor potential channels, is required for autophagy in multiple cell types by a mechanism that remains unclear. Here, we report that PKD2 forms a protein complex with BECN1 (beclin 1), a key protein required for the formation of autophagic vacuoles, by acting as a scaffold that interacts with several co-modulators via its coiled-coil domain (CCD). Our data identified a physical and functional interaction between PKD2 and BECN1, which depends on one out of two CCD domains (CC1), located in the carboxy-terminal tail of PKD2. In addition, depletion of intracellular Ca2+ with BAPTA-AM not only blunted starvation-induced autophagy but also disrupted the PKD2-BECN1 complex. Consistently, PKD2 overexpression triggered autophagy by increasing its interaction with BECN1, while overexpression of PKD2D509V, a Ca2+ channel activity-deficient mutant, did not induce autophagy and manifested diminished interaction with BECN1. Our findings show that the PKD2-BECN1 complex is required for the induction of autophagy, and its formation depends on the presence of the CC1 domain of PKD2 and on intracellular Ca2+ mobilization by PKD2. These results provide new insights regarding the molecular mechanisms by which PKD2 controls autophagy.Abbreviations: ADPKD: autosomal dominant polycystic kidney disease; ATG: autophagy-related; ATG14/ATG14L: autophagy related 14; Baf A1: bafilomycin A1; BCL2/Bcl-2: BCL2 apoptosis regulator; BCL2L1/BCL-XL: BCL2 like 1; BECN1: beclin 1; CCD: coiled-coil domain; EBSS: Earle's balanced salt solution; ER: endoplasmic reticulum; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; GOLGA2/GM130: golgin A2; GST: glutathione s-transferase; LAMP1: lysosomal associated membrane protein 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MTORC1: mechanistic target of rapamycin kinase complex 1; NBR1: NBR1 autophagy cargo receptor; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PKD2/PC2: polycystin 2, transient receptor potential cation channel; RTN4/NOGO: reticulon 4; RUBCN/RUBICON: rubicon autophagy regulator; SQSTM1/p62: sequestosome 1; UVRAG: UV radiation resistance associated; WIPI2: WD repeat domain, phosphoinositide interacting 2.
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Affiliation(s)
- Daniel Peña-Oyarzun
- Instituto de Investigación en Ciencias Odontológicas (ICOD), Facultad de Odontología, Universidad de Chile, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas & Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Marcelo Rodriguez-Peña
- Instituto de Investigación en Ciencias Odontológicas (ICOD), Facultad de Odontología, Universidad de Chile, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas & Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Francesca Burgos-Bravo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Angelo Vergara
- Instituto de Investigación en Ciencias Odontológicas (ICOD), Facultad de Odontología, Universidad de Chile, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas & Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Catalina Kretschmar
- Instituto de Investigación en Ciencias Odontológicas (ICOD), Facultad de Odontología, Universidad de Chile, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas & Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Cristian Sotomayor-Flores
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas & Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Cesar A. Ramirez-Sarmiento
- Institute for Biological and Medical Engineering, Facultades de Ingenieria, Medicina y Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Humbert De Smedt
- Department of Cellular and Molecular Medicine, Katholieke Universiteit Leuven, Belgium
| | - Montserrat Reyes
- Instituto de Investigación en Ciencias Odontológicas (ICOD), Facultad de Odontología, Universidad de Chile, Santiago, Chile
- Department of Pathology and Oral Medicine, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - William Perez
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Vicente A. Torres
- Instituto de Investigación en Ciencias Odontológicas (ICOD), Facultad de Odontología, Universidad de Chile, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas & Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Eugenia Morselli
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Francisco Altamirano
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Christian A. M. Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Joseph A. Hill
- Cardiology Division, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sergio Lavandero
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas & Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
- Cardiology Division, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Alfredo Criollo
- Instituto de Investigación en Ciencias Odontológicas (ICOD), Facultad de Odontología, Universidad de Chile, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas & Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Autophagy Research Center, Universidad de Chile, Santiago, Chile
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12
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Barz S, Kriegenburg F, Sánchez-Martín P, Kraft C. Small but mighty: Atg8s and Rabs in membrane dynamics during autophagy. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119064. [PMID: 34048862 PMCID: PMC8261831 DOI: 10.1016/j.bbamcr.2021.119064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/04/2021] [Accepted: 05/21/2021] [Indexed: 11/17/2022]
Abstract
Autophagy is a degradative pathway during which autophagosomes are formed that enwrap cytosolic material destined for turnover within the lytic compartment. Autophagosome biogenesis requires controlled lipid and membrane rearrangements to allow the formation of an autophagosomal seed and its subsequent elongation into a fully closed and fusion-competent double membrane vesicle. Different membrane remodeling events are required, which are orchestrated by the distinct autophagy machinery. An important player among these autophagy proteins is the small lipid-modifier Atg8. Atg8 proteins facilitate various aspects of autophagosome formation and serve as a binding platform for autophagy factors. Also Rab GTPases have been implicated in autophagosome biogenesis. As Atg8 proteins interact with several Rab GTPase regulators, they provide a possible link between autophagy progression and Rab GTPase activity. Here, we review central aspects in membrane dynamics during autophagosome biogenesis with a focus on Atg8 proteins and selected Rab GTPases.
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Affiliation(s)
- Saskia Barz
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
| | - Franziska Kriegenburg
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Pablo Sánchez-Martín
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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13
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de Jong F, Munnik T. Attracted to membranes: lipid-binding domains in plants. PLANT PHYSIOLOGY 2021; 185:707-723. [PMID: 33793907 PMCID: PMC8133573 DOI: 10.1093/plphys/kiaa100] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/11/2020] [Indexed: 05/18/2023]
Abstract
Membranes are essential for cells and organelles to function. As membranes are impermeable to most polar and charged molecules, they provide electrochemical energy to transport molecules across and create compartmentalized microenvironments for specific enzymatic and cellular processes. Membranes are also responsible for guided transport of cargoes between organelles and during endo- and exocytosis. In addition, membranes play key roles in cell signaling by hosting receptors and signal transducers and as substrates and products of lipid second messengers. Anionic lipids and their specific interaction with target proteins play an essential role in these processes, which are facilitated by specific lipid-binding domains. Protein crystallography, lipid-binding studies, subcellular localization analyses, and computer modeling have greatly advanced our knowledge over the years of how these domains achieve precision binding and what their function is in signaling and membrane trafficking, as well as in plant development and stress acclimation.
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Affiliation(s)
- Femke de Jong
- Cluster Green Life Sciences, Section Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Teun Munnik
- Cluster Green Life Sciences, Section Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
- Author for communication:
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14
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Allen EA, Amato C, Fortier TM, Velentzas P, Wood W, Baehrecke EH. A conserved myotubularin-related phosphatase regulates autophagy by maintaining autophagic flux. J Cell Biol 2021; 219:152081. [PMID: 32915229 PMCID: PMC7594499 DOI: 10.1083/jcb.201909073] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 06/23/2020] [Accepted: 08/03/2020] [Indexed: 12/27/2022] Open
Abstract
Macroautophagy (autophagy) targets cytoplasmic cargoes to the lysosome for degradation. Like all vesicle trafficking, autophagy relies on phosphoinositide identity, concentration, and localization to execute multiple steps in this catabolic process. Here, we screen for phosphoinositide phosphatases that influence autophagy in Drosophila and identify CG3530. CG3530 is homologous to the human MTMR6 subfamily of myotubularin-related 3-phosphatases, and therefore, we named it dMtmr6. dMtmr6, which is required for development and viability in Drosophila, functions as a regulator of autophagic flux in multiple Drosophila cell types. The MTMR6 family member MTMR8 has a similar function in autophagy of higher animal cells. Decreased dMtmr6 and MTMR8 function results in autophagic vesicle accumulation and influences endolysosomal homeostasis.
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Affiliation(s)
- Elizabeth A Allen
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Clelia Amato
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Tina M Fortier
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Panagiotis Velentzas
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Will Wood
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Eric H Baehrecke
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
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15
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Cestari I, Stuart K. The phosphoinositide regulatory network in Trypanosoma brucei: Implications for cell-wide regulation in eukaryotes. PLoS Negl Trop Dis 2020; 14:e0008689. [PMID: 33119588 PMCID: PMC7595295 DOI: 10.1371/journal.pntd.0008689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The unicellular eukaryote Trypanosoma brucei undergoes extensive cellular and developmental changes during its life cycle. These include regulation of mammalian stage surface antigen variation and surface composition changes between life stages; switching between glycolysis and oxidative phosphorylation; differential mRNA editing; and changes in posttranscriptional gene expression, protein trafficking, organellar function, and cell morphology. These diverse events are coordinated and controlled throughout parasite development, maintained in homeostasis at each life stage, and are essential for parasite survival in both the host and insect vector. Described herein are the enzymes and metabolites of the phosphatidylinositol (PI) cellular regulatory network, its integration with other cellular regulatory systems that collectively control and coordinate these numerous cellular processes, including cell development and differentiation and the many associated complex processes in multiple subcellular compartments. We conclude that this regulation is the product of the organization of these enzymes within the cellular architecture, their activities, metabolite fluxes, and responses to environmental changes via signal transduction and other processes. We describe a paradigm for how these enzymes and metabolites could function to control and coordinate multiple cellular functions. The significance of the PI system's regulatory functions in single-celled eukaryotes to metazoans and their potential as chemotherapeutic targets are indicated.
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Affiliation(s)
- Igor Cestari
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
- * E-mail: (IC); (KS)
| | - Kenneth Stuart
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- * E-mail: (IC); (KS)
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16
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Oelschlaegel D, Weiss Sadan T, Salpeter S, Krug S, Blum G, Schmitz W, Schulze A, Michl P. Cathepsin Inhibition Modulates Metabolism and Polarization of Tumor-Associated Macrophages. Cancers (Basel) 2020; 12:cancers12092579. [PMID: 32927704 PMCID: PMC7563557 DOI: 10.3390/cancers12092579] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 08/21/2020] [Accepted: 09/01/2020] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Stroma-infiltrating tumor-associated macrophages (TAM) play an important role in regulating tumor progression and chemoresistance. Many tumor-infiltrating macrophage populations can be identified by preferential expression of distinct marker genes associated with an M2 phenotype and may execute tumor-promoting functions by enhancing tissue remodeling, facilitating angiogenesis, and suppressing immune responses. In this study, we aimed to characterize the impact of cathepsins in maintaining the TAM phenotype. For this purpose, we investigated the molecular effects of cathepsin inhibition on the viability and polarization of human primary macrophages as well as its metabolic consequences. Pharmacological inhibition of cathepsins B, L, and S using a novel inhibitor, GB111-NH2, led to a polarization shift from M2- to M1 macrophages, associated with distinct alterations in lysosomal signaling and lipid metabolism. This could be therapeutically exploited in tumors with strong infiltration of M2-macrophages, thereby possibly reverting M2 polarization, overcoming drug resistance, and improving the prognosis of our patients. Abstract Stroma-infiltrating immune cells, such as tumor-associated macrophages (TAM), play an important role in regulating tumor progression and chemoresistance. These effects are mostly conveyed by secreted mediators, among them several cathepsin proteases. In addition, increasing evidence suggests that stroma-infiltrating immune cells are able to induce profound metabolic changes within the tumor microenvironment. In this study, we aimed to characterize the impact of cathepsins in maintaining the TAM phenotype in more detail. For this purpose, we investigated the molecular effects of pharmacological cathepsin inhibition on the viability and polarization of human primary macrophages as well as its metabolic consequences. Pharmacological inhibition of cathepsins B, L, and S using a novel inhibitor, GB111-NH2, led to changes in cellular recycling processes characterized by an increased expression of autophagy- and lysosome-associated marker genes and reduced adenosine triphosphate (ATP) content. Decreased cathepsin activity in primary macrophages further led to distinct changes in fatty acid metabolites associated with increased expression of key modulators of fatty acid metabolism, such as fatty acid synthase (FASN) and acid ceramidase (ASAH1). The altered fatty acid profile was associated with an increased synthesis of the pro-inflammatory prostaglandin PGE2, which correlated with the upregulation of numerous NFkB-dependent pro-inflammatory mediators, including interleukin-1 (IL-1), interleukin-6 (IL-6), C-C motif chemokine ligand 2 (CCL2), and tumor necrosis factor-alpha (TNFα). Our data indicate a novel link between cathepsin activity and metabolic reprogramming in macrophages, demonstrated by a profound impact on autophagy and fatty acid metabolism, which facilitates a pro-inflammatory micromilieu generally associated with enhanced tumor elimination. These results provide a strong rationale for therapeutic cathepsin inhibition to overcome the tumor-promoting effects of the immune-evasive tumor micromilieu.
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Affiliation(s)
- Diana Oelschlaegel
- Department of Internal Medicine I, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (D.O.); (S.K.)
| | - Tommy Weiss Sadan
- Institute for Drug Research, Hebrew University of Jerusalem, Jerusalem 9112102, Israel; (T.W.S.); (S.S.); (G.B.)
| | - Seth Salpeter
- Institute for Drug Research, Hebrew University of Jerusalem, Jerusalem 9112102, Israel; (T.W.S.); (S.S.); (G.B.)
| | - Sebastian Krug
- Department of Internal Medicine I, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (D.O.); (S.K.)
| | - Galia Blum
- Institute for Drug Research, Hebrew University of Jerusalem, Jerusalem 9112102, Israel; (T.W.S.); (S.S.); (G.B.)
| | - Werner Schmitz
- Department of Biochemistry and Molecular Biology, Theodor-Boveri-Institute, Biocenter, 97074 Würzburg, Germany; (W.S.); (A.S.)
| | - Almut Schulze
- Department of Biochemistry and Molecular Biology, Theodor-Boveri-Institute, Biocenter, 97074 Würzburg, Germany; (W.S.); (A.S.)
| | - Patrick Michl
- Department of Internal Medicine I, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (D.O.); (S.K.)
- Correspondence: ; Tel.: +49-345-557-2661; Fax: +49-345-557-225
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17
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Kim Y, Kim SH. WD40-Repeat Proteins in Ciliopathies and Congenital Disorders of Endocrine System. Endocrinol Metab (Seoul) 2020; 35:494-506. [PMID: 32894826 PMCID: PMC7520596 DOI: 10.3803/enm.2020.302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/10/2020] [Indexed: 12/23/2022] Open
Abstract
WD40-repeat (WDR)-containing proteins constitute an evolutionarily conserved large protein family with a broad range of biological functions. In human proteome, WDR makes up one of the most abundant protein-protein interaction domains. Members of the WDR protein family play important roles in nearly all major cellular signalling pathways. Mutations of WDR proteins have been associated with various human pathologies including neurological disorders, cancer, obesity, ciliopathies and endocrine disorders. This review provides an updated overview of the biological functions of WDR proteins and their mutations found in congenital disorders. We also highlight the significant role of WDR proteins in ciliopathies and endocrine disorders. The new insights may help develop therapeutic approaches targeting WDR motifs.
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Affiliation(s)
- Yeonjoo Kim
- Cell Biology Research Centre, Molecular and Clinical Sciences Research Institute, St. George’s, University of London, London, UK
| | - Soo-Hyun Kim
- Cell Biology Research Centre, Molecular and Clinical Sciences Research Institute, St. George’s, University of London, London, UK
- Corresponding author: Soo-Hyun Kim Cell Biology Research Centre, Molecular and Clinical Sciences Research Institute, St. George’s, University of London, Cranmer Terrace, London SW17 0RE, UK Tel: +44-208-266-6198, E-mail:
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18
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Olivença DV, Voit EO, Pinto FR. ENaC regulation by phospholipids and DGK explained through mathematical modeling. Sci Rep 2020; 10:13952. [PMID: 32811866 PMCID: PMC7435262 DOI: 10.1038/s41598-020-70630-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/21/2020] [Indexed: 01/16/2023] Open
Abstract
Cystic fibrosis is a condition caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR). It is also thought to increase the activity of epithelial sodium channels (ENaC). The altered function of these ion channels is one of the causes of the thick dehydrated mucus that characterizes the disease and is partially responsible for recurrent pulmonary infections and inflammation events that ultimately destroy the lungs of affected subjects. Phosphoinositides are signaling lipids that regulate numerous cellular processes and membrane proteins, including ENaC. Inhibition of diacylglycerol kinase (DGK), an enzyme of the phosphoinositide pathway, reduces ENaC function. We propose a computational analysis that is based on the combination of two existing mathematical models: one representing the dynamics of phosphoinositides and the other explaining how phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) influences ENaC activity and, consequently, airway surface liquid. This integrated model permits, for the first time, a detailed assessment of the intricate interactions between DGK and ENaC and is consistent with available literature data. In particular, the computational approach allows comparisons of two competing hypotheses regarding the regulation of ENaC. The results strongly suggest that the regulation of ENaC is primarily exerted through the control of PI(4,5)P2 production by type-I phosphatidylinositol-4-phosphate 5-kinase (PIP5KI), which in turn is controlled by phosphatidic acid (PA), the product of the DGK reaction.
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Affiliation(s)
- Daniel V. Olivença
- Faculty of Sciences, BioISI – Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016 Lisbon, Portugal
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic Drive, Atlanta, GA 30332-2000 USA
| | - Eberhard O. Voit
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic Drive, Atlanta, GA 30332-2000 USA
| | - Francisco R. Pinto
- Faculty of Sciences, BioISI – Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016 Lisbon, Portugal
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19
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Hollenstein DM, Kraft C. Autophagosomes are formed at a distinct cellular structure. Curr Opin Cell Biol 2020; 65:50-57. [PMID: 32203894 PMCID: PMC7588827 DOI: 10.1016/j.ceb.2020.02.012] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/13/2020] [Accepted: 02/20/2020] [Indexed: 11/09/2022]
Abstract
Autophagy is characterized by the formation of double-membrane vesicles called autophagosomes, which deliver bulk cytoplasmic material to the lytic compartment of the cell for degradation. Autophagosome formation is initiated by assembly and recruitment of the core autophagy machinery to distinct cellular sites, referred to as phagophore assembly sites (PAS) in yeast or autophagosome formation sites in other organisms. A large number of autophagy proteins involved in the formation of autophagosomes has been identified; however, how the individual components of the PAS are assembled and how they function to generate autophagosomes remains a fundamental question. Here, we highlight recent studies that provide molecular insights into PAS organization and the role of the endoplasmic reticulum and the vacuole in autophagosome formation.
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Affiliation(s)
- David M Hollenstein
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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20
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Shen W, Wei J, Gao C. Functional Analysis of Plant FYVE Domain Proteins in Endosomal Trafficking. Methods Mol Biol 2020; 2177:83-94. [PMID: 32632807 DOI: 10.1007/978-1-0716-0767-1_8] [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] [Indexed: 04/11/2023]
Abstract
The FYVE domain is a double zinc finger-like domain that predominantly binds phosphatidylinositol 3-phosphate. The FYVE domain is usually found in proteins primarily involved in regulating various aspects of endomembrane homeostasis, including endosome tethering, endocytic recycling, membrane protein sorting, and autophagosome maturation. Whereas FYVE domain proteins have been extensively studied in mammals and yeast, only a few FYVE domain proteins have been identified and characterized in plants. Here, by using as an example FREE1 (FYVE DOMAIN PROTEIN REQUIRED FOR ENDOSOMAL SORTING 1), a protein previously identified by us as a critical factor for endosomal trafficking, we describe methods to determine its lipid binding properties and endosomal localization. In addition, we also demonstrate a method to quickly test whether an FYVE domain protein is involved in endosomal sorting in plant cells.
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Affiliation(s)
- Wenjin Shen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Juan Wei
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China.
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21
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Abstract
Neurodegenerative diseases are, at present, major socio-economic burdens without effective treatments and their increasing prevalence means that these diseases will be a challenge for future generations. Neurodegenerative diseases may differ in etiology and pathology but are often caused by the accumulation of dysfunctional and aggregation-prone proteins. Autophagy, a conserved cellular mechanism, deals with cellular stress and waste product build-up and has been shown to reduce the accumulation of dysfunctional proteins in animal models of neurodegenerative diseases. Historically, progress in understanding the precise function of lipids has traditionally been far behind other biological molecules (like proteins) but emerging works demonstrate the importance of lipids in the autophagy pathway and how the disturbance of lipid metabolism is connected to neurodegeneration. Here we review how altered autophagy and the disturbance of lipid metabolism, particularly of phosphoinositols and sphingolipids, feature in neurodegenerative diseases and address work from the field that suggests that these potentially offer an opportunity of therapeutic intervention.
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Affiliation(s)
- Sergio Hernandez-Diaz
- Université de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, 33000, Bordeaux, France.,CNRS, Institut des Maladies Neurodégénératives, UMR 5293, 33000, Bordeaux, France
| | - Sandra-Fausia Soukup
- Université de Bordeaux, Institut des Maladies Neurodégénératives, UMR 5293, 33000, Bordeaux, France.,CNRS, Institut des Maladies Neurodégénératives, UMR 5293, 33000, Bordeaux, France
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22
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Müller R, Citir M, Hauke S, Schultz C. Synthesis and Cellular Labeling of Caged Phosphatidylinositol Derivatives. Chemistry 2019; 26:384-389. [PMID: 31550056 PMCID: PMC6973124 DOI: 10.1002/chem.201903704] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/22/2019] [Indexed: 01/25/2023]
Abstract
Phosphatidylinositol (PI) is the biosynthetic precursor for seven phosphoinositides, important signaling lipids in cells. A membrane‐permeant caged PI derivative featuring a photo‐removable coumarinyl group masking the negative charge of the phosphate, as well as two enzymatically removable butyrate esters for increased lipophilicity and for preventing phosphate migration, were synthesized. Rapid cell entry and cellular labeling in fixed cells was demonstrated by a photo‐cross‐linkable diazirine followed by attachment of a fluorophore through click chemistry. Using this technique, we found that the multifunctional caged PI derivative resided predominantly at internal membranes but rapidly changed to the plasma membrane after uncaging. Accordingly, a preliminary proteomic analysis of the lipid–protein conjugates revealed that the two major PI transport proteins PITPα and β were prime targets of the photo‐cross‐linked PI derivative.
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Affiliation(s)
- Rainer Müller
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Mevlut Citir
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Sebastian Hauke
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Carsten Schultz
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR, 97239-3098, USA
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23
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Clement M, Raffort J, Lareyre F, Tsiantoulas D, Newland S, Lu Y, Masters L, Harrison J, Saveljeva S, Ma MKL, Ozsvar-Kozma M, Lam BYH, Yeo GSH, Binder CJ, Kaser A, Mallat Z. Impaired Autophagy in CD11b + Dendritic Cells Expands CD4 + Regulatory T Cells and Limits Atherosclerosis in Mice. Circ Res 2019; 125:1019-1034. [PMID: 31610723 PMCID: PMC6844650 DOI: 10.1161/circresaha.119.315248] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Supplemental Digital Content is available in the text. Atherosclerosis is a chronic inflammatory disease. Recent studies have shown that dysfunctional autophagy in endothelial cells, smooth muscle cells, and macrophages, plays a detrimental role during atherogenesis, leading to the suggestion that autophagy-stimulating approaches may provide benefit.
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Affiliation(s)
- Marc Clement
- From the Division of Cardiovascular Medicine, University of Cambridge, Cambridge, United Kingdom (M.C., J.R., F.L., D.T., S.N., Y.L., L.M., J.H., Z.M.)
| | - Juliette Raffort
- From the Division of Cardiovascular Medicine, University of Cambridge, Cambridge, United Kingdom (M.C., J.R., F.L., D.T., S.N., Y.L., L.M., J.H., Z.M.).,Université CÔte d'Azur, Institut National de la Santé et de la Recherche Médicale, Centre Mediterranéen de Recherche Moléculaire, University Hospital of Nice, France (J.R., F.L.)
| | - Fabien Lareyre
- From the Division of Cardiovascular Medicine, University of Cambridge, Cambridge, United Kingdom (M.C., J.R., F.L., D.T., S.N., Y.L., L.M., J.H., Z.M.).,Université CÔte d'Azur, Institut National de la Santé et de la Recherche Médicale, Centre Mediterranéen de Recherche Moléculaire, University Hospital of Nice, France (J.R., F.L.)
| | - Dimitrios Tsiantoulas
- From the Division of Cardiovascular Medicine, University of Cambridge, Cambridge, United Kingdom (M.C., J.R., F.L., D.T., S.N., Y.L., L.M., J.H., Z.M.)
| | - Stephen Newland
- From the Division of Cardiovascular Medicine, University of Cambridge, Cambridge, United Kingdom (M.C., J.R., F.L., D.T., S.N., Y.L., L.M., J.H., Z.M.)
| | - Yuning Lu
- From the Division of Cardiovascular Medicine, University of Cambridge, Cambridge, United Kingdom (M.C., J.R., F.L., D.T., S.N., Y.L., L.M., J.H., Z.M.)
| | - Leanne Masters
- From the Division of Cardiovascular Medicine, University of Cambridge, Cambridge, United Kingdom (M.C., J.R., F.L., D.T., S.N., Y.L., L.M., J.H., Z.M.)
| | - James Harrison
- From the Division of Cardiovascular Medicine, University of Cambridge, Cambridge, United Kingdom (M.C., J.R., F.L., D.T., S.N., Y.L., L.M., J.H., Z.M.)
| | - Svetlana Saveljeva
- Department of Gastroenterology and Hepatology, University of Cambridge, United Kingdom (S.S., A.K.)
| | - Marcella K L Ma
- MRC Metabolic Diseases Unit, University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Genomics and Transcriptomics Core, Addenbrooke's Hospital, Cambridge, United Kingdom (M.K.L.M., B.Y.H.L., G.S.H.Y.)
| | - Maria Ozsvar-Kozma
- Department of Laboratory Medicine, Medical University of Vienna and Center for Molecular Medicine (CeMM) of the Austrian Academy of Sciences Vienna, Austria (M.O.-K., C.J.B)
| | - Brian Y H Lam
- MRC Metabolic Diseases Unit, University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Genomics and Transcriptomics Core, Addenbrooke's Hospital, Cambridge, United Kingdom (M.K.L.M., B.Y.H.L., G.S.H.Y.)
| | - Giles S H Yeo
- MRC Metabolic Diseases Unit, University of Cambridge Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Genomics and Transcriptomics Core, Addenbrooke's Hospital, Cambridge, United Kingdom (M.K.L.M., B.Y.H.L., G.S.H.Y.)
| | - Christoph J Binder
- Department of Laboratory Medicine, Medical University of Vienna and Center for Molecular Medicine (CeMM) of the Austrian Academy of Sciences Vienna, Austria (M.O.-K., C.J.B)
| | - Arthur Kaser
- Department of Gastroenterology and Hepatology, University of Cambridge, United Kingdom (S.S., A.K.)
| | - Ziad Mallat
- From the Division of Cardiovascular Medicine, University of Cambridge, Cambridge, United Kingdom (M.C., J.R., F.L., D.T., S.N., Y.L., L.M., J.H., Z.M.).,Institut National de la Santé et de la Recherche Médicale, Paris Cardiovascular Research Center, France (Z.M.)
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24
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Cernikova L, Faso C, Hehl AB. Roles of Phosphoinositides and Their binding Proteins in Parasitic Protozoa. Trends Parasitol 2019; 35:996-1008. [PMID: 31615721 DOI: 10.1016/j.pt.2019.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 12/16/2022]
Abstract
Phosphoinositides (or phosphatidylinositol phosphates, PIPs) are low-abundance membrane phospholipids that act, in conjunction with their binding partners, as important constitutive signals defining biochemical organelle identity as well as membrane trafficking and signal transduction at eukaryotic cellular membranes. In this review, we present roles for PIP residues and PIP-binding proteins in endocytosis and autophagy in protist parasites such as Trypanosoma brucei, Toxoplasma gondii, Plasmodium falciparum, Entamoeba histolytica, and Giardia lamblia. Molecular parasitologists with an interest in comparative cell and molecular biology of membrane trafficking in protist lineages beyond the phylum Apicomplexa, along with cell and molecular biologists generally interested in the diversification of membrane trafficking in eukaryotes, will hopefully find this review to be a useful resource.
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Affiliation(s)
- Lenka Cernikova
- Institute of Parasitology, University of Zurich (ZH), Zurich, Switzerland
| | - Carmen Faso
- Institute of Parasitology, University of Zurich (ZH), Zurich, Switzerland; Institute of Cell Biology, University of Bern (BE), Bern, Switzerland
| | - Adrian B Hehl
- Institute of Parasitology, University of Zurich (ZH), Zurich, Switzerland.
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25
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Wang H, Lo WT, Haucke V. Phosphoinositide switches in endocytosis and in the endolysosomal system. Curr Opin Cell Biol 2019; 59:50-57. [DOI: 10.1016/j.ceb.2019.03.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/08/2019] [Accepted: 03/19/2019] [Indexed: 02/07/2023]
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26
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de la Ballina LR, Munson MJ, Simonsen A. Lipids and Lipid-Binding Proteins in Selective Autophagy. J Mol Biol 2019; 432:135-159. [PMID: 31202884 DOI: 10.1016/j.jmb.2019.05.051] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 02/07/2023]
Abstract
Eukaryotic cells have the capacity to degrade intracellular components through a lysosomal degradation pathway called macroautophagy (henceforth referred to as autophagy) in which superfluous or damaged cytosolic entities are engulfed and separated from the rest of the cell constituents into double membraned vesicles known as autophagosomes. Autophagosomes then fuse with endosomes and lysosomes, where cargo is broken down into basic building blocks that are released to the cytoplasm for the cell to reuse. Autophagic degradation can target either cytoplasmic material in bulk (non-selective autophagy) or particular cargo in what is called selective autophagy. Proper autophagic turnover requires the orchestrated participation of several players that need to be tightly and temporally coordinated. Whereas a large number of autophagy-related (ATG) proteins have been identified and their functions and regulation are starting to be understood, there is substantially less knowledge regarding the specific lipids constituting the autophagic membranes as well as their role in initiating, enabling or regulating the autophagic process. This review focuses on lipids and their corresponding binding proteins that are crucial in the process of selective autophagy.
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Affiliation(s)
- Laura R de la Ballina
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Michael J Munson
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
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27
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The role of LRRK2 in cytoskeletal dynamics. Biochem Soc Trans 2018; 46:1653-1663. [PMID: 30467120 DOI: 10.1042/bst20180469] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/16/2018] [Accepted: 10/24/2018] [Indexed: 12/11/2022]
Abstract
Leucine-rich repeat kinase 2 (LRRK2), a complex kinase/GTPase mutated in Parkinson's disease, has been shown to physically and functionally interact with cytoskeletal-related components in different brain cells. Neurons greatly rely on a functional cytoskeleton for many homeostatic processes such as local and long-distance vesicle transport, synaptic plasticity, and dendrites/axons growth and remodeling. Here, we will review the available data linking LRRK2 and the cytoskeleton, and discuss how this may be functionally relevant for the well-established roles of LRRK2 in intracellular trafficking pathways and outgrowth of neuronal processes in health and disease conditions.
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28
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Nascimbeni AC, Codogno P, Morel E. Local detection of PtdIns3P at autophagosome biogenesis membrane platforms. Autophagy 2017; 13:1602-1612. [PMID: 28813193 DOI: 10.1080/15548627.2017.1341465] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Phosphatidylinositol 3-phosphate (PtdIns3P) is a key player of membrane trafficking regulation, mostly synthesized by the PIK3C3 lipid kinase. The presence of PtdIns3P on endosomes has been demonstrated; however, the role and dynamics of the pool of PtdIns3P dedicated to macroautophagy/autophagy remains elusive. Here we addressed this question by studying the mobilization of PtdIns3P in time and space during autophagosome biogenesis. We compared different dyes known to specifically detect PtdIns3P by fluorescence microscopy analysis, based on PtdIns3P-binding FYVE and PX domains, and show that these transfected dyes induce defects in endosomal dynamics as well as artificial and sustained autophagosome formation. In contrast, indirect use of recombinant FYVE enabled us to track and discriminate endosomal and autophagosomal pools of PtdIns3P. We used this method to analyze localization and dynamics of PtdIns3P subdomains on the endoplasmic reticulum, at sites of pre-autophagosome associated protein recruitment such as the PtdIns3P-binding ZFYVE1/DFCP1 and WIPI2 autophagy regulators. This approach thus revealed the presence of a specific pool of PtdIns3P at the site where autophagosome assembly is initiated.
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Affiliation(s)
- Anna Chiara Nascimbeni
- a Cell Biology Department , Institut Necker-Enfants Malades (INEM) , INSERM U1151-CNRS UMR 8253, Paris , France.,b Université Paris Descartes-Sorbonne Paris Cité , Paris , France
| | - Patrice Codogno
- a Cell Biology Department , Institut Necker-Enfants Malades (INEM) , INSERM U1151-CNRS UMR 8253, Paris , France.,b Université Paris Descartes-Sorbonne Paris Cité , Paris , France
| | - Etienne Morel
- a Cell Biology Department , Institut Necker-Enfants Malades (INEM) , INSERM U1151-CNRS UMR 8253, Paris , France.,b Université Paris Descartes-Sorbonne Paris Cité , Paris , France
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29
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Shengjuler D, Sun S, Cremer PS, Cameron CE. PIP-on-a-chip: A Label-free Study of Protein-phosphoinositide Interactions. J Vis Exp 2017:55869. [PMID: 28784961 PMCID: PMC5613778 DOI: 10.3791/55869] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Numerous cellular proteins interact with membrane surfaces to affect essential cellular processes. These interactions can be directed towards a specific lipid component within a membrane, as in the case of phosphoinositides (PIPs), to ensure specific subcellular localization and/or activation. PIPs and cellular PIP-binding domains have been studied extensively to better understand their role in cellular physiology. We applied a pH modulation assay on supported lipid bilayers (SLBs) as a tool to study protein-PIP interactions. In these studies, pH sensitive ortho-Sulforhodamine B conjugated phosphatidylethanolamine is used to detect protein-PIP interactions. Upon binding of a protein to a PIP-containing membrane surface, the interfacial potential is modulated (i.e. change in local pH), shifting the protonation state of the probe. A case study of the successful usage of the pH modulation assay is presented by using phospholipase C delta1 Pleckstrin Homology (PLC-δ1 PH) domain and phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) interaction as an example. The apparent dissociation constant (Kd,app) for this interaction was 0.39 ± 0.05 µM, similar to Kd,app values obtained by others. As previously observed, the PLC-δ1 PH domain is PI(4,5)P2 specific, shows weaker binding towards phosphatidylinositol 4-phosphate, and no binding to pure phosphatidylcholine SLBs. The PIP-on-a-chip assay is advantageous over traditional PIP-binding assays, including but not limited to low sample volume and no ligand/receptor labeling requirements, the ability to test high- and low-affinity membrane interactions with both small and large molecules, and improved signal to noise ratio. Accordingly, the usage of the PIP-on-a-chip approach will facilitate the elucidation of mechanisms of a wide range of membrane interactions. Furthermore, this method could potentially be used in identifying therapeutics that modulate protein's capacity to interact with membranes.
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Affiliation(s)
- Djoshkun Shengjuler
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University;
| | - Simou Sun
- Department of Chemistry, The Pennsylvania State University
| | - Paul S Cremer
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University; Department of Chemistry, The Pennsylvania State University;
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University;
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30
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Tipping the scales: Lessons from simple model systems on inositol imbalance in neurological disorders. Eur J Cell Biol 2017; 96:154-163. [PMID: 28153412 DOI: 10.1016/j.ejcb.2017.01.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/18/2017] [Accepted: 01/21/2017] [Indexed: 11/20/2022] Open
Abstract
Inositol and inositol-containing compounds have signalling and regulatory roles in many cellular processes, suggesting that inositol imbalance may lead to wide-ranging changes in cellular functions. Indeed, changes in inositol-dependent signalling have been implicated in various diseases and cellular functions such as autophagy, and these changes have often been proposed as therapeutic targets. However, few studies have highlighted the links between inositol depletion and the downstream effects on inositol phosphates and phosphoinositides in disease states. For this research, many advances have employed simple model systems that include the social amoeba D. discoideum and the yeast S. cerevisiae, since these models enable a range of experimental approaches that are not possible in mammalian models. In this review, we discuss recent findings initiated in simple model systems and translated to higher model organisms where the effect of altered inositol, inositol phosphate and phosphoinositide levels impact on bipolar disorder, Alzheimer disease, epilepsy and autophagy.
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31
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Just W. . FEBS Lett 2016; 590:2325-6. [DOI: 10.1002/1873-3468.12305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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