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Mohan J, Moparthi SB, Girard-Blanc C, Campisi D, Blanchard S, Nugues C, Rama S, Salles A, Pénard E, Vassilopoulos S, Wollert T. ATG16L1 induces the formation of phagophore-like membrane cups. Nat Struct Mol Biol 2024; 31:1448-1459. [PMID: 38834913 DOI: 10.1038/s41594-024-01300-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 03/28/2024] [Indexed: 06/06/2024]
Abstract
The hallmark of non-selective autophagy is the formation of cup-shaped phagophores that capture bulk cytoplasm. The process is accompanied by the conjugation of LC3B to phagophores by an E3 ligase complex comprising ATG12-ATG5 and ATG16L1. Here we combined two complementary reconstitution approaches to reveal the function of LC3B and its ligase complex during phagophore expansion. We found that LC3B forms together with ATG12-ATG5-ATG16L1 a membrane coat that remodels flat membranes into cups that closely resemble phagophores. Mechanistically, we revealed that cup formation strictly depends on a close collaboration between LC3B and ATG16L1. Moreover, only LC3B, but no other member of the ATG8 protein family, promotes cup formation. ATG16L1 truncates that lacked the C-terminal membrane binding domain catalyzed LC3B lipidation but failed to assemble coats, did not promote cup formation and inhibited the biogenesis of non-selective autophagosomes. Our results thus demonstrate that ATG16L1 and LC3B induce and stabilize the characteristic cup-like shape of phagophores.
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Affiliation(s)
- Jagan Mohan
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, Paris, France
| | - Satish B Moparthi
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, Paris, France
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Association Institut de Myologie, Centre de Recherche en Myologie, Paris, France
| | - Christine Girard-Blanc
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, Paris, France
| | - Daniele Campisi
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, Paris, France
| | - Stéphane Blanchard
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, Paris, France
| | - Charlotte Nugues
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, Paris, France
| | - Sowmya Rama
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, Paris, France
| | - Audrey Salles
- Unit of Technology and Service Photonic BioImaging (UTechS PBI), C2RT, Institut Pasteur, Université de Paris, Paris, France
| | - Esthel Pénard
- Ultrastructural BioImaging Core Facility (UBI), C2RT, Institut Pasteur, Université Paris Cité, Paris, France
| | - Stéphane Vassilopoulos
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Association Institut de Myologie, Centre de Recherche en Myologie, Paris, France.
| | - Thomas Wollert
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, Paris, France.
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2
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Maciąg F, Chhikara A, Heine M. Calcium channel signalling at neuronal endoplasmic reticulum-plasma membrane junctions. Biochem Soc Trans 2024; 52:1617-1629. [PMID: 38934485 DOI: 10.1042/bst20230819] [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: 03/27/2024] [Revised: 05/22/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Neurons are highly specialised cells that need to relay information over long distances and integrate signals from thousands of synaptic inputs. The complexity of neuronal function is evident in the morphology of their plasma membrane (PM), by far the most intricate of all cell types. Yet, within the neuron lies an organelle whose architecture adds another level to this morphological sophistication - the endoplasmic reticulum (ER). Neuronal ER is abundant in the cell body and extends to distant axonal terminals and postsynaptic dendritic spines. It also adopts specialised structures like the spine apparatus in the postsynapse and the cisternal organelle in the axon initial segment. At membrane contact sites (MCSs) between the ER and the PM, the two membranes come in close proximity to create hubs of lipid exchange and Ca2+ signalling called ER-PM junctions. The development of electron and light microscopy techniques extended our knowledge on the physiological relevance of ER-PM MCSs. Equally important was the identification of ER and PM partners that interact in these junctions, most notably the STIM-ORAI and VAP-Kv2.1 pairs. The physiological functions of ER-PM junctions in neurons are being increasingly explored, but their molecular composition and the role in the dynamics of Ca2+ signalling are less clear. This review aims to outline the current state of research on the topic of neuronal ER-PM contacts. Specifically, we will summarise the involvement of different classes of Ca2+ channels in these junctions, discuss their role in neuronal development and neuropathology and propose directions for further research.
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Affiliation(s)
- Filip Maciąg
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, Hanns-Dieter Hüsch Weg 15, 55128 Mainz, Germany
| | - Arun Chhikara
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, Hanns-Dieter Hüsch Weg 15, 55128 Mainz, Germany
| | - Martin Heine
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, Hanns-Dieter Hüsch Weg 15, 55128 Mainz, Germany
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3
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Pradel B, Cantaloube G, Villares M, Deffieu MS, Robert-Hebmann V, Lucansky V, Faure M, Chazal N, Gaudin R, Espert L. LC3B conjugation machinery promotes autophagy-independent HIV-1 entry in CD4 + T lymphocytes. Autophagy 2024; 20:1825-1836. [PMID: 38566318 PMCID: PMC11262235 DOI: 10.1080/15548627.2024.2338573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 03/29/2024] [Indexed: 04/04/2024] Open
Abstract
HIV-1 entry into CD4+ T lymphocytes relies on the viral and cellular membranes' fusion, leading to viral capsid delivery in the target cell cytoplasm. Atg8/LC3B conjugation to lipids, process named Atg8ylation mainly studied in the context of macroautophagy/autophagy, occurs transiently in the early stages of HIV-1 replication in CD4+ T lymphocytes. Despite numerous studies investigating the HIV-1-autophagy interplays, the Atg8ylation impact in these early stages of infection remains unknown. Here we found that HIV-1 exposure leads to the rapid LC3B enrichment toward the target cell plasma membrane, in close proximity with the incoming viral particles. Furthermore, we demonstrated that Atg8ylation is a key event facilitating HIV-1 entry in target CD4+ T cells. Interestingly, this effect is independent of canonical autophagy as ATG13 silencing does not prevent HIV-1 entry. Together, our results provide an unconventional role of LC3B conjugation subverted by HIV-1 to achieve a critical step of its replication cycle.Abbreviations: BafA1: bafilomycin A1; BlaM: beta-lactamase; CD4+ TL: CD4+ T lymphocytes; PtdIns3K-BECN1 complex: BECN1-containing class III phosphatidylinositol 3-kinase complex; Env: HIV-1 envelope glycoproteins; HIV-1: type 1 human immunodeficiency virus; PM: plasma membrane; PtdIns3P: phosphatidylinositol-3-phosphate; VLP: virus-like particle.
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Affiliation(s)
- Baptiste Pradel
- University of Montpellier, CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), Montpellier, France
| | - Guilhem Cantaloube
- University of Montpellier, CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), Montpellier, France
| | - Marie Villares
- University of Montpellier, CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), Montpellier, France
| | - Maïka S. Deffieu
- University of Montpellier, CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), Montpellier, France
| | - Véronique Robert-Hebmann
- University of Montpellier, CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), Montpellier, France
| | - Vincent Lucansky
- University of Montpellier, CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), Montpellier, France
- Jessenius Faculty of Medicine in Martin (JFMED CU), Department of Pathophysiology, Comenius University in Bratislava, Martin, Slovakia
| | - Mathias Faure
- CIRI, University of Lyon, Inserm U1111, Claude Bernard University Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Nathalie Chazal
- University of Montpellier, CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), Montpellier, France
| | - Raphaël Gaudin
- University of Montpellier, CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), Montpellier, France
| | - Lucile Espert
- University of Montpellier, CNRS, Institut de Recherche en Infectiologie de Montpellier (IRIM), Montpellier, France
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Liu S, Su L, Li J, Zhang Y, Hu X, Wang P, Liu P, Ye J. Inhibition of miR-146b-5p alleviates isoprenaline-induced cardiac hypertrophy via regulating DFCP1. Mol Cell Endocrinol 2024; 589:112252. [PMID: 38649132 DOI: 10.1016/j.mce.2024.112252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
Pathological cardiac hypertrophy often precedes heart failure due to various stimuli, yet effective clinical interventions remain limited. Recently, microRNAs (miRNAs) have been identified as critical regulators of cardiovascular development. In this study, we investigated the role of miR-146b-5p and its underlying mechanisms of action in cardiac hypertrophy. Isoprenaline (ISO) treatment induced significant hypertrophy and markedly enhanced the expression of miR-146b-5p in cultured neonatal rat cardiomyocytes and hearts of C57BL/6 mice. Transfection with the miR-146b-5p mimic led to cardiomyocyte hypertrophy accompanied by autophagy inhibition. Conversely, miR-146b-5p inhibition significantly alleviated ISO-induced autophagy depression, thereby mitigating cardiac hypertrophy both in vitro and in vivo. Our results showed that the autophagy-related mediator double FYVE domain-containing protein 1 (DFCP1) is a target of miR-146b-5p. MiR-146b-5p blocked autophagic flux in cardiomyocytes by suppressing DFCP1, thus contributing to hypertrophy. These findings revealed that miR-146b-5p is a potential regulator of autophagy associated with the onset of cardiac hypertrophy, suggesting a possible therapeutic strategy involving the inhibition of miR-146b-5p.
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Affiliation(s)
- Siling Liu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, China
| | - Linjie Su
- School of Pharmaceutical Sciences, Sun Yat-Sen University, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, China
| | - Jie Li
- School of Pharmaceutical Sciences, Sun Yat-Sen University, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, China
| | - Yuexin Zhang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, China
| | - Xiaopei Hu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, China
| | - Pengcheng Wang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, China
| | - Peiqing Liu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, China.
| | - Jiantao Ye
- School of Pharmaceutical Sciences, Sun Yat-Sen University, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, China.
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5
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Kumar A, Krausko M, Jásik J. SYNAPTOTAGMIN 4 is expressed mainly in the phloem and participates in abiotic stress tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2024; 15:1363555. [PMID: 39011301 PMCID: PMC11246894 DOI: 10.3389/fpls.2024.1363555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 06/04/2024] [Indexed: 07/17/2024]
Abstract
Plant synaptotagmins structurally resemble animal synaptotagmins and extended-synaptotagmins. Animal synaptotagmins are well-characterized calcium sensors in membrane trafficking, and extended-synaptotagmins mediate lipid transfer at the endoplasmic reticulum-plasma membrane contact sites. Here, we characterize SYNAPTOTAGMIN 4 (SYT4), which belongs to the six-member family in Arabidopsis. Fluorometric GUS assay showed that the SYT4 promoter was strongest in roots and the least active in rosettes and cauline leaves, which was confirmed by qPCR. In seedlings, promoter activity was influenced by several factors, such as plant growth regulators, mannitol, sucrose, polyethylene glycol and cold. GUS histochemistry revealed SYT4 promoter activity in the phloem of all organs and even almost exclusively in sieve element precursors and differentiating sieve elements. Accordingly, the SYT-GFP fusion protein also accumulated in these cells with maximal abundance in sieve element precursors. The protein formed a network in the cytoplasm, but during sieve tube differentiation, it deposited at the cell periphery and disappeared from mature tubes. Using photoconvertible fluorescence technology, we showed that a high abundance of SYT4 protein in meristematic protophloem cells was due to its extensive synthesis. SYT4 protein synthesis was interrupted in differentiating sieve elements, but protein degradation was also reduced. In addition to phloem, the fusion protein was detected in shoot and root stem cell niche as early as the late heart stage of the embryo. We isolated and molecularly and biologically characterized five syt4 T-DNA insertion alleles and subjected them to phenotype analysis. The allele with the C2B domain interrupted by an T-DNA insertion exhibits increased sensitivity to factors such as auxins, osmotics, salicylic acid, sodium chloride, and the absence of sucrose in the root growth test.
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Affiliation(s)
- Ajay Kumar
- Department of Experimental Plant Biology, Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Miroslav Krausko
- Department of Experimental Plant Biology, Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Ján Jásik
- Department of Experimental Plant Biology, Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
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6
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Nähse V, Stenmark H, Schink KO. Omegasomes control formation, expansion, and closure of autophagosomes. Bioessays 2024; 46:e2400038. [PMID: 38724256 DOI: 10.1002/bies.202400038] [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: 02/15/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 05/28/2024]
Abstract
Autophagy, an essential cellular process for maintaining cellular homeostasis and eliminating harmful cytoplasmic objects, involves the de novo formation of double-membraned autophagosomes that engulf and degrade cellular debris, protein aggregates, damaged organelles, and pathogens. Central to this process is the phagophore, which forms from donor membranes rich in lipids synthesized at various cellular sites, including the endoplasmic reticulum (ER), which has emerged as a primary source. The ER-associated omegasomes, characterized by their distinctive omega-shaped structure and accumulation of phosphatidylinositol 3-phosphate (PI3P), play a pivotal role in autophagosome formation. Omegasomes are thought to serve as platforms for phagophore assembly by recruiting essential proteins such as DFCP1/ZFYVE1 and facilitating lipid transfer to expand the phagophore. Despite the critical importance of phagophore biogenesis, many aspects remain poorly understood, particularly the complete range of proteins involved in omegasome dynamics, and the detailed mechanisms of lipid transfer and membrane contact site formation.
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Affiliation(s)
- Viola Nähse
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Harald Stenmark
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Kay O Schink
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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7
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Ye Z, Ng CP, Liu H, Bao Q, Xu S, Zu D, He Y, Huang Y, Al-Aidaroos AQO, Guo K, Li J, Yaw LP, Xiong Q, Thura M, Zheng W, Guan F, Cheng X, Shi Y, Zeng Q. PRL1 and PRL3 promote macropinocytosis via its lipid phosphatase activity. Theranostics 2024; 14:3423-3438. [PMID: 38948056 PMCID: PMC11209707 DOI: 10.7150/thno.93127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 05/11/2024] [Indexed: 07/02/2024] Open
Abstract
PRL1 and PRL3, members of the protein tyrosine phosphatase family, have been associated with cancer metastasis and poor prognosis. Despite extensive research on their protein phosphatase activity, their potential role as lipid phosphatases remains elusive. Methods: We conducted comprehensive investigations to elucidate the lipid phosphatase activity of PRL1 and PRL3 using a combination of cellular assays, biochemical analyses, and protein interactome profiling. Functional studies were performed to delineate the impact of PRL1/3 on macropinocytosis and its implications in cancer biology. Results: Our study has identified PRL1 and PRL3 as lipid phosphatases that interact with phosphoinositide (PIP) lipids, converting PI(3,4)P2 and PI(3,5)P2 into PI(3)P on the cellular membranes. These enzymatic activities of PRLs promote the formation of membrane ruffles, membrane blebbing and subsequent macropinocytosis, facilitating nutrient extraction, cell migration, and invasion, thereby contributing to tumor development. These enzymatic activities of PRLs promote the formation of membrane ruffles, membrane blebbing and subsequent macropinocytosis. Additionally, we found a correlation between PRL1/3 expression and glioma development, suggesting their involvement in glioma progression. Conclusions: Combining with the knowledge that PRLs have been identified to be involved in mTOR, EGFR and autophagy, here we concluded the physiological role of PRL1/3 in orchestrating the nutrient sensing, absorbing and recycling via regulating macropinocytosis through its lipid phosphatase activity. This mechanism could be exploited by tumor cells facing a nutrient-depleted microenvironment, highlighting the potential therapeutic significance of targeting PRL1/3-mediated macropinocytosis in cancer treatment.
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Affiliation(s)
- Zu Ye
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, 310022, China
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Republic of Singapore, Singapore 138673
| | - Chee Ping Ng
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Republic of Singapore, Singapore 138673
| | - Haidong Liu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, 310022, China
| | - Qimei Bao
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, 310022, China
| | - Shengfeng Xu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Dan Zu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, 310022, China
| | - Yanhua He
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, 310022, China
| | - Yixing Huang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- National Clinical Research Center for Children's Health, Department of Pulmonology of Children's Hospital, Department of Biochemistry, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Abdul Qader Omer Al-Aidaroos
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Republic of Singapore, Singapore 138673
| | - Ke Guo
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Republic of Singapore, Singapore 138673
| | - Jie Li
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Republic of Singapore, Singapore 138673
| | - Lai Ping Yaw
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Republic of Singapore, Singapore 138673
| | - Qiancheng Xiong
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Republic of Singapore, Singapore 138673
| | - Min Thura
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Republic of Singapore, Singapore 138673
| | - Weihui Zheng
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Republic of Singapore, Singapore 138673
| | - Fenghui Guan
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Xiangdong Cheng
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou, 310022, China
| | - Yin Shi
- National Clinical Research Center for Children's Health, Department of Pulmonology of Children's Hospital, Department of Biochemistry, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qi Zeng
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Republic of Singapore, Singapore 138673
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Muramoto M, Mineoka N, Fukuda K, Kuriyama S, Masatani T, Fujita A. Coordinated regulation of phosphatidylinositol 4-phosphate and phosphatidylserine levels by Osh4p and Osh5p is an essential regulatory mechanism in autophagy. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184308. [PMID: 38437942 DOI: 10.1016/j.bbamem.2024.184308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 01/26/2024] [Accepted: 02/26/2024] [Indexed: 03/06/2024]
Abstract
Macroautophagy (hereafter autophagy) is an intracellular degradative pathway in budding yeast cells. Certain lipid types play essential roles in autophagy; yet the precise mechanisms regulating lipid composition during autophagy remain unknown. Here, we explored the role of the Osh family proteins in the modulating lipid composition during autophagy in budding yeast. Our results showed that osh1-osh7∆ deletions lead to autophagic dysfunction, with impaired GFP-Atg8 processing and the absence of autophagosomes and autophagic bodies in the cytosol and vacuole, respectively. Freeze-fracture electron microscopy (EM) revealed elevated phosphatidylinositol 4-phosphate (PtdIns(4)P) levels in cytoplasmic and luminal leaflets of autophagic bodies and vacuolar membranes in all deletion mutants. Phosphatidylserine (PtdSer) levels were significantly decreased in the autophagic bodies and vacuolar membranes in osh4∆ and osh5∆ mutants, whereas no significant changes were observed in other osh deletion mutants. Furthermore, we identified defects in autophagic processes in the osh4∆ and osh5∆ mutants, including rare autophagosome formation in the osh5∆ mutant and accumulation of autophagic bodies in the vacuole in the osh4∆ mutant, even in the absence of the proteinase inhibitor PMSF. These findings suggest that Osh4p and Osh5p play crucial roles in the transport of PtdSer to autophagic bodies and autophagosome membranes, respectively. The precise control of lipid composition in the membranes of autophagosomes and autophagic bodies by Osh4p and Osh5p represents an important regulatory mechanism in autophagy.
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Affiliation(s)
- Moe Muramoto
- Department of Molecular and Cell Biology and Biochemistry, Basic Veterinary Science, Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Nanaru Mineoka
- Department of Molecular and Cell Biology and Biochemistry, Basic Veterinary Science, Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Kayoko Fukuda
- Department of Molecular and Cell Biology and Biochemistry, Basic Veterinary Science, Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Sayuri Kuriyama
- Department of Molecular and Cell Biology and Biochemistry, Basic Veterinary Science, Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Tatsunori Masatani
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Center for One Medicine Innovative Translational Research (COMIT), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Akikazu Fujita
- Department of Molecular and Cell Biology and Biochemistry, Basic Veterinary Science, Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan.
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9
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Renna FJ, Gonzalez CD, Vaccaro MI. Decoding the Versatile Landscape of Autophagic Protein VMP1 in Cancer: A Comprehensive Review across Tissue Types and Regulatory Mechanisms. Int J Mol Sci 2024; 25:3758. [PMID: 38612567 PMCID: PMC11011780 DOI: 10.3390/ijms25073758] [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: 02/26/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Autophagy, a catabolic process orchestrating the degradation of proteins and organelles within lysosomes, is pivotal for maintaining cellular homeostasis. However, its dual role in cancer involves preventing malignant transformation while fostering progression and therapy resistance. Vacuole Membrane Protein 1 (VMP1) is an essential autophagic protein whose expression, per se, triggers autophagy, being present in the whole autophagic flux. In pancreatic cancer, VMP1-whose expression is linked to the Kirsten Rat Sarcoma Virus (KRAS) oncogene-significantly contributes to disease promotion, progression, and chemotherapy resistance. This investigation extends to breast cancer, colon cancer, hepatocellular carcinoma, and more, highlighting VMP1's nuanced nature, contingent on specific tissue contexts. The examination of VMP1's interactions with micro-ribonucleic acids (miRNAs), including miR-21, miR-210, and miR-124, enhances our understanding of its regulatory network in cancer. Additionally, this article discusses VMP1 gene fusions, especially with ribosomal protein S6 kinase B1 (RPS6KB1), shedding light on potential implications for tumor malignancy. By deciphering the molecular mechanisms linking VMP1 to cancer progression, this exploration paves the way for innovative therapeutic strategies to disrupt these pathways and potentially improve treatment outcomes.
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Affiliation(s)
- Felipe J. Renna
- Instituto de Bioquimica y Medicina Molecular Prof Alberto Boveris (IBIMOL), CONICET, Universidad de Buenos Aires, Buenos Aires C1113AAC, Argentina;
| | - Claudio D. Gonzalez
- Instituto de Investigaciones, IUC, Medicina Traslacional, Hospital Universitario CEMIC, Buenos Aires C1431FWN, Argentina;
| | - Maria I. Vaccaro
- Instituto de Bioquimica y Medicina Molecular Prof Alberto Boveris (IBIMOL), CONICET, Universidad de Buenos Aires, Buenos Aires C1113AAC, Argentina;
- Instituto de Investigaciones, IUC, Medicina Traslacional, Hospital Universitario CEMIC, Buenos Aires C1431FWN, Argentina;
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10
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Gheitasi H, Sabbaghian M, Fadaee M, Mohammadzadeh N, Shekarchi AA, Poortahmasebi V. The relationship between autophagy and respiratory viruses. Arch Microbiol 2024; 206:136. [PMID: 38436746 DOI: 10.1007/s00203-024-03838-3] [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: 11/26/2023] [Revised: 01/05/2024] [Accepted: 01/06/2024] [Indexed: 03/05/2024]
Abstract
Respiratory viruses have caused severe global health problems and posed essential challenges to the medical community. In recent years, the role of autophagy as a critical process in cells in viral respiratory diseases has been noticed. One of the vital catabolic biological processes in the body is autophagy. Autophagy contributes to energy recovery by targeting and selectively directing foreign microorganisms, organelles, and senescent intracellular proteins to the lysosome for degradation and phagocytosis. Activation or suppression of autophagy is often initiated when foreign pathogenic organisms such as viruses infect cells. Because of its antiviral properties, several viruses may escape or resist this process by encoding viral proteins. Viruses can also use autophagy to enhance their replication or prolong the persistence of latent infections. Here, we provide an overview of autophagy and respiratory viruses such as coronavirus, rhinovirus, parainfluenza, influenza, adenovirus, and respiratory syncytial virus, and examine the interactions between them and the role of autophagy in the virus-host interaction process and the resulting virus replication strategy.
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Affiliation(s)
- Hamidreza Gheitasi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Sabbaghian
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Manouchehr Fadaee
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nader Mohammadzadeh
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Akbar Shekarchi
- Department of Pathology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahdat Poortahmasebi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
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11
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Semenova MG, Petina AN, Fedorova EE. Autophagy and Symbiosis: Membranes, ER, and Speculations. Int J Mol Sci 2024; 25:2918. [PMID: 38474164 DOI: 10.3390/ijms25052918] [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: 12/27/2023] [Revised: 02/19/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
The interaction of plants and soil bacteria rhizobia leads to the formation of root nodule symbiosis. The intracellular form of rhizobia, the symbiosomes, are able to perform the nitrogen fixation by converting atmospheric dinitrogen into ammonia, which is available for plants. The symbiosis involves the resource sharing between two partners, but this exchange does not include equivalence, which can lead to resource scarcity and stress responses of one of the partners. In this review, we analyze the possible involvement of the autophagy pathway in the process of the maintenance of the nitrogen-fixing bacteria intracellular colony and the changes in the endomembrane system of the host cell. According to in silico expression analysis, ATG genes of all groups were expressed in the root nodule, and the expression was developmental zone dependent. The analysis of expression of genes involved in the response to carbon or nitrogen deficiency has shown a suboptimal access to sugars and nitrogen in the nodule tissue. The upregulation of several ER stress genes was also detected. Hence, the root nodule cells are under heavy bacterial infection, carbon deprivation, and insufficient nitrogen supply, making nodule cells prone to autophagy. We speculate that the membrane formation around the intracellular rhizobia may be quite similar to the phagophore formation, and the induction of autophagy and ER stress are essential to the success of this process.
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Affiliation(s)
- Maria G Semenova
- Timiryazev Institute of Plant Physiology, Russian Academy of Science, 127276 Moscow, Russia
| | - Alekandra N Petina
- Timiryazev Institute of Plant Physiology, Russian Academy of Science, 127276 Moscow, Russia
| | - Elena E Fedorova
- Timiryazev Institute of Plant Physiology, Russian Academy of Science, 127276 Moscow, Russia
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12
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Ma L, Han T, Zhan YA. Mechanism and role of mitophagy in the development of severe infection. Cell Death Discov 2024; 10:88. [PMID: 38374038 PMCID: PMC10876966 DOI: 10.1038/s41420-024-01844-4] [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: 10/23/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
Mitochondria produce adenosine triphosphate and potentially contribute to proinflammatory responses and cell death. Mitophagy, as a conservative phenomenon, scavenges waste mitochondria and their components in the cell. Recent studies suggest that severe infections develop alongside mitochondrial dysfunction and mitophagy abnormalities. Restoring mitophagy protects against excessive inflammation and multiple organ failure in sepsis. Here, we review the normal mitophagy process, its interaction with invading microorganisms and the immune system, and summarize the mechanism of mitophagy dysfunction during severe infection. We highlight critical role of normal mitophagy in preventing severe infection.
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Affiliation(s)
- Lixiu Ma
- Department of Respiratory and Critical Care Medicine, the 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Tianyu Han
- Jiangxi Institute of Respiratory Disease, the 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Yi-An Zhan
- Department of Respiratory and Critical Care Medicine, the 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China.
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13
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Hu Y, Ye R, Su J, Rui Y, Yu XF. cGAS-STING-mediated novel nonclassic antiviral activities. J Med Virol 2024; 96:e29403. [PMID: 38293806 DOI: 10.1002/jmv.29403] [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: 10/28/2023] [Revised: 12/13/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024]
Abstract
Stimulatorof interferon genes (STING) is an intracellular sensor of cyclic dinucleotides involved in the innate immune response against pathogen- or self-derived DNA. For years, interferon (IFN) induction of cyclic GMP-AMP synthase (cGAS)-STING has been considered as a canonical pattern defending the host from viral invasion. The mechanism of the cGAS-STING-IFN pathway has been well-illustrated. However, other signalling cascades driven by cGAS-STING have emerged in recent years and some of them have been found to possess antiviral ability independent of IFN. Here, we summarize the current progress on cGAS-STING-mediated nonclassic antiviral activities with an emphasis on the nuclear factor-κB and autophagy pathways, which are the most-studied pathways. In addition, we briefly present the primordial function of the cGAS-STING pathway in primitive species to show the importance of IFN-unrelated antiviral activity from an evolutionary angle. Finally, we discuss open questions that need to be solved for further exploitation of this field.
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Affiliation(s)
- Ying Hu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine; Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang, China
| | - Runxin Ye
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine; Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang, China
| | - Jiaming Su
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine; Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yajuan Rui
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine; Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiao-Fang Yu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine; Zhejiang Provincial Clinical Research Center for Cancer, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
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14
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Nagdev PK, Agnivesh PK, Roy A, Sau S, Kalia NP. Exploring and exploiting the host cell autophagy during Mycobacterium tuberculosis infection. Eur J Clin Microbiol Infect Dis 2023; 42:1297-1315. [PMID: 37740791 DOI: 10.1007/s10096-023-04663-0] [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: 04/10/2023] [Accepted: 09/06/2023] [Indexed: 09/25/2023]
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis, is a fatal infectious disease that prevails to be the second leading cause of death from a single infectious agent despite the availability of multiple drugs for treatment. The current treatment regimen involves the combination of several drugs for 6 months that remain ineffective in completely eradicating the infection because of several drawbacks, such as the long duration of treatment and the side effects of drugs causing non-adherence of patients to the treatment regimen. Autophagy is an intracellular degradative process that eliminates pathogens at the early stages of infection. Mycobacterium tuberculosis's unique autophagy-blocking capability makes it challenging to eliminate compared to usual pathogens. The present review discusses recent advances in autophagy-inhibiting factors and mechanisms that could be exploited to identify autophagy-inducing chemotherapeutics that could be used as adjunctive therapy with the existing first-line anti-TB agent to shorten the duration of therapy and enhance cure rates from multidrug-resistant tuberculosis (MDR-TB) and extreme drug-resistant tuberculosis (XDR-TB).
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Affiliation(s)
- Pavan Kumar Nagdev
- Department of Biological Sciences (Pharmacology and Toxicology), National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Puja Kumari Agnivesh
- Department of Biological Sciences (Pharmacology and Toxicology), National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Arnab Roy
- Department of Biological Sciences (Pharmacology and Toxicology), National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Shashikanta Sau
- Department of Biological Sciences (Pharmacology and Toxicology), National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Nitin Pal Kalia
- Department of Biological Sciences (Pharmacology and Toxicology), National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India.
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15
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Banerjee C, Mehra D, Song D, Mancebo A, Park JM, Kim DH, Puchner EM. ULK1 forms distinct oligomeric states and nanoscopic structures during autophagy initiation. SCIENCE ADVANCES 2023; 9:eadh4094. [PMID: 37774021 PMCID: PMC10541014 DOI: 10.1126/sciadv.adh4094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
Autophagy induction involves extensive molecular and membrane reorganization. Despite substantial progress, the mechanism underlying autophagy initiation remains poorly understood. Here, we used quantitative photoactivated localization microscopy with single-molecule sensitivity to analyze the nanoscopic distribution of endogenous ULK1, the kinase that triggers autophagy. Under amino acid starvation, ULK1 formed large clusters containing up to 161 molecules at the endoplasmic reticulum. Cross-correlation analysis revealed that ULK1 clusters engaging in autophagosome formation require 30 or more molecules. The ULK1 structures with more than the threshold number contained varying levels of Atg13, Atg14, Atg16, LC3B, GEC1, and WIPI2. We found that ULK1 activity is dispensable for the initial clustering of ULK1, but necessary for the subsequent expansion of the clusters, which involves interaction with Atg14, Atg16, and LC3B and relies on Vps34 activity. This quantitative analysis at the single-molecule level has provided unprecedented insights into the behavior of ULK1 during autophagy initiation.
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Affiliation(s)
- Chiranjib Banerjee
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Dushyant Mehra
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Minneapolis, MN, USA
- Department of Biomedical Engineering and Physiology, Mayo Clinic, Rochester, MN, USA
| | - Daihyun Song
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Angel Mancebo
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Ji-Man Park
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Do-Hyung Kim
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Elias M. Puchner
- School of Physics and Astronomy, University of Minnesota, Twin Cities, Minneapolis, MN, USA
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16
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Li S, Zhang M, Ge L. Reconstitution of membrane contact by unilamellar vesicles. BIOPHYSICS REPORTS 2023; 9:188-194. [PMID: 38516622 PMCID: PMC10951472 DOI: 10.52601/bpr.2023.230011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 09/12/2023] [Indexed: 03/23/2024] Open
Abstract
Eukaryotic cells compartmentalize diverse biochemical functions within organelles defined by intracellular membranes. Recent focus has intensified on studying the interactions among organelles and the role of membrane contacts in maintaining cellular balance. While analyzing these contacts mainly involves fluorescence and electron microscopy, as well as biochemical cell fractionation, understanding their mechanisms and responses to genetic and environmental changes remains challenging. Here we describe an approach employing in vitro reconstitution of membrane contacts using unilamellar vesicles. This technique offers insights into contact mechanisms when combined with established methods like fluorescence imaging and mass spectrometry, potentially deepening our understanding of membrane contacts and organelle networks.
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Affiliation(s)
- Shulin Li
- State Key Laboratory of Membrane Biology, Beijing 100101, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Min Zhang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Liang Ge
- State Key Laboratory of Membrane Biology, Beijing 100101, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
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17
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Elander PH, Holla S, Sabljić I, Gutierrez-Beltran E, Willems P, Bozhkov PV, Minina EA. Interactome of Arabidopsis ATG5 Suggests Functions beyond Autophagy. Int J Mol Sci 2023; 24:12300. [PMID: 37569688 PMCID: PMC10418956 DOI: 10.3390/ijms241512300] [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: 07/05/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Autophagy is a catabolic pathway capable of degrading cellular components ranging from individual molecules to organelles. Autophagy helps cells cope with stress by removing superfluous or hazardous material. In a previous work, we demonstrated that transcriptional upregulation of two autophagy-related genes, ATG5 and ATG7, in Arabidopsis thaliana positively affected agronomically important traits: biomass, seed yield, tolerance to pathogens and oxidative stress. Although the occurrence of these traits correlated with enhanced autophagic activity, it is possible that autophagy-independent roles of ATG5 and ATG7 also contributed to the phenotypes. In this study, we employed affinity purification and LC-MS/MS to identify the interactome of wild-type ATG5 and its autophagy-inactive substitution mutant, ATG5K128R Here we present the first interactome of plant ATG5, encompassing not only known autophagy regulators but also stress-response factors, components of the ubiquitin-proteasome system, proteins involved in endomembrane trafficking, and potential partners of the nuclear fraction of ATG5. Furthermore, we discovered post-translational modifications, such as phosphorylation and acetylation present on ATG5 complex components that are likely to play regulatory functions. These results strongly indicate that plant ATG5 complex proteins have roles beyond autophagy itself, opening avenues for further investigations on the complex roles of autophagy in plant growth and stress responses.
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Affiliation(s)
- Pernilla H. Elander
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750-07 Uppsala, Sweden; (P.H.E.); (S.H.); (I.S.); (P.V.B.)
| | - Sanjana Holla
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750-07 Uppsala, Sweden; (P.H.E.); (S.H.); (I.S.); (P.V.B.)
| | - Igor Sabljić
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750-07 Uppsala, Sweden; (P.H.E.); (S.H.); (I.S.); (P.V.B.)
| | - Emilio Gutierrez-Beltran
- Instituto de Bioquımica Vegetal y Fotosıntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Cientıficas, 41092 Sevilla, Spain;
- Departamento de Bioquimica Vegetal y Biologia Molecular, Facultad de Biologia, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Peter V. Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750-07 Uppsala, Sweden; (P.H.E.); (S.H.); (I.S.); (P.V.B.)
| | - Elena A. Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750-07 Uppsala, Sweden; (P.H.E.); (S.H.); (I.S.); (P.V.B.)
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18
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Olivas TJ, Wu Y, Yu S, Luan L, Choi P, Guinn ED, Nag S, De Camilli PV, Gupta K, Melia TJ. ATG9 vesicles comprise the seed membrane of mammalian autophagosomes. J Cell Biol 2023; 222:e202208088. [PMID: 37115958 PMCID: PMC10148236 DOI: 10.1083/jcb.202208088] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 03/20/2023] [Accepted: 04/05/2023] [Indexed: 04/30/2023] Open
Abstract
As the autophagosome forms, its membrane surface area expands rapidly, while its volume is kept low. Protein-mediated transfer of lipids from another organelle to the autophagosome likely drives this expansion, but as these lipids are only introduced into the cytoplasmic-facing leaflet of the organelle, full membrane growth also requires lipid scramblase activity. ATG9 harbors scramblase activity and is essential to autophagosome formation; however, whether ATG9 is integrated into mammalian autophagosomes remains unclear. Here we show that in the absence of lipid transport, ATG9 vesicles are already competent to collect proteins found on mature autophagosomes, including LC3-II. Further, we use styrene-maleic acid lipid particles to reveal the nanoscale organization of protein on LC3-II membranes; ATG9 and LC3-II are each fully integrated into expanding autophagosomes. The ratios of these two proteins at different stages of maturation demonstrate that ATG9 proteins are not continuously integrated, but rather are present on the seed vesicles only and become diluted in the expanding autophagosome membrane.
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Affiliation(s)
- Taryn J. Olivas
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
| | - Yumei Wu
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Neuroscience, School of Medicine, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, School of Medicine, Yale University, New Haven, CT, USA
- Program in Cellular Neuroscience Neurodegeneration and Repair, School of Medicine, Yale University, New Haven, CT, USA
| | - Shenliang Yu
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
| | - Lin Luan
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
| | - Peter Choi
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
| | - Emily D. Guinn
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
| | - Shanta Nag
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
| | - Pietro V. De Camilli
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Neuroscience, School of Medicine, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, School of Medicine, Yale University, New Haven, CT, USA
- Program in Cellular Neuroscience Neurodegeneration and Repair, School of Medicine, Yale University, New Haven, CT, USA
| | - Kallol Gupta
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Thomas J. Melia
- Department of Cell Biology, School of Medicine, Yale University, New Haven, CT, USA
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19
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Papin L, Lehmann M, Lagisquet J, Maarifi G, Robert-Hebmann V, Mariller C, Guerardel Y, Espert L, Haucke V, Blanchet FP. The Autophagy Nucleation Factor ATG9 Forms Nanoclusters with the HIV-1 Receptor DC-SIGN and Regulates Early Antiviral Autophagy in Human Dendritic Cells. Int J Mol Sci 2023; 24:ijms24109008. [PMID: 37240354 DOI: 10.3390/ijms24109008] [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: 04/13/2023] [Revised: 05/08/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Dendritic cells (DC) are critical cellular mediators of host immunity, notably by expressing a broad panel of pattern recognition receptors. One of those receptors, the C-type lectin receptor DC-SIGN, was previously reported as a regulator of endo/lysosomal targeting through functional connections with the autophagy pathway. Here, we confirmed that DC-SIGN internalization intersects with LC3+ autophagy structures in primary human monocyte-derived dendritic cells (MoDC). DC-SIGN engagement promoted autophagy flux which coincided with the recruitment of ATG-related factors. As such, the autophagy initiation factor ATG9 was found to be associated with DC-SIGN very early upon receptor engagement and required for an optimal DC-SIGN-mediated autophagy flux. The autophagy flux activation upon DC-SIGN engagement was recapitulated using engineered DC-SIGN-expressing epithelial cells in which ATG9 association with the receptor was also confirmed. Finally, Stimulated emission depletion (STED) microscopy performed in primary human MoDC revealed DC-SIGN-dependent submembrane nanoclusters formed with ATG9, which was required to degrade incoming viruses and further limit DC-mediated transmission of HIV-1 infection to CD4+ T lymphocytes. Our study unveils a physical association between the Pattern Recognition Receptor DC-SIGN and essential components of the autophagy pathway contributing to early endocytic events and the host's antiviral immune response.
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Affiliation(s)
- Laure Papin
- Institut de Recherche en Infectiologie de Montpellier-IRIM-CNRS UMR9004, University of Montpellier, 34090 Montpellier, France
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Justine Lagisquet
- Institut de Recherche en Infectiologie de Montpellier-IRIM-CNRS UMR9004, University of Montpellier, 34090 Montpellier, France
| | - Ghizlane Maarifi
- Institut de Recherche en Infectiologie de Montpellier-IRIM-CNRS UMR9004, University of Montpellier, 34090 Montpellier, France
| | - Véronique Robert-Hebmann
- Institut de Recherche en Infectiologie de Montpellier-IRIM-CNRS UMR9004, University of Montpellier, 34090 Montpellier, France
| | - Christophe Mariller
- Univ. Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Yann Guerardel
- Univ. Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
- Institute for Glyco-Core Research (iGCORE), Gifu University, Gifu 501-1112, Japan
| | - Lucile Espert
- Institut de Recherche en Infectiologie de Montpellier-IRIM-CNRS UMR9004, University of Montpellier, 34090 Montpellier, France
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Fabien P Blanchet
- Institut de Recherche en Infectiologie de Montpellier-IRIM-CNRS UMR9004, University of Montpellier, 34090 Montpellier, France
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20
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Zhang Y, Weng J, Huan L, Sheng S, Xu F. Mitophagy in atherosclerosis: from mechanism to therapy. Front Immunol 2023; 14:1165507. [PMID: 37261351 PMCID: PMC10228545 DOI: 10.3389/fimmu.2023.1165507] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/12/2023] [Indexed: 06/02/2023] Open
Abstract
Mitophagy is a type of autophagy that can selectively eliminate damaged and depolarized mitochondria to maintain mitochondrial activity and cellular homeostasis. Several pathways have been found to participate in different steps of mitophagy. Mitophagy plays a significant role in the homeostasis and physiological function of vascular endothelial cells, vascular smooth muscle cells, and macrophages, and is involved in the development of atherosclerosis (AS). At present, many medications and natural chemicals have been shown to alter mitophagy and slow the progression of AS. This review serves as an introduction to the field of mitophagy for researchers interested in targeting this pathway as part of a potential AS management strategy.
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Affiliation(s)
- Yanhong Zhang
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiajun Weng
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Traditional Chinese Medicine Clinical Medical School (Xiyuan), Peking University, Beijing, China
- Department of Integrated Traditional and Western Medicine, Peking University Health Science Center, Beijing, China
| | - Luyao Huan
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Graduate School of Beijing University of Chinese Medicine, Beijing, China
| | - Song Sheng
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Fengqin Xu
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Traditional Chinese Medicine Clinical Medical School (Xiyuan), Peking University, Beijing, China
- Department of Integrated Traditional and Western Medicine, Peking University Health Science Center, Beijing, China
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21
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Assi M, Kimmelman AC. Impact of context-dependent autophagy states on tumor progression. NATURE CANCER 2023; 4:596-607. [PMID: 37069394 PMCID: PMC10542907 DOI: 10.1038/s43018-023-00546-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 03/20/2023] [Indexed: 04/19/2023]
Abstract
Macroautophagy is a cellular quality-control process that degrades proteins, protein aggregates and damaged organelles. Autophagy plays a fundamental role in cancer where, in the presence of stressors (for example, nutrient starvation, hypoxia, mechanical pressure), tumor cells activate it to degrade intracellular substrates and provide energy. Cell-autonomous autophagy in tumor cells and cell-nonautonomous autophagy in the tumor microenvironment and in the host converge on mechanisms that modulate metabolic fitness, DNA integrity and immune escape and, consequently, support tumor growth. In this Review, we will discuss insights into the tumor-modulating roles of autophagy in different contexts and reflect on how future studies using physiological culture systems may help to understand the complexity and open new therapeutic avenues.
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Affiliation(s)
- Mohamad Assi
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Alec C Kimmelman
- Department of Radiation Oncology, New York University Langone Health, New York, NY, USA.
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA.
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22
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Liu L, Tang Y, Zhou Z, Huang Y, Zhang R, Lyu H, Xiao S, Guo D, Ali DW, Michalak M, Chen XZ, Zhou C, Tang J. Membrane Curvature: The Inseparable Companion of Autophagy. Cells 2023; 12:1132. [PMID: 37190041 PMCID: PMC10136490 DOI: 10.3390/cells12081132] [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: 12/07/2022] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Autophagy is a highly conserved recycling process of eukaryotic cells that degrades protein aggregates or damaged organelles with the participation of autophagy-related proteins. Membrane bending is a key step in autophagosome membrane formation and nucleation. A variety of autophagy-related proteins (ATGs) are needed to sense and generate membrane curvature, which then complete the membrane remodeling process. The Atg1 complex, Atg2-Atg18 complex, Vps34 complex, Atg12-Atg5 conjugation system, Atg8-phosphatidylethanolamine conjugation system, and transmembrane protein Atg9 promote the production of autophagosomal membranes directly or indirectly through their specific structures to alter membrane curvature. There are three common mechanisms to explain the change in membrane curvature. For example, the BAR domain of Bif-1 senses and tethers Atg9 vesicles to change the membrane curvature of the isolation membrane (IM), and the Atg9 vesicles are reported as a source of the IM in the autophagy process. The amphiphilic helix of Bif-1 inserts directly into the phospholipid bilayer, causing membrane asymmetry, and thus changing the membrane curvature of the IM. Atg2 forms a pathway for lipid transport from the endoplasmic reticulum to the IM, and this pathway also contributes to the formation of the IM. In this review, we introduce the phenomena and causes of membrane curvature changes in the process of macroautophagy, and the mechanisms of ATGs in membrane curvature and autophagosome membrane formation.
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Affiliation(s)
- Lei Liu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Yu Tang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Zijuan Zhou
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China
| | - Yuan Huang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Rui Zhang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Hao Lyu
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Shuai Xiao
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Dong Guo
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Declan William Ali
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Marek Michalak
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Xing-Zhen Chen
- Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Cefan Zhou
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
| | - Jingfeng Tang
- Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan 430068, China
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23
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Wang P, Duckney P, Gao E, Hussey PJ, Kriechbaumer V, Li C, Zang J, Zhang T. Keep in contact: multiple roles of endoplasmic reticulum-membrane contact sites and the organelle interaction network in plants. THE NEW PHYTOLOGIST 2023; 238:482-499. [PMID: 36651025 DOI: 10.1111/nph.18745] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Functional regulation and structural maintenance of the different organelles in plants contribute directly to plant development, reproduction and stress responses. To ensure these activities take place effectively, cells have evolved an interconnected network amongst various subcellular compartments, regulating rapid signal transduction and the exchange of biomaterial. Many proteins that regulate membrane connections have recently been identified in plants, and this is the first step in elucidating both the mechanism and function of these connections. Amongst all organelles, the endoplasmic reticulum is the key structure, which likely links most of the different subcellular compartments through membrane contact sites (MCS) and the ER-PM contact sites (EPCS) have been the most intensely studied in plants. However, the molecular composition and function of plant MCS are being found to be different from other eukaryotic systems. In this article, we will summarise the most recent advances in this field and discuss the mechanism and biological relevance of these essential links in plants.
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Affiliation(s)
- Pengwei Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Patrick Duckney
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Erlin Gao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Patrick J Hussey
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Verena Kriechbaumer
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Chengyang Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Jingze Zang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Tong Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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24
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Wang Y, Li Z, Wang X, Zhao Z, Jiao L, Liu R, Wang K, Ma R, Yang Y, Chen G, Wang Y, Bian X. Insights into membrane association of the SMP domain of extended synaptotagmin. Nat Commun 2023; 14:1504. [PMID: 36932127 PMCID: PMC10023780 DOI: 10.1038/s41467-023-37202-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
The Synaptotagmin-like Mitochondrial-lipid-binding Protein (SMP) domain is a newly identified lipid transfer module present in proteins that regulate lipid homeostasis at membrane contact sites (MCSs). However, how the SMP domain associates with the membrane to extract and unload lipids is unclear. Here, we performed in vitro DNA brick-assisted lipid transfer assays and in silico molecular dynamics simulations to investigate the molecular basis of the membrane association by the SMP domain of extended synaptotagmin (E-Syt), which tethers the tubular endoplasmic reticulum (ER) to the plasma membrane (PM). We demonstrate that the SMP domain uses its tip region to recognize the extremely curved subdomain of tubular ER and the acidic-lipid-enriched PM for highly efficient lipid transfer. Supporting these findings, disruption of these mechanisms results in a defect in autophagosome biogenesis contributed by E-Syt. Our results suggest a model that provides a coherent picture of the action of the SMP domain at MCSs.
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Affiliation(s)
- Yunyun Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, China
| | - Zhenni Li
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, China
| | - Xinyu Wang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Ziyuan Zhao
- College of Life Sciences, Nankai University, Tianjin, China
| | - Li Jiao
- College of Life Sciences, Nankai University, Tianjin, China
| | - Ruming Liu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Keying Wang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Rui Ma
- College of Physical Science and Technology, Xiamen University, Xiamen, China
| | - Yang Yang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guo Chen
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, China
| | - Yong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, China.
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, China.
| | - Xin Bian
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, China.
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25
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Lipids in Mitochondrial Macroautophagy: Phase Behavior of Bilayers Containing Cardiolipin and Ceramide. Int J Mol Sci 2023; 24:ijms24065080. [PMID: 36982156 PMCID: PMC10049649 DOI: 10.3390/ijms24065080] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/09/2023] Open
Abstract
Cardiolipin (CL) is a key lipid for damaged mitochondrial recognition by the LC3/GABARAP human autophagy proteins. The role of ceramide (Cer) in this process is unclear, but CL and Cer have been proposed to coexist in mitochondria under certain conditions. Varela et al. showed that in model membranes composed of egg sphingomyelin (eSM), dioleoyl phosphatidylethanolamine (DOPE), and CL, the addition of Cer enhanced the binding of LC3/GABARAP proteins to bilayers. Cer gave rise to lateral phase separation of Cer-rich rigid domains but protein binding took place mainly in the fluid continuous phase. In the present study, a biophysical analysis of bilayers composed of eSM, DOPE, CL, and/or Cer was attempted to understand the relevance of this lipid coexistence. Bilayers were studied by differential scanning calorimetry, confocal fluorescence microscopy, and atomic force microscopy. Upon the addition of CL and Cer, one continuous phase and two segregated ones were formed. In bilayers with egg phosphatidylcholine instead of eSM, in which the binding of LC3/GABARAP proteins hardly increased with Cer in the former study, a single segregated phase was formed. Assuming that phase separation at the nanoscale is ruled by the same principles acting at the micrometer scale, it is proposed that Cer-enriched rigid nanodomains, stabilized by eSM:Cer interactions formed within the DOPE- and CL-enriched fluid phase, result in structural defects at the rigid/fluid nanointerfaces, thus hypothetically facilitatingLC3/GABARAP protein interaction.
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26
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Autophagy in Inflammatory Response against SARS-CoV-2. Int J Mol Sci 2023; 24:ijms24054928. [PMID: 36902354 PMCID: PMC10002778 DOI: 10.3390/ijms24054928] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
The coronavirus disease pandemic, which profoundly reshaped the world in 2019 (COVID-19), and is currently ongoing, has affected over 200 countries, caused over 500 million cumulative cases, and claimed the lives of over 6.4 million people worldwide as of August 2022. The causative agent is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Depicting this virus' life cycle and pathogenic mechanisms, as well as the cellular host factors and pathways involved during infection, has great relevance for the development of therapeutic strategies. Autophagy is a catabolic process that sequesters damaged cell organelles, proteins, and external invading microbes, and delivers them to the lysosomes for degradation. Autophagy would be involved in the entry, endo, and release, as well as the transcription and translation, of the viral particles in the host cell. Secretory autophagy would also be involved in developing the thrombotic immune-inflammatory syndrome seen in a significant number of COVID-19 patients that can lead to severe illness and even death. This review aims to review the main aspects that characterize the complex and not yet fully elucidated relationship between SARS-CoV-2 infection and autophagy. It briefly describes the key concepts regarding autophagy and mentions its pro- and antiviral roles, while also noting the reciprocal effect of viral infection in autophagic pathways and their clinical aspects.
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27
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Zhang Y, Li H, Lv L, Lu K, Li H, Zhang W, Cui T. Autophagy: Dual roles and perspective for clinical treatment of colorectal cancer. Biochimie 2023; 206:49-60. [PMID: 36244578 DOI: 10.1016/j.biochi.2022.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/29/2022] [Accepted: 10/09/2022] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) raises concerns to people because of its high recurrence and metastasis rate, diagnosis challenges, and poor prognosis. Various studies have shown the association of altered autophagy with tumorigenesis, tumor-stroma interactions, and resistance to cancer therapy in CRC. Autophagy is a highly conserved cytosolic catabolic process in eukaryotes that plays distinct roles in CRC occurrence and progression. In early tumorigenesis, autophagy may inhibit tumor growth through diverse mechanisms, whereas it exhibits a tumor promoting function in CRC progression. This different functions of autophagy in CRC occurrence and progression make developing therapies targeting autophagy complicated. In this review, we discuss the classification and process of autophagy as well as its dual roles in CRC, functions in the tumor microenvironment, cross-talk with apoptosis, and potential usefulness as a CRC therapeutic target.
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Affiliation(s)
- Yabin Zhang
- West China Second University Hospital, State Key Laboratory of Biotherapy, Laboratory of Metabolomics and Gynecological Disease Research and Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, 610041, Chengdu, China
| | - Haiyan Li
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Liang Lv
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Kefeng Lu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Huihui Li
- West China Second University Hospital, State Key Laboratory of Biotherapy, Laboratory of Metabolomics and Gynecological Disease Research and Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, 610041, Chengdu, China
| | - Wenli Zhang
- Department of Orthopedics, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Tao Cui
- West China Second University Hospital, State Key Laboratory of Biotherapy, Laboratory of Metabolomics and Gynecological Disease Research and Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, 610041, Chengdu, China.
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28
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Moghimianavval H, Patel C, Mohapatra S, Hwang SW, Kayikcioglu T, Bashirzadeh Y, Liu AP, Ha T. Engineering Functional Membrane-Membrane Interfaces by InterSpy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202104. [PMID: 35618485 PMCID: PMC9789529 DOI: 10.1002/smll.202202104] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/26/2022] [Indexed: 06/15/2023]
Abstract
Engineering synthetic interfaces between membranes has potential applications in designing non-native cellular communication pathways and creating synthetic tissues. Here, InterSpy is introduced as a synthetic biology tool consisting of a heterodimeric protein engineered to form and maintain membrane-membrane interfaces between apposing synthetic as well as cell membranes through the SpyTag/SpyCatcher interaction. The inclusion of split fluorescent protein fragments in InterSpy allows tracking of the formation of a membrane-membrane interface and reconstitution of functional fluorescent protein in the space between apposing membranes. First, InterSpy is demonstrated by testing split protein designs using a mammalian cell-free expression (CFE) system. By utilizing co-translational helix insertion, cell-free synthesized InterSpy fragments are incorporated into the membrane of liposomes and supported lipid bilayers with the desired topology. Functional reconstitution of split fluorescent protein between the membranes is strictly dependent on SpyTag/SpyCatcher. Finally, InterSpy is demonstrated in mammalian cells by detecting fluorescence reconstitution of split protein at the membrane-membrane interface between two cells each expressing a component of InterSpy. InterSpy demonstrates the power of CFE systems in the functional reconstitution of synthetic membrane interfaces via proximity-inducing proteins. This technology may also prove useful where cell-cell contacts and communication are recreated in a controlled manner using minimal components.
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Affiliation(s)
- Hossein Moghimianavval
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Chintan Patel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sonisilpa Mohapatra
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sung-Won Hwang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Tunc Kayikcioglu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yashar Bashirzadeh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Allen P. Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Baltimore, MD 21205, USA
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29
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Capitanio C, Bieber A, Wilfling F. How Membrane Contact Sites Shape the Phagophore. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231162495. [PMID: 37366413 PMCID: PMC10243513 DOI: 10.1177/25152564231162495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/15/2023] [Accepted: 02/18/2023] [Indexed: 06/28/2023]
Abstract
During macroautophagy, phagophores establish multiple membrane contact sites (MCSs) with other organelles that are pivotal for proper phagophore assembly and growth. In S. cerevisiae, phagophore contacts have been observed with the vacuole, the ER, and lipid droplets. In situ imaging studies have greatly advanced our understanding of the structure and function of these sites. Here, we discuss how in situ structural methods like cryo-CLEM can give unprecedented insights into MCSs, and how they help to elucidate the structural arrangements of MCSs within cells. We further summarize the current knowledge of the contact sites in autophagy, focusing on autophagosome biogenesis in the model organism S. cerevisiae.
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Affiliation(s)
- Cristina Capitanio
- Department of Molecular Machines and
Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Aligning Science Across Parkinson's (ASAP)
Collaborative Research Network, Chevy Chase, MD, USA
| | - Anna Bieber
- Department of Molecular Machines and
Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Aligning Science Across Parkinson's (ASAP)
Collaborative Research Network, Chevy Chase, MD, USA
| | - Florian Wilfling
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt a. M., Germany
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30
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Da Graça J, Morel E. Canonical and Non-Canonical Roles of SNX1 and SNX2 in Endosomal Membrane Dynamics. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231217867. [PMID: 38033809 PMCID: PMC10683387 DOI: 10.1177/25152564231217867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023]
Abstract
Sorting nexins (SNXs) are a family of membrane-binding proteins known to play a critical role in regulating endocytic pathway sorting and endosomal membrane trafficking. Among them, SNX1 and SNX2 are members of the SNX-BAR subfamily and possess a membrane-curvature domain and a phosphoinositide-binding domain, which enables their stabilization at the phosphatidylinositol-3-phosphate (PI3P)-positive surface of endosomes. While their binding to PI3P-positive platforms facilitates interaction with endosomal partners and stabilization at the endosomal membrane, their SNX-BAR region is pivotal for generating membrane tubulation from endosomal compartments. In this context, their primary identified biological roles-and their partnership-are tightly associated with the retromer and endosomal SNX-BAR sorting complex for promoting exit 1 complex trafficking, facilitating the transport of cargoes from early endosomes to the secretory pathway. However, recent literature indicates that these proteins also possess biological functions in other aspects of endosomal features and sorting processes. Notably, SNX2 has been found to regulate endosome-endoplasmic reticulum (ER) contact sites through its interaction with VAP proteins at the ER membrane. Furthermore, data from our laboratory show that SNX1 and SNX2 are involved in the tubulation of early endosomes toward ER sites associated with autophagy initiation during starvation. These findings shed light on a novel role of SNXs in inter-organelle tethering and communication. In this concise review, we will explore the non-retromer functions of SNX1 and SNX2, specifically focusing on their involvement in endosomal membrane dynamics during stress sensing and autophagy-associated processes.
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Affiliation(s)
- Juliane Da Graça
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Paris, France
| | - Etienne Morel
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, Paris, France
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31
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Nieto-Garai JA, Olazar-Intxausti J, Anso I, Lorizate M, Terrones O, Contreras FX. Super-Resolution Microscopy to Study Interorganelle Contact Sites. Int J Mol Sci 2022; 23:15354. [PMID: 36499680 PMCID: PMC9739495 DOI: 10.3390/ijms232315354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/29/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Interorganelle membrane contact sites (MCS) are areas of close vicinity between the membranes of two organelles that are maintained by protein tethers. Recently, a significant research effort has been made to study MCS, as they are implicated in a wide range of biological functions, such as organelle biogenesis and division, apoptosis, autophagy, and ion and phospholipid homeostasis. Their composition, characteristics, and dynamics can be studied by different techniques, but in recent years super-resolution fluorescence microscopy (SRFM) has emerged as a powerful tool for studying MCS. In this review, we first explore the main characteristics and biological functions of MCS and summarize the different approaches for studying them. Then, we center on SRFM techniques that have been used to study MCS. For each of the approaches, we summarize their working principle, discuss their advantages and limitations, and explore the main discoveries they have uncovered in the field of MCS.
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Affiliation(s)
- Jon Ander Nieto-Garai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - June Olazar-Intxausti
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Itxaso Anso
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, 48903 Barakaldo, Spain
| | - Maier Lorizate
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Oihana Terrones
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Francesc-Xabier Contreras
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, 48940 Leioa, Spain
- Ikerbasque, Basque Foundation of Science, 48011 Bilbao, Spain
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Zwilling E, Reggiori F. Membrane Contact Sites in Autophagy. Cells 2022; 11:3813. [PMID: 36497073 PMCID: PMC9735501 DOI: 10.3390/cells11233813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022] Open
Abstract
Eukaryotes utilize different communication strategies to coordinate processes between different cellular compartments either indirectly, through vesicular transport, or directly, via membrane contact sites (MCSs). MCSs have been implicated in lipid metabolism, calcium signaling and the regulation of organelle biogenesis in various cell types. Several studies have shown that MCSs play a crucial role in the regulation of macroautophagy, an intracellular catabolic transport route that is characterized by the delivery of cargoes (proteins, protein complexes or aggregates, organelles and pathogens) to yeast and plant vacuoles or mammalian lysosomes, for their degradation and recycling into basic metabolites. Macroautophagy is characterized by the de novo formation of double-membrane vesicles called autophagosomes, and their biogenesis requires an enormous amount of lipids. MCSs appear to have a central role in this supply, as well as in the organization of the autophagy-related (ATG) machinery. In this review, we will summarize the evidence for the participation of specific MCSs in autophagosome formation, with a focus on the budding yeast and mammalian systems.
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Affiliation(s)
- Emma Zwilling
- Department of Biomedicine, Aarhus University, Ole Worms Allé 4, 8000C Aarhus, Denmark
| | - Fulvio Reggiori
- Department of Biomedicine, Aarhus University, Ole Worms Allé 4, 8000C Aarhus, Denmark
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Høegh-Guldbergs Gade 6B, 8000C Aarhus, Denmark
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Ng MYW, Charsou C, Lapao A, Singh S, Trachsel-Moncho L, Schultz SW, Nakken S, Munson MJ, Simonsen A. The cholesterol transport protein GRAMD1C regulates autophagy initiation and mitochondrial bioenergetics. Nat Commun 2022; 13:6283. [PMID: 36270994 PMCID: PMC9586981 DOI: 10.1038/s41467-022-33933-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/05/2022] [Indexed: 12/25/2022] Open
Abstract
During autophagy, cytosolic cargo is sequestered into double-membrane vesicles called autophagosomes. The contributions of specific lipids, such as cholesterol, to the membranes that form the autophagosome, remain to be fully characterized. Here, we demonstrate that short term cholesterol depletion leads to a rapid induction of autophagy and a corresponding increase in autophagy initiation events. We further show that the ER-localized cholesterol transport protein GRAMD1C functions as a negative regulator of starvation-induced autophagy and that both its cholesterol transport VASt domain and membrane binding GRAM domain are required for GRAMD1C-mediated suppression of autophagy initiation. Similar to its yeast orthologue, GRAMD1C associates with mitochondria through its GRAM domain. Cells lacking GRAMD1C or its VASt domain show increased mitochondrial cholesterol levels and mitochondrial oxidative phosphorylation, suggesting that GRAMD1C may facilitate cholesterol transfer at ER-mitochondria contact sites. Finally, we demonstrate that expression of GRAMD family proteins is linked to clear cell renal carcinoma survival, highlighting the pathophysiological relevance of cholesterol transport proteins.
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Affiliation(s)
- Matthew Yoke Wui Ng
- grid.5510.10000 0004 1936 8921Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway ,grid.5510.10000 0004 1936 8921Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0450 Oslo, Norway
| | - Chara Charsou
- grid.5510.10000 0004 1936 8921Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway ,grid.5510.10000 0004 1936 8921Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0450 Oslo, Norway
| | - Ana Lapao
- grid.5510.10000 0004 1936 8921Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway ,grid.5510.10000 0004 1936 8921Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0450 Oslo, Norway
| | - Sakshi Singh
- grid.5510.10000 0004 1936 8921Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway ,grid.5510.10000 0004 1936 8921Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0450 Oslo, Norway
| | - Laura Trachsel-Moncho
- grid.5510.10000 0004 1936 8921Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway ,grid.5510.10000 0004 1936 8921Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0450 Oslo, Norway
| | - Sebastian W. Schultz
- grid.5510.10000 0004 1936 8921Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0450 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital Montebello, 0379 Oslo, Norway
| | - Sigve Nakken
- grid.5510.10000 0004 1936 8921Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0450 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital Montebello, 0379 Oslo, Norway
| | - Michael J. Munson
- grid.5510.10000 0004 1936 8921Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway ,grid.5510.10000 0004 1936 8921Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0450 Oslo, Norway ,grid.418151.80000 0001 1519 6403Present Address: Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anne Simonsen
- grid.5510.10000 0004 1936 8921Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0372 Oslo, Norway ,grid.5510.10000 0004 1936 8921Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, 0450 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital Montebello, 0379 Oslo, Norway
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Schmitt D, Bozkurt S, Henning‐Domres P, Huesmann H, Eimer S, Bindila L, Behrends C, Boyle E, Wilfling F, Tascher G, Münch C, Behl C, Kern A. Lipid and protein content profiling of isolated native autophagic vesicles. EMBO Rep 2022; 23:e53065. [PMID: 36215690 PMCID: PMC9724672 DOI: 10.15252/embr.202153065] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022] Open
Abstract
Autophagy is responsible for clearance of an extensive portfolio of cargoes, which are sequestered into vesicles, called autophagosomes, and are delivered to lysosomes for degradation. The pathway is highly dynamic and responsive to several stress conditions. However, the phospholipid composition and protein contents of human autophagosomes under changing autophagy rates are elusive so far. Here, we introduce an antibody-based FACS-mediated approach for the isolation of native autophagic vesicles and ensured the quality of the preparations. Employing quantitative lipidomics, we analyze phospholipids present within human autophagic vesicles purified upon basal autophagy, starvation, and proteasome inhibition. Importantly, besides phosphoglycerides, we identify sphingomyelin within autophagic vesicles and show that the phospholipid composition is unaffected by the different conditions. Employing quantitative proteomics, we obtain cargo profiles of autophagic vesicles isolated upon the different treatment paradigms. Interestingly, starvation shows only subtle effects, while proteasome inhibition results in the enhanced presence of ubiquitin-proteasome pathway factors within autophagic vesicles. Thus, here we present a powerful method for the isolation of native autophagic vesicles, which enabled profound phospholipid and cargo analyses.
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Affiliation(s)
- Daniel Schmitt
- The Autophagy Lab, Institute of PathobiochemistryUniversity Medical Center of the Johannes Gutenberg UniversityMainzGermany
| | - Süleyman Bozkurt
- Institute of Biochemistry II, Faculty of MedicineGoethe UniversityFrankfurt am MainGermany
| | - Pascale Henning‐Domres
- The Autophagy Lab, Institute of PathobiochemistryUniversity Medical Center of the Johannes Gutenberg UniversityMainzGermany
| | - Heike Huesmann
- The Autophagy Lab, Institute of PathobiochemistryUniversity Medical Center of the Johannes Gutenberg UniversityMainzGermany
| | - Stefan Eimer
- Department of Structural Cell BiologyInstitute for Cell Biology and Neuroscience, Goethe UniversityFrankfurt am MainGermany
| | - Laura Bindila
- Clinical Lipidomics Unit, Institute of Physiological ChemistryUniversity Medical Center of the Johannes Gutenberg UniversityMainzGermany
| | - Christian Behrends
- Munich Cluster for Systems Neurology (SyNergy)Ludwig‐Maximilians‐UniversityMunichGermany
| | - Emily Boyle
- Mechanisms of Cellular Quality ControlMax Planck Institute of BiophysicsFrankfurt am MainGermany
| | - Florian Wilfling
- Mechanisms of Cellular Quality ControlMax Planck Institute of BiophysicsFrankfurt am MainGermany
| | - Georg Tascher
- Institute of Biochemistry II, Faculty of MedicineGoethe UniversityFrankfurt am MainGermany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of MedicineGoethe UniversityFrankfurt am MainGermany
| | - Christian Behl
- The Autophagy Lab, Institute of PathobiochemistryUniversity Medical Center of the Johannes Gutenberg UniversityMainzGermany
| | - Andreas Kern
- The Autophagy Lab, Institute of PathobiochemistryUniversity Medical Center of the Johannes Gutenberg UniversityMainzGermany
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Berth SH, Rich DJ, Lloyd TE. The role of autophagic kinases in regulation of axonal function. Front Cell Neurosci 2022; 16:996593. [PMID: 36226074 PMCID: PMC9548526 DOI: 10.3389/fncel.2022.996593] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
Autophagy is an essential process for maintaining cellular homeostasis. Highlighting the importance of proper functioning of autophagy in neurons, disruption of autophagy is a common finding in neurodegenerative diseases. In recent years, evidence has emerged for the role of autophagy in regulating critical axonal functions. In this review, we discuss kinase regulation of autophagy in neurons, and provide an overview of how autophagic kinases regulate axonal processes, including axonal transport and axonal degeneration and regeneration. We also examine mechanisms for disruption of this process leading to neurodegeneration, focusing on the role of TBK1 in pathogenesis of Amyotrophic Lateral Sclerosis.
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36
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Extended-synaptotagmin 1 engages in unconventional protein secretion mediated via SEC22B + vesicle pathway in liver cancer. Proc Natl Acad Sci U S A 2022; 119:e2202730119. [PMID: 36044553 PMCID: PMC9457520 DOI: 10.1073/pnas.2202730119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein secretion in cancer cells defines tumor survival and progression by orchestrating the microenvironment. Studies suggest the occurrence of active secretion of cytosolic proteins in liver cancer and their involvement in tumorigenesis. Here, we investigated the identification of extended-synaptotagmin 1 (E-Syt1), an endoplasmic reticulum (ER)-bound protein, as a key mediator for cytosolic protein secretion at the ER-plasma membrane (PM) contact sites. Cytosolic proteins interacted with E-Syt1 on the ER, and then localized spatially inside SEC22B+ vesicles of liver cancer cells. Consequently, SEC22B on the vesicle tethered to the PM via Q-SNAREs (SNAP23, SNX3, and SNX4) for their secretion. Furthermore, inhibiting the interaction of protein kinase Cδ (PKCδ), a liver cancer-specific secretory cytosolic protein, with E-Syt1 by a PKCδ antibody, decreased in both PKCδ secretion and tumorigenicity. Results reveal the role of ER-PM contact sites in cytosolic protein secretion and provide a basis for ER-targeting therapy for liver cancer.
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Vaccaro MI, Mitchell F, Rivera F, Gonzalez CD. Protein expression in exocrine pancreatic diseases. Focus on VMP1 mediated autophagy. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 132:175-197. [PMID: 36088075 DOI: 10.1016/bs.apcsb.2022.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The exocrine pancreas produces enzymes involved in the digestive process whereas endocrine pancreas mainly regulates glucose metabolism. Diseases of the exocrine pancreas are characterized by high morbidity and mortality. Acute pancreatitis is a painful disease in which pancreatic secretory proteins are prematurely activated causing the digestion of the gland. Pancreatic adenocarcinoma is one of the most malignant cancers due to its resistance to treatment, its late diagnosis and high capacity for metastasis. Autophagy is a catabolic process that aims at degrading cytoplasmic contents and damaged organelles, to preserve cell viability and homeostasis. VMP1 is a transmembrane protein that plays a key role in triggering autophagy and being part of the autophagosome membrane. A specific type of selective autophagy pathway called zymophagy protects the pancreas against self-digestion in the setting of acute pancreatitis by sequestering intracellularly activated zymogen granules. Mitophagy is also responsible for maintaining pancreatitis as a mild disease by preserving mitochondrial function. Dysregulation of these selective autophagic processes by pancreatitis itself constitutes a risk factor for development of severe disease. In pancreatic adenocarcinoma, VMP1 mediated autophagy promotes cancer cell survival and resistance to chemotherapy. Therefore, it is relevant to highlight a role for controlling VMP1 expression and targeting VMP1 molecular pathways to improve exocrine pancreatic diseases prognosis.
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Affiliation(s)
- Maria I Vaccaro
- University of Buenos Aires, CONICET, Institute for Biochemistry and Molecular Medicine, Department of Pathophysiology, Buenos Aires, Argentina; CEMIC University Hospital, Unit of Translational Medical Research, Buenos Aires, Argentina.
| | - Florencia Mitchell
- CEMIC University Institute, School of Medicine, Department of Pharmacology, Buenos Aires, Argentina
| | - Francisco Rivera
- CEMIC University Institute, School of Medicine, Department of Pharmacology, Buenos Aires, Argentina
| | - Claudio D Gonzalez
- CEMIC University Hospital, Unit of Translational Medical Research, Buenos Aires, Argentina; CEMIC University Institute, School of Medicine, Department of Pharmacology, Buenos Aires, Argentina
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Xu J, Elshazly AM, Gewirtz DA. The Cytoprotective, Cytotoxic and Nonprotective Functional Forms of Autophagy Induced by Microtubule Poisons in Tumor Cells—Implications for Autophagy Modulation as a Therapeutic Strategy. Biomedicines 2022; 10:biomedicines10071632. [PMID: 35884937 PMCID: PMC9312878 DOI: 10.3390/biomedicines10071632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 12/12/2022] Open
Abstract
Microtubule poisons, as is the case with other antitumor drugs, routinely promote autophagy in tumor cells. However, the nature and function of the autophagy, in terms of whether it is cytoprotective, cytotoxic or nonprotective, cannot be predicted; this likely depends on both the type of drug studied as well as the tumor cell under investigation. In this article, we explore the literature relating to the spectrum of microtubule poisons and the nature of the autophagy induced. We further speculate as to whether autophagy inhibition could be a practical strategy for improving the response to cancer therapy involving these drugs that have microtubule function as a primary target.
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Affiliation(s)
- Jingwen Xu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China;
| | - Ahmed M. Elshazly
- Massey Cancer Center, Department of Pharmacology and Toxicology, Virginia Commonwealth University, 401 College St., Richmond, VA 23298, USA;
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - David A. Gewirtz
- Massey Cancer Center, Department of Pharmacology and Toxicology, Virginia Commonwealth University, 401 College St., Richmond, VA 23298, USA;
- Correspondence:
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Majeed ST, Majeed R, Andrabi KI. Expanding the view of the molecular mechanisms of autophagy pathway. J Cell Physiol 2022; 237:3257-3277. [DOI: 10.1002/jcp.30819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 01/18/2023]
Affiliation(s)
- Sheikh Tahir Majeed
- Department of Biotechnology Central University of Kashmir Ganderbal Jammu and Kashmir India
- Growth Factor Signaling Laboratory, Department of Biotechnology University of Kashmir Srinagar Jammu and Kashmir India
| | - Rabiya Majeed
- Growth Factor Signaling Laboratory, Department of Biotechnology University of Kashmir Srinagar Jammu and Kashmir India
- Department of Biochemistry University of Kashmir Srinagar Jammu and Kashmir India
| | - Khurshid I. Andrabi
- Growth Factor Signaling Laboratory, Department of Biotechnology University of Kashmir Srinagar Jammu and Kashmir India
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Deretic V, Lazarou M. A guide to membrane atg8ylation and autophagy with reflections on immunity. J Cell Biol 2022; 221:e202203083. [PMID: 35699692 PMCID: PMC9202678 DOI: 10.1083/jcb.202203083] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/16/2022] [Accepted: 05/26/2022] [Indexed: 12/11/2022] Open
Abstract
The process of membrane atg8ylation, defined herein as the conjugation of the ATG8 family of ubiquitin-like proteins to membrane lipids, is beginning to be appreciated in its broader manifestations, mechanisms, and functions. Classically, membrane atg8ylation with LC3B, one of six mammalian ATG8 family proteins, has been viewed as the hallmark of canonical autophagy, entailing the formation of characteristic double membranes in the cytoplasm. However, ATG8s are now well described as being conjugated to single membranes and, most recently, proteins. Here we propose that the atg8ylation is coopted by multiple downstream processes, one of which is canonical autophagy. We elaborate on these biological outputs, which impact metabolism, quality control, and immunity, emphasizing the context of inflammation and immunological effects. In conclusion, we propose that atg8ylation is a modification akin to ubiquitylation, and that it is utilized by different systems participating in membrane stress responses and membrane remodeling activities encompassing autophagy and beyond.
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Affiliation(s)
- Vojo Deretic
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Michael Lazarou
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
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Duckney PJ, Wang P, Hussey PJ. Membrane contact sites and cytoskeleton-membrane interactions in autophagy. FEBS Lett 2022; 596:2093-2103. [PMID: 35648104 PMCID: PMC9545284 DOI: 10.1002/1873-3468.14414] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 11/23/2022]
Abstract
In Eukaryotes, organelle interactions occur at specialised contact sites between organelle membranes. Contact sites are regulated by specialised tethering proteins, which bring organelle membranes into close proximity, and facilitate functional crosstalk between compartments. While contact site proteins are well characterised in mammals and yeast, the regulators of plant contact site formation are only now beginning to emerge. Having unique subcellular structures, plants must also utilise unique mechanisms of organelle interaction to regulate plant‐specific functions. The recently characterised NETWORKED proteins are the first dedicated family of plant‐specific contact site proteins. Research into the NET proteins and their interacting partners continues to uncover plant‐specific mechanisms of organelle interaction and the importance of these organelle contacts to plant life. Moreover, it is becoming increasingly apparent that organelle interactions are fundamental to autophagy in plants. Here, we will present recent developments in our understanding of the mechanisms of plant organelle interactions, their functions, and emerging roles in autophagy.
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Affiliation(s)
| | - Pengwei Wang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
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de la Cruz-Ojeda P, Flores-Campos R, Navarro-Villarán E, Muntané J. The Role of Non-Coding RNAs in Autophagy During Carcinogenesis. Front Cell Dev Biol 2022; 10:799392. [PMID: 35309939 PMCID: PMC8926078 DOI: 10.3389/fcell.2022.799392] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/18/2022] [Indexed: 12/12/2022] Open
Abstract
Macroautophagy (autophagy herein) is a cellular stress response and a survival pathway involved in self-renewal and quality control processes to maintain cellular homeostasis. The alteration of autophagy has been implicated in numerous diseases such as cancer where it plays a dual role. Autophagy serves as a tumor suppressor in the early phases of cancer formation with the restoration of homeostasis and eliminating cellular altered constituents, yet in later phases, autophagy may support and/or facilitate tumor growth, metastasis and may contribute to treatment resistance. Key components of autophagy interact with either pro- and anti-apoptotic factors regulating the proximity of tumor cells to apoptotic cliff promoting cell survival. Autophagy is regulated by key cell signaling pathways such as Akt (protein kinase B, PKB), mammalian target of rapamycin (mTOR) and AMP-activated protein kinase (AMPK) involved in cell survival and metabolism. The expression of critical members of upstream cell signaling, as well as those directly involved in the autophagic and apoptotic machineries are regulated by microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Consequently, non-coding RNAs play a relevant role in carcinogenesis and treatment response in cancer. The review is an update of the current knowledge in the regulation by miRNA and lncRNA of the autophagic components and their functional impact to provide an integrated and comprehensive regulatory network of autophagy in cancer.
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Affiliation(s)
- Patricia de la Cruz-Ojeda
- Institute of Biomedicine of Seville (IBiS), Hospital University "Virgen del Rocío"/CSIC/University of Seville, Seville, Spain.,Department of Medical Physiology and Biophysics, University of Seville, Seville, Spain.,Networked Biomedical Research Center Hepatic and Digestive Diseases (CIBEREHD o Ciberehd), Institute of Health Carlos III, Madrid, Spain
| | - Rocío Flores-Campos
- Institute of Biomedicine of Seville (IBiS), Hospital University "Virgen del Rocío"/CSIC/University of Seville, Seville, Spain
| | - Elena Navarro-Villarán
- Institute of Biomedicine of Seville (IBiS), Hospital University "Virgen del Rocío"/CSIC/University of Seville, Seville, Spain.,Department of Medical Physiology and Biophysics, University of Seville, Seville, Spain.,Networked Biomedical Research Center Hepatic and Digestive Diseases (CIBEREHD o Ciberehd), Institute of Health Carlos III, Madrid, Spain
| | - Jordi Muntané
- Institute of Biomedicine of Seville (IBiS), Hospital University "Virgen del Rocío"/CSIC/University of Seville, Seville, Spain.,Department of Medical Physiology and Biophysics, University of Seville, Seville, Spain.,Networked Biomedical Research Center Hepatic and Digestive Diseases (CIBEREHD o Ciberehd), Institute of Health Carlos III, Madrid, Spain
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Lapaquette P, Ducreux A, Basmaciyan L, Paradis T, Bon F, Bataille A, Winckler P, Hube B, d’Enfert C, Esclatine A, Dubus E, Bringer MA, Morel E, Dalle F. Membrane protective role of autophagic machinery during infection of epithelial cells by Candida albicans. Gut Microbes 2022; 14:2004798. [PMID: 35086419 PMCID: PMC8803057 DOI: 10.1080/19490976.2021.2004798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Candida albicans (C. albicans) is an opportunistic pathogen causing infections ranging from superficial to life-threatening disseminated infections. In a susceptible host, C. albicans is able to translocate through the gut barrier, promoting its dissemination into deeper organs. C. albicans hyphae can invade human epithelial cells by two well-documented mechanisms: epithelial-driven endocytosis and C. albicans-driven active penetration. One mechanism by which host cells protect themselves against intracellular C. albicans is termed autophagy. The protective role of autophagy during C. albicans infection has been investigated in myeloid cells; however, far less is known regarding the role of this process during the infection of epithelial cells. In the present study, we investigated the role of autophagy-related proteins during the infection of epithelial cells, including intestinal epithelial cells and gut explants, by C. albicans. Using cell imaging, we show that key molecular players of the autophagy machinery (LC3-II, PI3P, ATG16L1, and WIPI2) were recruited at Candida invasion sites. We deepened these observations by electron microscopy analyses that reveal the presence of autophagosomes in the vicinity of invading hyphae. Importantly, these events occur during active penetration of C. albicans into host cells and are associated with plasma membrane damage. In this context, we show that the autophagy-related key proteins ATG5 and ATG16L1 contribute to plasma membrane repair mediated by lysosomal exocytosis and participate in protecting epithelial cells against C. albicans-induced cell death. Our findings provide a novel mechanism by which epithelial cells, forming the first line of defense against C. albicans in the gut, can react to limit C. albicans invasion.
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Affiliation(s)
- Pierre Lapaquette
- Univ. Bourgogne Franche-Comté, Agrosup Dijon, UMR PAM A 02.102, Dijon, France,CONTACT Pierre Lapaquette Univ. Bourgogne Franche-Comté, Agrosup Dijon, UMR PAM A 02.102, Dijon, France
| | - Amandine Ducreux
- Univ. Bourgogne Franche-Comté, Agrosup Dijon, UMR PAM A 02.102, Dijon, France
| | - Louise Basmaciyan
- Univ. Bourgogne Franche-Comté, Agrosup Dijon, UMR PAM A 02.102, Dijon, France,Laboratoire de Parasitologie-Mycologie, Plateforme de Biologie Hospitalo-Universitaire Gérard Mack, Dijon, France
| | - Tracy Paradis
- Univ. Bourgogne Franche-Comté, Agrosup Dijon, UMR PAM A 02.102, Dijon, France
| | - Fabienne Bon
- Univ. Bourgogne Franche-Comté, Agrosup Dijon, UMR PAM A 02.102, Dijon, France
| | | | - Pascale Winckler
- Univ. Bourgogne Franche-Comté, Agrosup Dijon, UMR PAM A 02.102, Dijon, France,Dimacell Imaging Facility, Agrosup Dijon, INRA, INSERM, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany,Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Christophe d’Enfert
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, USC2019 INRA, Paris, France
| | - Audrey Esclatine
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Elisabeth Dubus
- Centre des Sciences du Goût et de l’Alimentation, AgroSup Dijon, CNRS, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Marie-Agnès Bringer
- Centre des Sciences du Goût et de l’Alimentation, AgroSup Dijon, CNRS, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Etienne Morel
- Institut Necker Enfants-Malades (INEM), INSERM U1151-CNRS UMR 8253, Université de Paris, Paris, France
| | - Frédéric Dalle
- Univ. Bourgogne Franche-Comté, Agrosup Dijon, UMR PAM A 02.102, Dijon, France,Laboratoire de Parasitologie-Mycologie, Plateforme de Biologie Hospitalo-Universitaire Gérard Mack, Dijon, France,Frédéric Dalle Laboratoire de Parasitologie-Mycologie
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Visintin R, Ray SK. Specific microRNAs for Modulation of Autophagy in Spinal Cord Injury. Brain Sci 2022; 12:247. [PMID: 35204010 PMCID: PMC8870708 DOI: 10.3390/brainsci12020247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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
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Li S, Yan R, Xu J, Zhao S, Ma X, Sun Q, Zhang M, Li Y, Liu JJG, Chen L, Li S, Xu K, Ge L. A new type of ERGIC-ERES membrane contact mediated by TMED9 and SEC12 is required for autophagosome biogenesis. Cell Res 2022; 32:119-138. [PMID: 34561617 PMCID: PMC8461442 DOI: 10.1038/s41422-021-00563-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/23/2021] [Indexed: 02/08/2023] Open
Abstract
Under stress, the endomembrane system undergoes reorganization to support autophagosome biogenesis, which is a central step in autophagy. How the endomembrane system remodels has been poorly understood. Here we identify a new type of membrane contact formed between the ER-Golgi intermediate compartment (ERGIC) and the ER-exit site (ERES) in the ER-Golgi system, which is essential for promoting autophagosome biogenesis induced by different stress stimuli. The ERGIC-ERES contact is established by the interaction between TMED9 and SEC12 which generates a short distance opposition (as close as 2-5 nm) between the two compartments. The tight membrane contact allows the ERES-located SEC12 to transactivate COPII assembly on the ERGIC. In addition, a portion of SEC12 also relocates to the ERGIC. Through both mechanisms, the ERGIC-ERES contact promotes formation of the ERGIC-derived COPII vesicle, a membrane precursor of the autophagosome. The ERGIC-ERES contact is physically and functionally different from the TFG-mediated ERGIC-ERES adjunction involved in secretory protein transport, and therefore defines a unique endomembrane structure generated upon stress conditions for autophagic membrane formation.
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Affiliation(s)
- Shulin Li
- State Key Laboratory of Membrane Biology, Beijing, China ,grid.452723.50000 0004 7887 9190Tsinghua-Peking Center for Life Sciences, Beijing, China ,grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua University, Beijing, China
| | - Rui Yan
- grid.47840.3f0000 0001 2181 7878Department of Chemistry, University of California, Berkeley, CA USA
| | - Jialu Xu
- grid.452723.50000 0004 7887 9190Tsinghua-Peking Center for Life Sciences, Beijing, China ,grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua University, Beijing, China ,Beijing Advanced Innovation Center for Structural Biology, Beijing, China
| | - Shiqun Zhao
- grid.11135.370000 0001 2256 9319Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China ,grid.419265.d0000 0004 1806 6075National Center for Nanoscience and Technology, Beijing, China
| | - Xinyu Ma
- State Key Laboratory of Membrane Biology, Beijing, China ,grid.452723.50000 0004 7887 9190Tsinghua-Peking Center for Life Sciences, Beijing, China ,grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua University, Beijing, China
| | - Qiming Sun
- grid.13402.340000 0004 1759 700XDepartment of Biochemistry, Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang China
| | - Min Zhang
- State Key Laboratory of Membrane Biology, Beijing, China ,grid.452723.50000 0004 7887 9190Tsinghua-Peking Center for Life Sciences, Beijing, China ,grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua University, Beijing, China
| | - Ying Li
- State Key Laboratory of Membrane Biology, Beijing, China ,grid.452723.50000 0004 7887 9190Tsinghua-Peking Center for Life Sciences, Beijing, China ,grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua University, Beijing, China
| | - Jun-Jie Gogo Liu
- grid.452723.50000 0004 7887 9190Tsinghua-Peking Center for Life Sciences, Beijing, China ,grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua University, Beijing, China ,Beijing Advanced Innovation Center for Structural Biology, Beijing, China
| | - Liangyi Chen
- grid.11135.370000 0001 2256 9319Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China ,grid.419265.d0000 0004 1806 6075National Center for Nanoscience and Technology, Beijing, China
| | - Sai Li
- grid.452723.50000 0004 7887 9190Tsinghua-Peking Center for Life Sciences, Beijing, China ,grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua University, Beijing, China ,Beijing Advanced Innovation Center for Structural Biology, Beijing, China
| | - Ke Xu
- grid.47840.3f0000 0001 2181 7878Department of Chemistry, University of California, Berkeley, CA USA
| | - Liang Ge
- State Key Laboratory of Membrane Biology, Beijing, China ,grid.452723.50000 0004 7887 9190Tsinghua-Peking Center for Life Sciences, Beijing, China ,grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua University, Beijing, China
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46
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ER-phagy requires the assembly of actin at sites of contact between the cortical ER and endocytic pits. Proc Natl Acad Sci U S A 2022; 119:2117554119. [PMID: 35101986 PMCID: PMC8833162 DOI: 10.1073/pnas.2117554119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/24/2021] [Indexed: 01/03/2023] Open
Abstract
Portions of the endoplasmic reticulum (ER) are degraded by autophagy (ER-phagy) in response to starvation or the accumulation of misfolded proteins. We show that ER-phagy requires assembly of actin at sites of contact between the edges of ER sheets and endocytic pits on the plasma membrane. Actin assembly may help to bring an element of the ER carrying the selective autophagy receptor Atg40 into the cell interior, where it associates with Atg11, a scaffold needed to recruit components for autophagosome assembly. Understanding the mechanism by which regions of the ER are selected for degradation and sequestered within autophagosomes may help in the development of novel approaches to treat diseases that result from the accumulation of misfolded proteins within the ER. Fragments of the endoplasmic reticulum (ER) are selectively delivered to the lysosome (mammals) or vacuole (yeast) in response to starvation or the accumulation of misfolded proteins through an autophagic process known as ER-phagy. A screen of the Saccharomyces cerevisiae deletion library identified end3Δ as a candidate knockout strain that is defective in ER-phagy during starvation conditions, but not bulk autophagy. We find that loss of End3 and its stable binding partner Pan1, or inhibition of the Arp2/3 complex that is coupled by the End3-Pan1 complex to endocytic pits, blocks the association of the cortical ER autophagy receptor, Atg40, with the autophagosomal assembly scaffold protein Atg11. The membrane contact site module linking the rim of cortical ER sheets and endocytic pits, consisting of Scs2 or Scs22, Osh2 or Osh3, and Myo3 or Myo5, is also needed for ER-phagy. Both Atg40 and Scs2 are concentrated at the edges of ER sheets and can be cross-linked to each other. Our results are consistent with a model in which actin assembly at sites of contact between the cortical ER and endocytic pits contributes to ER sequestration into autophagosomes.
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Kumar S, Javed R, Mudd M, Pallikkuth S, Lidke KA, Jain A, Tangavelou K, Gudmundsson SR, Ye C, Rusten TE, Anonsen JH, Lystad AH, Claude-Taupin A, Simonsen A, Salemi M, Phinney B, Li J, Guo LW, Bradfute SB, Timmins GS, Eskelinen EL, Deretic V. Mammalian hybrid pre-autophagosomal structure HyPAS generates autophagosomes. Cell 2021; 184:5950-5969.e22. [PMID: 34741801 PMCID: PMC8616855 DOI: 10.1016/j.cell.2021.10.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 05/12/2021] [Accepted: 10/15/2021] [Indexed: 12/14/2022]
Abstract
The biogenesis of mammalian autophagosomes remains to be fully defined. Here, we used cellular and in vitro membrane fusion analyses to show that autophagosomes are formed from a hitherto unappreciated hybrid membrane compartment. The autophagic precursors emerge through fusion of FIP200 vesicles, derived from the cis-Golgi, with endosomally derived ATG16L1 membranes to generate a hybrid pre-autophagosomal structure, HyPAS. A previously unrecognized apparatus defined here controls HyPAS biogenesis and mammalian autophagosomal precursor membranes. HyPAS can be modulated by pharmacological agents whereas its formation is inhibited upon severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or by expression of SARS-CoV-2 nsp6. These findings reveal the origin of mammalian autophagosomal membranes, which emerge via convergence of secretory and endosomal pathways, and show that this process is targeted by microbial factors such as coronaviral membrane-modulating proteins.
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Affiliation(s)
- Suresh Kumar
- Autophagy Inflammation and Metabolism Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Ruheena Javed
- Autophagy Inflammation and Metabolism Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Michal Mudd
- Autophagy Inflammation and Metabolism Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Sandeep Pallikkuth
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | - Keith A Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | - Ashish Jain
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Karthikeyan Tangavelou
- Autophagy Inflammation and Metabolism Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | | | - Chunyan Ye
- Center for Global Health, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | | | | | | | - Aurore Claude-Taupin
- Autophagy Inflammation and Metabolism Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Anne Simonsen
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Michelle Salemi
- Proteomics Core, University of California Davis, Davis, CA, USA
| | - Brett Phinney
- Proteomics Core, University of California Davis, Davis, CA, USA
| | - Jing Li
- Department of Surgery, University of Virginia, Charlottesville, VA, USA
| | - Lian-Wang Guo
- Department of Surgery, University of Virginia, Charlottesville, VA, USA
| | - Steven B Bradfute
- Center for Global Health, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Graham S Timmins
- Autophagy Inflammation and Metabolism Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; School of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | | | - Vojo Deretic
- Autophagy Inflammation and Metabolism Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
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48
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Mailler E, Guardia CM, Bai X, Jarnik M, Williamson CD, Li Y, Maio N, Golden A, Bonifacino JS. The autophagy protein ATG9A enables lipid mobilization from lipid droplets. Nat Commun 2021; 12:6750. [PMID: 34799570 PMCID: PMC8605025 DOI: 10.1038/s41467-021-26999-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 10/26/2021] [Indexed: 01/18/2023] Open
Abstract
The multispanning membrane protein ATG9A is a scramblase that flips phospholipids between the two membrane leaflets, thus contributing to the expansion of the phagophore membrane in the early stages of autophagy. Herein, we show that depletion of ATG9A does not only inhibit autophagy but also increases the size and/or number of lipid droplets in human cell lines and C. elegans. Moreover, ATG9A depletion blocks transfer of fatty acids from lipid droplets to mitochondria and, consequently, utilization of fatty acids in mitochondrial respiration. ATG9A localizes to vesicular-tubular clusters (VTCs) that are tightly associated with an ER subdomain enriched in another multispanning membrane scramblase, TMEM41B, and also in close proximity to phagophores, lipid droplets and mitochondria. These findings indicate that ATG9A plays a critical role in lipid mobilization from lipid droplets to autophagosomes and mitochondria, highlighting the importance of ATG9A in both autophagic and non-autophagic processes.
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Affiliation(s)
- Elodie Mailler
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Carlos M Guardia
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Xiaofei Bai
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michal Jarnik
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Chad D Williamson
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Nunziata Maio
- Metals Biology and Molecular Medicine Group, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Andy Golden
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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49
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Autophagy Dysregulation in Diabetic Kidney Disease: From Pathophysiology to Pharmacological Interventions. Cells 2021; 10:cells10092497. [PMID: 34572148 PMCID: PMC8469825 DOI: 10.3390/cells10092497] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 09/04/2021] [Accepted: 09/09/2021] [Indexed: 12/18/2022] Open
Abstract
Diabetic kidney disease (DKD) is a frequent, potentially devastating complication of diabetes mellitus. Several factors are involved in its pathophysiology. At a cellular level, diabetic kidney disease is associated with many structural and functional alterations. Autophagy is a cellular mechanism that transports intracytoplasmic components to lysosomes to preserve cellular function and homeostasis. Autophagy integrity is essential for cell homeostasis, its alteration can drive to cell damage or death. Diabetic kidney disease is associated with profound autophagy dysregulation. Autophagy rate and flux alterations were described in several models of diabetic kidney disease. Some of them are closely linked with disease progression and severity. Some antidiabetic agents have shown significant effects on autophagy. A few of them have also demonstrated to modify disease progression and improved outcomes in affected patients. Other drugs also target autophagy and are being explored for clinical use in patients with diabetic kidney disease. The modulation of autophagy could be relevant for the pharmacological treatment and prevention of this disease in the future. Therefore, this is an evolving area that requires further experimental and clinical research. Here we discuss the relationship between autophagy and Diabetic kidney disease and the potential value of autophagy modulation as a target for pharmacological intervention.
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50
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Tu YXI, Sydor AM, Coyaud E, Laurent EMN, Dyer D, Mellouk N, St-Germain J, Vernon RM, Forman-Kay JD, Li T, Hua R, Zhao K, Ridgway ND, Kim PK, Raught B, Brumell JH. Global Proximity Interactome of the Human Macroautophagy Pathway. Autophagy 2021; 18:1174-1186. [PMID: 34524948 PMCID: PMC9196747 DOI: 10.1080/15548627.2021.1965711] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Macroautophagy is a highly conserved eukaryotic cellular pathway involving the engulfment of macromolecules, organelles, and invading microbes by a double-membrane compartment and subsequent lysosomal degradation. The mechanisms that regulate macroautophagy, and the interaction of its components with other cellular pathways, have remained unclear. Here, we performed proximity-dependent biotin identification (BioID) on 39 core human macroautophagy proteins, identifying over 700 unique high confidence proximity interactors with new putative connections between macroautophagic and essential cellular processes. Of note, we identify members of the OSBPL (oxysterol binding protein like) family as Atg8-family protein interactors. We subsequently conducted comprehensive screens of the OSBPL family for LC3B-binding and roles in xenophagy and aggrephagy. OSBPL7 and OSBPL11 emerged as novel lipid transfer proteins required for macroautophagy of selective cargo. Altogether, our proximity interaction map provides a valuable resource for the study of autophagy and highlights the critical role of membrane contact site proteins in the pathway.
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Affiliation(s)
- Yi Xin Iris Tu
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Andrew M Sydor
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Estelle M N Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Diana Dyer
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Nora Mellouk
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Robert M Vernon
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Julie D Forman-Kay
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Taoyingnan Li
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Rong Hua
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Kexin Zhao
- Departments of Pediatrics and Biochemistry and Molecular Biology, Atlantic Research Centre, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Neale D Ridgway
- Departments of Pediatrics and Biochemistry and Molecular Biology, Atlantic Research Centre, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Peter K Kim
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John H Brumell
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,SickKids IBD Centre, Hospital for Sick Children, Toronto, Ontario, Canada
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