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Broadbent DG, Barnaba C, Perez GI, Schmidt JC. Quantitative analysis of autophagy reveals the role of ATG9 and ATG2 in autophagosome formation. J Cell Biol 2023; 222:e202210078. [PMID: 37115157 PMCID: PMC10148237 DOI: 10.1083/jcb.202210078] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/03/2023] [Accepted: 03/17/2023] [Indexed: 04/29/2023] Open
Abstract
Autophagy is a catabolic pathway required for the recycling of cytoplasmic materials. To define the mechanisms underlying autophagy it is critical to quantitatively characterize the dynamic behavior of autophagy factors in living cells. Using a panel of cell lines expressing HaloTagged autophagy factors from their endogenous loci, we analyzed the abundance, single-molecule dynamics, and autophagosome association kinetics of autophagy proteins involved in autophagosome biogenesis. We demonstrate that autophagosome formation is inefficient and ATG2-mediated tethering to donor membranes is a key commitment step in autophagosome formation. Furthermore, our observations support the model that phagophores are initiated by the accumulation of autophagy factors on mobile ATG9 vesicles, and that the ULK1 complex and PI3-kinase form a positive feedback loop required for autophagosome formation. Finally, we demonstrate that the duration of autophagosome biogenesis is ∼110 s. In total, our work provides quantitative insight into autophagosome biogenesis and establishes an experimental framework to analyze autophagy in human cells.
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Affiliation(s)
- David G. Broadbent
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Carlo Barnaba
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Gloria I. Perez
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Jens C. Schmidt
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
- Department of Obstetrics and Gynecology, Michigan State University, East Lansing, MI, USA
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2
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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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Zhang JM, Wang ZG, He ZY, Qin L, Wang J, Zhu WT, Qi J. Cyclic mechanical strain with high-tensile triggers autophagy in growth plate chondrocytes. J Orthop Surg Res 2022; 17:191. [PMID: 35346257 PMCID: PMC8962562 DOI: 10.1186/s13018-022-03081-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/16/2022] [Indexed: 01/18/2023] Open
Abstract
Abstract
Background
Mechanical loading has been widely considered to be essential for growth plate to maintain metabolism and development. Cyclic mechanical strain has been demonstrated to induce autophagy, whereas the relationship between cyclic tensile strain (CTS) and autophagy in growth plate chondrocytes (GPCs) is not clear. The objective of this study was to investigate whether CTS can regulate autophagy in GPCs in vitro and explore the potential mechanisms of this regulation.
Methods
The 2-week-old Sprague–Dawley rat GPCs were subjected to CTS of varying magnitude and duration at a frequency of 2.0 Hz. The mRNA levels of autophagy-related genes were measured by RT-qPCR. The autophagy in GPCs was verified by transmission electron microscopy (TME), immunofluorescence and Western blotting. The fluorescence-activated cell sorting (FACS) was employed to detect the percentage of apoptotic and necrotic cells.
Results
In GPCs, CTS significantly increased the mRNA and protein levels of autophagy-related genes, such as LC3, ULK1, ATG5 and BECN1 in a magnitude- and time-dependent manner. There was no significant difference in the proportion of apoptotic and necrotic cells between control group and CTS group. The autophagy inhibitors, 3-methyladenine (3MA) and chloroquine (CQ) reversed the CTS-induced autophagy via promoting the formation of autophagosomes. Cytochalasin D (cytoD), an inhibitor of G-actin polymerization into F-actin, could effectively block the CTS-induced autophagy in GPCs.
Conclusion
Cyclic mechanical strain with high-tensile triggers autophagy in GPCs, which can be suppressed by 3MA and CQ, and cytoskeletal F-actin microfilaments organization plays a key role in chondrocytes’ response to mechanical loading.
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Zaki Mahdi N. Investigation of the Lethal Effect of Purified Arginine Deiminase Purified from Lactobacillus plantarum p5 on Murine Mammary Adenocarcinoma and Vero cell Lines. ARCHIVES OF RAZI INSTITUTE 2022; 77:241-247. [PMID: 35891771 PMCID: PMC9288635 DOI: 10.22092/ari.2021.356587.1873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/04/2021] [Indexed: 05/25/2023]
Abstract
Cancer is one of the most serious diseases facing humanity; accordingly, it is urgent to find a cure that is rarely harmful to the patient as much as possible. It has been approved that arginine deiminase (ADI) can hydrolyze the plasma arginine to citrulline. This hydrolysis activity and reduction in the amount of intercellular arginine suppress lipopolysaccharide-induced nitric oxide synthesis. On the other hand, arginine depletion arrests the cell cycle at the G1 phase; therefore, ADI has been considered a powerful anticancer agent. The current study aimed to investigate the lethal effects of ADI purified from the Lactobacillus plantarum p5 strain on murine mammary adenocarcinoma and Vero cell lines. Anti-proliferative activity of ADI against murine mammary adenocarcinoma) AMN3) cell line was evaluated after different incubation times (3, 6, 24, 48, and 72 h) of exposure to 1 µg/mL of ADI, compared to Vero (non-cancer cell line) transformed cell line with same conditions. The autophagy process in cancer cells was recognized after three hours of incubation with ADI which was clearly observed in the AMN3 cell line under an inverted microscope. The first stages of the programmed cell death (apoptosis) pathway were only observed in AMN3 cells after 24 h of incubation with ADI, and this process continued with the time until they reached the last stages of apoptosis after 72 h of incubation. The results of the current study showed that the AMN3 cell line was auxotrophic for arginine because it could not produce it in the presence of enzyme which had a robust activity to kill these cancer cells; however, Vero non-cancer cell line survived in the presence of ADI because it had the ability to produce arginine.
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Affiliation(s)
- N Zaki Mahdi
- Department of Biology, College of Sciences, Mustansiriyah University, Baghdad, Iraq
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Wang Y, Li Y, Wei F, Duan Y. Optical Imaging Paves the Way for Autophagy Research. Trends Biotechnol 2017; 35:1181-1193. [PMID: 28916049 PMCID: PMC7114199 DOI: 10.1016/j.tibtech.2017.08.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 01/02/2023]
Abstract
Autophagy is a degradation process in eukaryotic cells that recycles cellular components for nutrition supply under environmental stress and plays a double-edged role in development of major human diseases. Noninvasive optical imaging enables us to clearly visualize various classes of structures involved in autophagy at macroscopic and microscopic dynamic levels. In this review, we discuss important trends of emerging optical imaging technologies used to explore autophagy and provide insights into the mechanistic investigation and structural study of autophagy in mammalian cells. Some exciting new prospects and future research directions regarding optical imaging techniques in this field are also highlighted.
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Affiliation(s)
- Yimin Wang
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Yu Li
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Fujing Wei
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China.
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Wang L, Kim JY, Liu HM, Lai MMC, Ou JHJ. HCV-induced autophagosomes are generated via homotypic fusion of phagophores that mediate HCV RNA replication. PLoS Pathog 2017; 13:e1006609. [PMID: 28931085 PMCID: PMC5621699 DOI: 10.1371/journal.ppat.1006609] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 09/29/2017] [Accepted: 08/26/2017] [Indexed: 12/21/2022] Open
Abstract
Hepatitis C virus (HCV) induces autophagy to promote its replication, including its RNA replication, which can take place on double-membrane vesicles known as autophagosomes. However, how HCV induces the biogenesis of autophagosomes and how HCV RNA replication complex may be assembled on autophagosomes were largely unknown. During autophagy, crescent membrane structures known as phagophores first appear in the cytoplasm, which then progress to become autophagosomes. By conducting electron microscopy and in vitro membrane fusion assay, we found that phagophores induced by HCV underwent homotypic fusion to generate autophagosomes in a process dependent on the SNARE protein syntaxin 7 (STX7). Further analyses by live-cell imaging and fluorescence microscopy indicated that HCV-induced phagophores originated from the endoplasmic reticulum (ER). Interestingly, comparing with autophagy induced by nutrient starvation, the progression of phagophores to autophagosomes induced by HCV took significantly longer time, indicating fundamental differences in the biogenesis of autophagosomes induced by these two different stimuli. As the knockdown of STX7 to inhibit the formation of autophagosomes did not affect HCV RNA replication, and purified phagophores could mediate HCV RNA replication, the assembly of the HCV RNA replication complex on autophagosomes apparently took place during the formative stage of phagophores. These findings provided important information for understanding how HCV controlled and modified this important cellular pathway for its own replication. Autophagy is a catabolic process that is important for maintaining cellular homeostasis. During autophagy, crescent membrane structures known as phagophores first appear in the cytoplasm, which then expand to form enclosed double-membrane vesicles known as autophagosomes. It has been shown that hepatitis C virus (HCV) induces autophagy and uses autophagosomal membranes for its RNA replication. In this report, we studied the biogenesis pathway of HCV-induced autophagosomes and demonstrated that phagophores induced by HCV originated from the endoplasmic reticulum and undergo homotypic fusion to generate autophagosomes, and that the HCV RNA replication complex is assembled on phagophores prior to the formation of autophagosomes. These findings provided important information for understanding how an RNA virus controls this important cellular pathway for its replication.
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Affiliation(s)
- Linya Wang
- Department of Molecular Microbiology and Immunology, University of Southern California, Keck School of Medicine, Los Angeles, California, United States of America
| | - Ja Yeon Kim
- Department of Molecular Microbiology and Immunology, University of Southern California, Keck School of Medicine, Los Angeles, California, United States of America
| | - Helene Minyi Liu
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Michael M. C. Lai
- Department of Molecular Microbiology and Immunology, University of Southern California, Keck School of Medicine, Los Angeles, California, United States of America
- Research Center for Emerging Viruses, China Medical University Hospital and China Medical University, Taichung, Taiwan
| | - Jing-hsiung James Ou
- Department of Molecular Microbiology and Immunology, University of Southern California, Keck School of Medicine, Los Angeles, California, United States of America
- * E-mail:
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Karanasios E, Walker SA, Okkenhaug H, Manifava M, Hummel E, Zimmermann H, Ahmed Q, Domart MC, Collinson L, Ktistakis NT. Autophagy initiation by ULK complex assembly on ER tubulovesicular regions marked by ATG9 vesicles. Nat Commun 2016; 7:12420. [PMID: 27510922 PMCID: PMC4987534 DOI: 10.1038/ncomms12420] [Citation(s) in RCA: 213] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 06/30/2016] [Indexed: 12/11/2022] Open
Abstract
Autophagosome formation requires sequential translocation of autophagy-specific proteins to membranes enriched in PI3P and connected to the ER. Preceding this, the earliest autophagy-specific structure forming de novo is a small punctum of the ULK1 complex. The provenance of this structure and its mode of formation are unknown. We show that the ULK1 structure emerges from regions, where ATG9 vesicles align with the ER and its formation requires ER exit and coatomer function. Super-resolution microscopy reveals that the ULK1 compartment consists of regularly assembled punctate elements that cluster in progressively larger spherical structures and associates uniquely with the early autophagy machinery. Correlative electron microscopy after live imaging shows tubulovesicular membranes present at the locus of this structure. We propose that the nucleation of autophagosomes occurs in regions, where the ULK1 complex coalesces with ER and the ATG9 compartment.
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Affiliation(s)
| | - Simon A. Walker
- Signalling Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Hanneke Okkenhaug
- Signalling Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Maria Manifava
- Signalling Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Eric Hummel
- Carl Zeiss Microscopy GmbH, Munich 81379, Germany
| | | | - Qashif Ahmed
- Signalling Programme, The Babraham Institute, Cambridge CB22 3AT, UK
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Dynamics of autophagosome formation: a pulse and a sequence of waves. Biochem Soc Trans 2015; 42:1389-95. [PMID: 25233420 DOI: 10.1042/bst20140183] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Autophagosomes form in eukaryotic cells in response to starvation or to other stress conditions brought about by the unwanted presence in the cytosol of pathogens, damaged organelles or aggregated protein assemblies. The uniqueness of autophagosomes is that they form de novo and that they are the only double-membraned vesicles known in cells, having arisen from flat membrane sheets which have expanded and self-closed. The various steps describing their formation as well as most of the protein and lipid components involved have been identified. Furthermore, the hierarchical relationships among the components are well documented, and the mechanistic rationale for some of these hierarchies has been revealed. In the present review, we try to provide a current view of the process of autophagosome formation in mammalian cells, emphasizing along the way gaps in our knowledge that need additional work.
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