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Wang N, Shibata Y, Paulo JA, Gygi SP, Rapoport TA. A conserved membrane curvature-generating protein is crucial for autophagosome formation in fission yeast. Nat Commun 2023; 14:4765. [PMID: 37553386 PMCID: PMC10409813 DOI: 10.1038/s41467-023-40530-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 07/26/2023] [Indexed: 08/10/2023] Open
Abstract
Organelles are shaped by curvature-generating proteins, which include the reticulons and REEPs that are involved in forming the endoplasmic reticulum (ER). A conserved REEP subfamily differs from the ER-shaping REEPs in abundance and membrane topology and has unidentified functions. Here, we show that Rop1, the single member of this family in the fission yeast Schizosacharomyces pombe, is crucial for the macroautophagy of organelles and cytosolic proteins. Rop1 is needed for the formation of phagophores, cup-like structures consisting of two closely apposed membrane sheets that encapsulate cargo. It is recruited at early stages to phagophores and is required for their maturation into autophagosomes. Rop1 function relies on its ability to generate high membrane curvature and on its colocalization with the autophagy component Atg2 that is thought to reside at the phagophore rim. We propose that Rop1 facilitates the formation and growth of the double-membrane structure of the autophagosome.
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Affiliation(s)
- Ning Wang
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Yoko Shibata
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.
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2
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Huang X, Yao J, Liu L, Luo Y, Yang A. Atg8-PE protein-based in vitro biochemical approaches to autophagy studies. Autophagy 2022; 18:2020-2035. [PMID: 35072587 PMCID: PMC9397461 DOI: 10.1080/15548627.2022.2025572] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Macroautophagy/autophagy is an evolutionarily conserved intracellular degradation pathway that maintains cellular homeostasis. Over the past two decades, a series of scientific breakthroughs have helped explain autophagy-related molecular mechanisms and physiological functions. This tremendous progress continues to depend largely on powerful research methods, specifically, various autophagy marker Atg8-PE protein-based methods for studying membrane dynamics and monitoring autophagic activity. Recently, several biochemical approaches have been successfully developed to produce the lipidated protein Atg8-PE or its mimics in vitro, including enzyme-mediated reconstitution systems, chemically defined reconstitution systems, cell-free lipidation systems and protein chemical synthesis. These approaches have contributed important insights into the mechanisms underlying Atg8-mediated membrane dynamics and protein-protein interactions, creating a new perspective in autophagy studies. In this review, we comprehensively summarize Atg8-PE protein-based in vitro biochemical approaches and recent advances to facilitate a better understanding of autophagy mechanisms. In addition, we highlight the advantages and disadvantages of various Atg8-PE protein-based approaches to provide general guidance for their use in studying autophagy.Abbreviations: ATG: autophagy related; ATP: adenosine triphosphate; COPII: coat protein complex II; DGS-NTA: 1,2-dioleoyl-sn-glycero-3-[(N-(5-amino-1-carboxypentyl)iminodiacetic acid)succinyl] (nickel salt); DPPE: 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine; DSPE: 1,2-distearoyl-sn-glycero-3-phosphoethanolamine; E. coli: Escherichia coli; EPL: expressed protein ligation; ERGIC: ER-Golgi intermediate compartment; GABARAP: GABA type A receptor-associated protein; GABARAPL1: GABA type A receptor associated protein like 1; GABARAPL2: GABA type A receptor associated protein like 2; GFP: green fluorescent protein; GUVs: giant unilamellar vesicles; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MBP: maltose binding protein; MEFs: mouse embryonic fibroblasts; MESNa: 2-mercaptoethanesulfonic acid sodium salt; NCL: native chemical ligation; NTA: nitrilotriacetic acid; PE: phosphatidylethanolamine; PS: phosphatidylserine; PtdIns3K: class III phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; SPPS: solid-phase peptide synthesis; TEV: tobacco etch virus; WT: wild-type.
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Affiliation(s)
- Xue Huang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Jia Yao
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Lu Liu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Yu Luo
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing, China,CONTACT Aimin Yang School of Life Sciences, Chongqing University, Chongqing, China
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3
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Miao L, Wang B, Zhang J, Yin L, Pu Y. Plasma metabolomic profiling in workers with noise-induced hearing loss: a pilot study. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:68539-68550. [PMID: 34275074 DOI: 10.1007/s11356-021-15468-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/12/2021] [Indexed: 05/09/2023]
Abstract
Noise-induced hearing loss (NIHL) remains a leading occupational related disease and is a serious public health problem. Hence, the identification of potential biomarkers for NIHL prevention and diagnosis has become an urgent work. To discover potential metabolic biomarkers of NIHL, plasma metabolomics analysis in 62 NIHL patients and 62 normal hearing controls was performed using ultrahigh-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry (UHPLC-Q-TOF MS). Orthogonal partial least square-discriminant analysis (OPLS-DA) model was applied to distinguish metabolite profile alterations in plasma samples between the two groups. The metabolites with a variable importance of projection (VIP) value > 1 and P value < 0.05 were considered to be potential metabolic biomarkers. KEGG database was performed to explore the involved pathways of potential biomarkers. Three autophagy-related genes (PI3K, AKT, and ATG5) were selected for further verification, and mRNA levels were detected using RT-qPCR analysis. Twenty plasma metabolites with VIP > 1 and P < 0.05 were significantly altered between the two groups. Totally, seven metabolic pathways involving the glycerophospholipid metabolism, glycosylphosphatidylinositol (GPI)-anchor biosynthesis, autophagy pathway, choline metabolism, the alpha-linolenic acid metabolism and linoleic acid metabolism, and retrograde endocannabinoid pathway were significantly related to NIHL. Furthermore, verification by RT-qPCR suggested that the mRNA expression levels of PI3K and AKT along with ATG5 were significantly lower in the NIHL patients compared with controls. In summary, the present study provides the first evidence that the identified aberrantly altered metabolites may be the potentially valuable biomarkers of NIHL for occupational noise-exposed workers. Autophagy signal pathway may be involved in the occurrence and development of NIHL. Moreover, this present study may be helpful to further better understand the metabolic changes in NIHL and be helpful for the understanding of pathogenic mechanism.
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Affiliation(s)
- Long Miao
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health Southeast University, Nanjing, 210009, People's Republic of China
| | - Boshen Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health Southeast University, Nanjing, 210009, People's Republic of China
| | - Juan Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health Southeast University, Nanjing, 210009, People's Republic of China
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health Southeast University, Nanjing, 210009, People's Republic of China
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health Southeast University, Nanjing, 210009, People's Republic of China.
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4
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Chen W, Shen T, Wang L, Lu K. Oligomerization of Selective Autophagy Receptors for the Targeting and Degradation of Protein Aggregates. Cells 2021; 10:cells10081989. [PMID: 34440758 PMCID: PMC8394947 DOI: 10.3390/cells10081989] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 02/05/2023] Open
Abstract
The selective targeting and disposal of solid protein aggregates are essential for cells to maintain protein homoeostasis. Autophagy receptors including p62, NBR1, Cue5/TOLLIP (CUET), and Tax1-binding protein 1 (TAX1BP1) proteins function in selective autophagy by targeting ubiquitinated aggregates through ubiquitin-binding domains. Here, we summarize previous beliefs and recent findings on selective receptors in aggregate autophagy. Since there are many reviews on selective autophagy receptors, we focus on their oligomerization, which enables receptors to function as pathway determinants and promotes phase separation.
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Affiliation(s)
- Wenjun Chen
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (W.C.); (T.S.); (L.W.)
- Department of Neurology, Shanxi Provincial People’s Hospital, Taiyuan 030012, China
| | - Tianyun Shen
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (W.C.); (T.S.); (L.W.)
| | - Lijun Wang
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (W.C.); (T.S.); (L.W.)
| | - Kefeng Lu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (W.C.); (T.S.); (L.W.)
- Correspondence:
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5
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Dong G, Zhao X, Guo J, Ma L, Zhou H, Liu Q, Zhao X, Wang C, Wu K. Functional expression and purification of recombinant full-length human ATG7 protein with HIV-1 Tat peptide in Escherichia coli. Protein Expr Purif 2021; 182:105844. [PMID: 33592251 DOI: 10.1016/j.pep.2021.105844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/18/2021] [Accepted: 02/09/2021] [Indexed: 01/07/2023]
Abstract
The human autophagy-related protein ATG7 (hATG7), an E1-like ubiquitin enzyme, activates two ubiquitin-like proteins, LC3 (Atg8) and Atg12, and promotes autophagosome formation. While hATG7 plays an essential role for the autophagy conjugation system, the production of full-length functional hATG7 in bacterial systems remains challenging. Previous studies have demonstrated that the HIV-1 virus-encoded Tat peptide ('GRKKRRQRRR') can increase the yield and solubility of heterologous proteins. Here, functional full-length hATG7 was expressed using the pET28b-Tat expression vector in the Escherichia coli BL21 (DE3) strain. Recombinant hATG7 protein aggregated as inclusion bodies while expressed with widely used prokaryotic expression plasmids. In contrast, the solubility of Tat-tagged hATG7 increased significantly with prolonged time compared to Tat-free hATG7. The recombinant proteins were purified to >90% homogeneity under native conditions with a single step of affinity chromatography purification. The results of in vitro pull-down and LC3B-I lipidation assays showed that Tat-tagged hATG7 directly interacted with LC3B-I and promoted LC3B-I lipidation, suggesting that Tat-tagged hATG7 has significant catalytic activity. Overall, this study provides a novel method for improving the functional expression of full-length hATG7 in bacterial systems by fusion with the Tat peptide, a process which may be applied in future studies of hATG7 structure and function.
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Affiliation(s)
- Guofu Dong
- Beijing Key Laboratory of Radiation Biology (No. BZ0325) and Department of Experimental Pathology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Xi Zhao
- Beijing Key Laboratory of Radiation Biology (No. BZ0325) and Department of Experimental Pathology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Junwang Guo
- Beijing Key Laboratory of Radiation Biology (No. BZ0325) and Department of Experimental Pathology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Lei Ma
- Beijing Key Laboratory of Radiation Biology (No. BZ0325) and Department of Experimental Pathology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Hongmei Zhou
- Beijing Key Laboratory of Radiation Biology (No. BZ0325) and Department of Experimental Pathology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Qi Liu
- Beijing Key Laboratory of Radiation Biology (No. BZ0325) and Department of Experimental Pathology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Xuelong Zhao
- Beijing Key Laboratory of Radiation Biology (No. BZ0325) and Department of Experimental Pathology, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Changzhen Wang
- Beijing Key Laboratory of Radiation Biology (No. BZ0325) and Department of Experimental Pathology, Beijing Institute of Radiation Medicine, Beijing, 100850, China.
| | - Ke Wu
- Beijing Key Laboratory of Radiation Biology (No. BZ0325) and Department of Experimental Pathology, Beijing Institute of Radiation Medicine, Beijing, 100850, China.
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6
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Wang S, Li Y, Ma C. Atg3 promotes Atg8 lipidation via altering lipid diffusion and rearrangement. Protein Sci 2020; 29:1511-1523. [PMID: 32277540 DOI: 10.1002/pro.3866] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/03/2020] [Accepted: 04/03/2020] [Indexed: 12/20/2022]
Abstract
Atg3-catalyzed transferring of Atg8 to phosphatidylethanolamine (PE) in the phagophore membrane is essential for autophagy. Previous studies have demonstrated that this process requires Atg3 to interact with the phagophore membrane via its N-terminal amphipathic helix. In this study, by using combined biochemical and biophysical approaches, our data showed that in addition to binding to the membranes, Atg3 attenuates lipid diffusion and enriches lipid molecules with smaller headgroup. Our data suggest that Atg3 promotes Atg8 lipidation via altering lipid diffusion and rearrangement.
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Affiliation(s)
- Shen Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yun Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian, China
| | - Cong Ma
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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7
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Abreu S, Kriegenburg F, Gómez-Sánchez R, Mari M, Sánchez-Wandelmer J, Skytte Rasmussen M, Soares Guimarães R, Zens B, Schuschnig M, Hardenberg R, Peter M, Johansen T, Kraft C, Martens S, Reggiori F. Conserved Atg8 recognition sites mediate Atg4 association with autophagosomal membranes and Atg8 deconjugation. EMBO Rep 2017; 18:765-780. [PMID: 28330855 DOI: 10.15252/embr.201643146] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 02/12/2017] [Accepted: 02/20/2017] [Indexed: 12/12/2022] Open
Abstract
Deconjugation of the Atg8/LC3 protein family members from phosphatidylethanolamine (PE) by Atg4 proteases is essential for autophagy progression, but how this event is regulated remains to be understood. Here, we show that yeast Atg4 is recruited onto autophagosomal membranes by direct binding to Atg8 via two evolutionarily conserved Atg8 recognition sites, a classical LC3-interacting region (LIR) at the C-terminus of the protein and a novel motif at the N-terminus. Although both sites are important for Atg4-Atg8 interaction in vivo, only the new N-terminal motif, close to the catalytic center, plays a key role in Atg4 recruitment to autophagosomal membranes and specific Atg8 deconjugation. We thus propose a model where Atg4 activity on autophagosomal membranes depends on the cooperative action of at least two sites within Atg4, in which one functions as a constitutive Atg8 binding module, while the other has a preference toward PE-bound Atg8.
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Affiliation(s)
- Susana Abreu
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Franziska Kriegenburg
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rubén Gómez-Sánchez
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Muriel Mari
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jana Sánchez-Wandelmer
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mads Skytte Rasmussen
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Rodrigo Soares Guimarães
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bettina Zens
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Martina Schuschnig
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Ralph Hardenberg
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Matthias Peter
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Terje Johansen
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Claudine Kraft
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Fulvio Reggiori
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands .,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
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