1
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Arines FM, Wielenga A, Henn D, Burata OE, Garcia FN, Stockbridge RB, Li M. Lysosomal membrane transporter purification and reconstitution for functional studies. Mol Biol Cell 2024; 35:ar28. [PMID: 38117592 PMCID: PMC10916862 DOI: 10.1091/mbc.e23-06-0259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/20/2023] [Accepted: 12/13/2023] [Indexed: 12/22/2023] Open
Abstract
Lysosomes achieve their function through numerous transporters that import or export nutrients across their membrane. However, technical challenges in membrane protein overexpression, purification, and reconstitution hinder our understanding of lysosome transporter function. Here, we developed a platform to overexpress and purify the putative lysine transporter Ypq1 using a constitutive overexpression system in protease- and ubiquitination-deficient yeast vacuoles. Using this method, we purified and reconstituted Ypq1 into proteoliposomes and showed lysine transport function, supporting its role as a basic amino acid transporter on the vacuole membrane. We also found that the absence of lysine destabilizes purified Ypq1 and causes it to aggregate, consistent with its propensity to be downregulated in vivo upon lysine starvation. Our approach may be useful for the biochemical characterization of many transporters and membrane proteins to understand organellar transport and regulation.
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Affiliation(s)
- Felichi Mae Arines
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Aleksander Wielenga
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Danielle Henn
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Olive E. Burata
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Francisco Narro Garcia
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Randy B. Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
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2
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Pascual-García S, Martínez-Peinado P, Pujalte-Satorre C, Navarro-Sempere A, Esteve-Girbés J, López-Jaén AB, Javaloyes-Antón J, Cobo-Velacoracho R, Navarro-Blasco FJ, Sempere-Ortells JM. Exosomal Osteoclast-Derived miRNA in Rheumatoid Arthritis: From Their Pathogenesis in Bone Erosion to New Therapeutic Approaches. Int J Mol Sci 2024; 25:1506. [PMID: 38338785 PMCID: PMC10855630 DOI: 10.3390/ijms25031506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease that causes inflammation, pain, and ultimately, bone erosion of the joints. The causes of this disease are multifactorial, including genetic factors, such as the presence of the human leukocyte antigen (HLA)-DRB1*04 variant, alterations in the microbiota, or immune factors including increased cytotoxic T lymphocytes (CTLs), neutrophils, or elevated M1 macrophages which, taken together, produce high levels of pro-inflammatory cytokines. In this review, we focused on the function exerted by osteoclasts on osteoblasts and other osteoclasts by means of the release of exosomal microRNAs (miRNAs). Based on a thorough revision, we classified these molecules into three categories according to their function: osteoclast inhibitors (miR-23a, miR-29b, and miR-214), osteoblast inhibitors (miR-22-3p, miR-26a, miR-27a, miR-29a, miR-125b, and miR-146a), and osteoblast enhancers (miR-20a, miR-34a, miR-96, miR-106a, miR-142, miR-199a, miR-324, and miR-486b). Finally, we analyzed potential therapeutic targets of these exosomal miRNAs, such as the use of antagomiRs, blockmiRs, agomiRs and competitive endogenous RNAs (ceRNAs), which are already being tested in murine and ex vivo models of RA. These strategies might have an important role in reestablishing the regulation of osteoclast and osteoblast differentiation making progress in the development of personalized medicine.
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Affiliation(s)
- Sandra Pascual-García
- Department of Biotechnology, University of Alicante, 03690 San Vicente del Raspeig, Spain
| | | | | | - Alicia Navarro-Sempere
- Department of Biotechnology, University of Alicante, 03690 San Vicente del Raspeig, Spain
| | - Jorge Esteve-Girbés
- Department of Legal Studies of the State, University of Alicante, 03690 San Vicente del Raspeig, Spain
| | - Ana B. López-Jaén
- Department of Biotechnology, University of Alicante, 03690 San Vicente del Raspeig, Spain
| | - Juan Javaloyes-Antón
- Department of Physics, Systems Engineering and Signal Theory, University of Alicante, 03690 San Vicente del Raspeig, Spain
| | - Raúl Cobo-Velacoracho
- Department of Biotechnology, University of Alicante, 03690 San Vicente del Raspeig, Spain
| | - Francisco J. Navarro-Blasco
- Department of Biotechnology, University of Alicante, 03690 San Vicente del Raspeig, Spain
- Rheumatology Unit, University General Hospital of Elche, 03203 Elche, Spain
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3
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Sakai Y, Oku M. ATG and ESCRT control multiple modes of microautophagy. FEBS Lett 2024; 598:48-58. [PMID: 37857501 DOI: 10.1002/1873-3468.14760] [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: 07/20/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 10/21/2023]
Abstract
The discovery of microautophagy, the direct engulfment of cytoplasmic material by the lysosome, dates back to 1966 in a morphological study of mammalian cells by Christian de Duve. Since then, studies on microautophagy have shifted toward the elucidation of the physiological significance of the process. However, in contrast to macroautophagy, studies on the molecular mechanisms of microautophagy have been limited. Only recent studies revealed that ATG proteins involved in macroautophagy are also operative in several types of microautophagy and that ESCRT proteins, responsible for the multivesicular body pathway, play a central role in most microautophagy processes. In this review, we summarize our current knowledge on the function of ATG and ESCRT proteins in microautophagy.
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Affiliation(s)
- Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Japan
| | - Masahide Oku
- Department of Bioscience and Biotechnology, Faculty of Bioenvironmental Sciences, Kyoto University of Advanced Science, Kameoka, Japan
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4
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Shi Y, Simpson S, Chen Y, Aull H, Benjamin J, Serra-Moreno R. Mutations accumulated in the Spike of SARS-CoV-2 Omicron allow for more efficient counteraction of the restriction factor BST2/Tetherin. PLoS Pathog 2024; 20:e1011912. [PMID: 38190411 PMCID: PMC10798645 DOI: 10.1371/journal.ppat.1011912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/19/2024] [Accepted: 12/19/2023] [Indexed: 01/10/2024] Open
Abstract
BST2/Tetherin is a restriction factor with broad antiviral activity against enveloped viruses, including coronaviruses. Specifically, BST2 traps nascent particles to membrane compartments, preventing their release and spread. In turn, viruses have evolved multiple mechanisms to counteract BST2. Here, we examined the interactions between BST2 and SARS-CoV-2. Our study shows that BST2 reduces SARS-CoV-2 virion release. However, the virus uses the Spike (S) protein to downregulate BST2. This requires a physical interaction between S and BST2, which routes BST2 for lysosomal degradation in a Clathtin- and ubiquitination-dependent manner. By surveying different SARS-CoV-2 variants of concern (Alpha-Omicron), we found that Omicron is more efficient at counteracting BST2, and that mutations in S account for its enhanced anti-BST2 activity. Mapping analyses revealed that several surfaces in the extracellular region of BST2 are required for an interaction with the Spike, and that the Omicron variant has changed its patterns of association with BST2 to improve its counteraction. Therefore, our study suggests that, besides enhancing receptor binding and evasion of neutralizing antibodies, mutations accumulated in the Spike afford more efficient counteraction of BST2, which highlights that BST2 antagonism is important for SARS-CoV-2 infectivity and spread.
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Affiliation(s)
- Yuhang Shi
- Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Sydney Simpson
- Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Yuexuan Chen
- Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Haley Aull
- Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Jared Benjamin
- Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Ruth Serra-Moreno
- Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
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5
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Fang S, Chen G, Wang Y, Ganti R, Chernova TA, Zhou L, Jacobs SE, Duong D, Kiyokawa H, Chernoff YO, Li M, Shcherbik N, Zhao B, Yin J. Profiling and verifying the substrates of E3 ubiquitin ligase Rsp5 in yeast cells. STAR Protoc 2023; 4:102489. [PMID: 37561636 PMCID: PMC10440593 DOI: 10.1016/j.xpro.2023.102489] [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: 02/07/2023] [Revised: 04/07/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023] Open
Abstract
Yeast is an essential model organism for studying protein ubiquitination pathways; however, identifying the direct substrates of E3 in the cell presents a challenge. Here, we present a protocol for using the orthogonal ubiquitin transfer (OUT) cascade to profile the substrate specificity of yeast E3 Rsp5. We describe steps for OUT profiling, proteomics analysis, in vitro and in cell ubiquitination, and stability assay. The protocol can be adapted for identifying and verifying the ubiquitination targets of other E3s in yeast. For complete details on the use and execution of this protocol, please refer to Wang et al.1.
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Affiliation(s)
- Shuai Fang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China; Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Geng Chen
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA; Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Yiyang Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA; Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Rakhee Ganti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Li Zhou
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Savannah E Jacobs
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Duc Duong
- Integrated Proteomics Core, Emory University, Atlanta, GA 30322, USA
| | - Hiroaki Kiyokawa
- Department of Pharmacology, Northwestern University, Chicago, IL 60611, USA
| | - Yury O Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ming Li
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48019, USA
| | - Natalia Shcherbik
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA.
| | - Bo Zhao
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.
| | - Jun Yin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
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6
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Yang H, Tan JX. Lysosomal quality control: molecular mechanisms and therapeutic implications. Trends Cell Biol 2023; 33:749-764. [PMID: 36717330 PMCID: PMC10374877 DOI: 10.1016/j.tcb.2023.01.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/29/2023]
Abstract
Lysosomes are essential catabolic organelles with an acidic lumen and dozens of hydrolytic enzymes. The detrimental consequences of lysosomal leakage have been well known since lysosomes were discovered during the 1950s. However, detailed knowledge of lysosomal quality control mechanisms has only emerged relatively recently. It is now clear that lysosomal leakage triggers multiple lysosomal quality control pathways that replace, remove, or directly repair damaged lysosomes. Here, we review how lysosomal damage is sensed and resolved in mammalian cells, with a focus on the molecular mechanisms underlying different lysosomal quality control pathways. We also discuss the clinical implications and therapeutic potential of these pathways.
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Affiliation(s)
- Haoxiang Yang
- Aging Institute, University of Pittsburgh School of Medicine/University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Jay Xiaojun Tan
- Aging Institute, University of Pittsburgh School of Medicine/University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA; Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
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7
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Wu H, Qian X, Liang G. The Role of Small Extracellular Vesicles Derived from Mesenchymal Stromal Cells on Myocardial Protection: a Review of Current Advances and Future Perspectives. Cardiovasc Drugs Ther 2023:10.1007/s10557-023-07472-x. [PMID: 37227567 DOI: 10.1007/s10557-023-07472-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/18/2023] [Indexed: 05/26/2023]
Abstract
Small extracellular vesicles (SEVs) secreted by mesenchymal stromal cells (MSCs) are considered one of the most promising biological therapies in recent years. The protective effect of MSCs-derived SEVs on myocardium is mainly related to their ability to deliver cargo, anti-inflammatory properties, promotion of angiogenesis, immunoregulation, and other factors. Herein, this review focuses on the biological properties, isolation methods, and functions of SEVs. Then, the roles and potential mechanisms of SEVs and engineered SEVs in myocardial protection are summarized. Finally, the current situation of clinical research on SEVs, the difficulties encountered, and the future fore-ground of SEVs are discussed. In conclusion, although there are some technical difficulties and conceptual contradictions in the research of SEVs, the unique biological functions of SEVs provide a new direction for the development of regenerative medicine. Further exploration is warranted to establish a solid experimental and theoretical basis for future clinical application of SEVs.
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Affiliation(s)
- Hongkun Wu
- School of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
- Center for Translational Medicine, Guizhou Medical University, Guiyang, Guizhou, China
- Department of Cardiac Surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Xingkai Qian
- Center for Translational Medicine, Guizhou Medical University, Guiyang, Guizhou, China
- Department of Cardiac Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Guiyou Liang
- Department of Cardiac Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China.
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8
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Arines FM, Wielenga A, Burata OE, Garcia FN, Stockbridge RB, Li M. Lysosome transporter purification and reconstitution identifies Ypq1 pH-gated lysine transport and regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.31.535002. [PMID: 37034749 PMCID: PMC10081341 DOI: 10.1101/2023.03.31.535002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Lysosomes achieve their function through numerous transporters that import or export nutrients across their membrane. However, technical challenges in membrane protein overexpression, purification, and reconstitution hinder our understanding of lysosome transporter function. Here, we developed a platform to overexpress and purify the putative lysine transporter Ypq1 using a constitutive overexpression system in protease- and ubiquitination-deficient yeast vacuoles. Using this method, we purified and reconstituted Ypq1 into proteoliposomes and showed lysine transport function, supporting its role as a basic amino acid transporter on the vacuole membrane. We also found that the absence of lysine destabilizes purified Ypq1 and causes it to aggregate, consistent with its propensity to be downregulated in vivo upon lysine starvation. Our approach may be useful for the biochemical characterization of many transporters and membrane proteins to understand organellar transport and regulation.
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Affiliation(s)
- Felichi Mae Arines
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Aleksander Wielenga
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Olive E. Burata
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francisco Narro Garcia
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Randy B. Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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9
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Shi G, Chiramel AI, Li T, Lai KK, Kenney AD, Zani A, Eddy AC, Majdoul S, Zhang L, Dempsey T, Beare PA, Kar S, Yewdell JW, Best SM, Yount JS, Compton AA. Rapalogs downmodulate intrinsic immunity and promote cell entry of SARS-CoV-2. J Clin Invest 2022; 132:e160766. [PMID: 36264642 PMCID: PMC9753997 DOI: 10.1172/jci160766] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/18/2022] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in immunocompromised individuals is associated with prolonged virus shedding and evolution of viral variants. Rapamycin and its analogs (rapalogs, including everolimus, temsirolimus, and ridaforolimus) are FDA approved as mTOR inhibitors for the treatment of human diseases, including cancer and autoimmunity. Rapalog use is commonly associated with an increased susceptibility to infection, which has been traditionally explained by impaired adaptive immunity. Here, we show that exposure to rapalogs increased susceptibility to SARS-CoV-2 infection in tissue culture and in immunologically naive rodents by antagonizing the cell-intrinsic immune response. We identified 1 rapalog (ridaforolimus) that was less potent in this regard and demonstrated that rapalogs promote spike-mediated entry into cells, by triggering the degradation of the antiviral proteins IFITM2 and IFITM3 via an endolysosomal remodeling program called microautophagy. Rapalogs that increased virus entry inhibited mTOR-mediated phosphorylation of the transcription factor TFEB, which facilitated its nuclear translocation and triggered microautophagy. In rodent models of infection, injection of rapamycin prior to and after virus exposure resulted in elevated SARS-CoV-2 replication and exacerbated viral disease, while ridaforolimus had milder effects. Overall, our findings indicate that preexisting use of certain rapalogs may elevate host susceptibility to SARS-CoV-2 infection and disease by activating lysosome-mediated suppression of intrinsic immunity.
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Affiliation(s)
- Guoli Shi
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute (NCI), NIH, Frederick, Maryland, USA
| | - Abhilash I. Chiramel
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Hamilton, Montana, USA
| | - Tiansheng Li
- Laboratory of Viral Diseases, NIAID, NIH, Bethesda, Maryland, USA
| | - Kin Kui Lai
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute (NCI), NIH, Frederick, Maryland, USA
| | - Adam D. Kenney
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Ashley Zani
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Adrian C. Eddy
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Saliha Majdoul
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute (NCI), NIH, Frederick, Maryland, USA
| | - Lizhi Zhang
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Tirhas Dempsey
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute (NCI), NIH, Frederick, Maryland, USA
| | - Paul A. Beare
- Laboratory of Bacteriology, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, USA
| | | | | | - Sonja M. Best
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Hamilton, Montana, USA
| | - Jacob S. Yount
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Alex A. Compton
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute (NCI), NIH, Frederick, Maryland, USA
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10
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Golden CK, Kazmirchuk TDD, McNally EK, El eissawi M, Gokbayrak ZD, Richard JD, Brett CL. A two-tiered system for selective receptor and transporter protein degradation. PLoS Genet 2022; 18:e1010446. [PMID: 36215320 PMCID: PMC9584418 DOI: 10.1371/journal.pgen.1010446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 10/20/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022] Open
Abstract
Diverse physiology relies on receptor and transporter protein down–regulation and degradation mediated by ESCRTs. Loss–of–function mutations in human ESCRT genes linked to cancers and neurological disorders are thought to block this process. However, when homologous mutations are introduced into model organisms, cells thrive and degradation persists, suggesting other mechanisms compensate. To better understand this secondary process, we studied degradation of transporter (Mup1) or receptor (Ste3) proteins when ESCRT genes (VPS27, VPS36) are deleted in Saccharomyces cerevisiae using live-cell imaging and organelle biochemistry. We find that endocytosis remains intact, but internalized proteins aberrantly accumulate on vacuolar lysosome membranes within cells. Here they are sorted for degradation by the intralumenal fragment (ILF) pathway, constitutively or when triggered by substrates, misfolding or TOR activation in vivo and in vitro. Thus, the ILF pathway functions as fail–safe layer of defense when ESCRTs disregard their clients, representing a two–tiered system that ensures degradation of surface polytopic proteins. Receptor, transporter and channel proteins on the plasma membranes (or surface) of all cells mediate extensive physiology. This requires precise control of their numbers, and damaged copies must be removed to prevent cytotoxicity. Their downregulation and degradation is mediated by lysosomes after endocytosis and entry into the multi–vesicular body (MVB) pathway which depends on ESCRTs (Endosomal Sorting Complexes Required for Transport). Loss–of–function mutations in ESCRT genes are linked to cancers and neurological disease, but cells survive and some proteins continue to be degraded. Herein, we use baker’s yeast (Saccharomyces cerevisiae) as model to better understand how surface proteins are degraded in cells missing ESCRT genes. Using fluorescence microscopy matched with biochemical and genetic approaches, we find that the methionine transporter Mup1 and G-protein coupled receptor Ste3 continue to be degraded when two ESCRT genes are deleted. They are endocytosed but rerouted to membranes of vacuolar lysosomes after stimuli are applied to trigger their downregulation. Here they are sorted into intralumenal fragments and degraded by acid hydrolases within vacuolar lysosomes upon homotypic membrane fusion. We propose that this intralumenal fragment (ILF) pathway functions as a secondary mechanism to degrade surface proteins with the canonical MVB pathway is disrupted.
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Affiliation(s)
| | | | - Erin Kate McNally
- Department of Biology, Concordia University, Montreal, Quebec, Canada
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11
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Zhang W, Yang X, Li Y, Yu L, Zhang B, Zhang J, Cho WJ, Venkatarangan V, Chen L, Burugula BB, Bui S, Wang Y, Duan C, Kitzman JO, Li M. GCAF(TMEM251) regulates lysosome biogenesis by activating the mannose-6-phosphate pathway. Nat Commun 2022; 13:5351. [PMID: 36096887 PMCID: PMC9468337 DOI: 10.1038/s41467-022-33025-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/29/2022] [Indexed: 11/09/2022] Open
Abstract
The mannose-6-phosphate (M6P) biosynthetic pathway for lysosome biogenesis has been studied for decades and is considered a well-understood topic. However, whether this pathway is regulated remains an open question. In a genome-wide CRISPR/Cas9 knockout screen, we discover TMEM251 as the first regulator of the M6P modification. Deleting TMEM251 causes mistargeting of most lysosomal enzymes due to their loss of M6P modification and accumulation of numerous undigested materials. We further demonstrate that TMEM251 localizes to the Golgi and is required for the cleavage and activity of GNPT, the enzyme that catalyzes M6P modification. In zebrafish, TMEM251 deletion leads to severe developmental defects including heart edema and skeletal dysplasia, which phenocopies Mucolipidosis Type II. Our discovery provides a mechanism for the newly discovered human disease caused by TMEM251 mutations. We name TMEM251 as GNPTAB cleavage and activity factor (GCAF) and its related disease as Mucolipidosis Type V.
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Affiliation(s)
- Weichao Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xi Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yingxiang Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Linchen Yu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Bokai Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jianchao Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Woo Jung Cho
- BRCF Microscopy Core, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Varsha Venkatarangan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Liang Chen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Bala Bharathi Burugula
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sarah Bui
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yanzhuang Wang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Cunming Duan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
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12
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Shi G, Chiramel AI, Li T, Lai KK, Kenney AD, Zani A, Eddy A, Majdoul S, Zhang L, Dempsey T, Beare PA, Kar S, Yewdell JW, Best SM, Yount JS, Compton AA. Rapalogs downmodulate intrinsic immunity and promote cell entry of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.04.15.440067. [PMID: 33880473 PMCID: PMC8057238 DOI: 10.1101/2021.04.15.440067] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 infection in immunocompromised individuals is associated with prolonged virus shedding and evolution of viral variants. Rapamycin and its analogs (rapalogs, including everolimus, temsirolimus, and ridaforolimus) are FDA-approved as mTOR inhibitors for the treatment of human diseases, including cancer and autoimmunity. Rapalog use is commonly associated with increased susceptibility to infection, which has been traditionally explained by impaired adaptive immunity. Here, we show that exposure to rapalogs increases susceptibility to SARS-CoV-2 infection in tissue culture and in immunologically naive rodents by antagonizing the cell-intrinsic immune response. By identifying one rapalog (ridaforolimus) that is less potent in this regard, we demonstrate that rapalogs promote Spike-mediated entry into cells by triggering the degradation of antiviral proteins IFITM2 and IFITM3 via an endolysosomal remodeling program called microautophagy. Rapalogs that increase virus entry inhibit the mTOR-mediated phosphorylation of the transcription factor TFEB, which facilitates its nuclear translocation and triggers microautophagy. In rodent models of infection, injection of rapamycin prior to and after virus exposure resulted in elevated SARS-CoV-2 replication and exacerbated viral disease, while ridaforolimus had milder effects. Overall, our findings indicate that preexisting use of certain rapalogs may elevate host susceptibility to SARS-CoV-2 infection and disease by activating lysosome-mediated suppression of intrinsic immunity.
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Affiliation(s)
- Guoli Shi
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Abhilash I. Chiramel
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - Tiansheng Li
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Kin Kui Lai
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Adam D. Kenney
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Ashley Zani
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Adrian Eddy
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Saliha Majdoul
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Lizhi Zhang
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Tirhas Dempsey
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Paul A. Beare
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | | | - Jonathan W. Yewdell
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Sonja M. Best
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA
| | - Jacob S. Yount
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Alex A. Compton
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
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13
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Arines FM, Li M. An optimized protocol to analyze membrane protein degradation in yeast using quantitative western blot and flow cytometry. STAR Protoc 2022; 3:101274. [PMID: 35403002 PMCID: PMC8987394 DOI: 10.1016/j.xpro.2022.101274] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2022] Open
Abstract
Membrane proteins (MPs) are essential in many cellular functions. To maintain proteostasis, MPs are downregulated via ubiquitination and degradation. Here, we describe an optimized protocol to analyze MP degradation using quantitative western blot and flow cytometry-based approaches. We use the degradation of Ypq1, a vacuole membrane lysine transporter, to demonstrate the protocol, which can be adapted for other organelle MPs and thus provide useful tools to study MP regulation in yeast and other model organisms. For complete details on the use and execution of this protocol, please refer to Arines et al. (2021) and Yang et al. (2020). Two complementary protocols for quantifying membrane protein degradation in yeast Measures the decrease of full-length protein by quantitative western blot Quantifies the quenching of GFP fluorescence by flow cytometry Adaptable to other fluorescent protein tags and mammalian cells
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14
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The role of K63-linked polyubiquitin in several types of autophagy. Biol Futur 2022; 73:137-148. [DOI: 10.1007/s42977-022-00117-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 04/05/2022] [Indexed: 01/08/2023]
Abstract
AbstractLysosomal-dependent self-degradative (autophagic) mechanisms are essential for the maintenance of normal homeostasis in all eukaryotic cells. Several types of such self-degradative and recycling pathways have been identified, based on how the cellular self material can incorporate into the lysosomal lumen. Ubiquitination, a well-known and frequently occurred posttranslational modification has essential role in all cell biological processes, thus in autophagy too. The second most common type of polyubiquitin chain is the K63-linked polyubiquitin, which strongly connects to some self-degradative mechanisms in the cells. In this review, we discuss the role of this type of polyubiquitin pattern in numerous autophagic processes.
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15
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α-Arrestins and Their Functions: From Yeast to Human Health. Int J Mol Sci 2022; 23:ijms23094988. [PMID: 35563378 PMCID: PMC9105457 DOI: 10.3390/ijms23094988] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/10/2022] Open
Abstract
α-Arrestins, also called arrestin-related trafficking adaptors (ARTs), constitute a large family of proteins conserved from yeast to humans. Despite their evolutionary precedence over their extensively studied relatives of the β-arrestin family, α-arrestins have been discovered relatively recently, and thus their properties are mostly unexplored. The predominant function of α-arrestins is the selective identification of membrane proteins for ubiquitination and degradation, which is an important element in maintaining membrane protein homeostasis as well as global cellular metabolisms. Among members of the arrestin clan, only α-arrestins possess PY motifs that allow canonical binding to WW domains of Rsp5/NEDD4 ubiquitin ligases and the subsequent ubiquitination of membrane proteins leading to their vacuolar/lysosomal degradation. The molecular mechanisms of the selective substrate’s targeting, function, and regulation of α-arrestins in response to different stimuli remain incompletely understood. Several functions of α-arrestins in animal models have been recently characterized, including redox homeostasis regulation, innate immune response regulation, and tumor suppression. However, the molecular mechanisms of α-arrestin regulation and substrate interactions are mainly based on observations from the yeast Saccharomyces cerevisiae model. Nonetheless, α-arrestins have been implicated in health disorders such as diabetes, cardiovascular diseases, neurodegenerative disorders, and tumor progression, placing them in the group of potential therapeutic targets.
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16
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Banjade S, Zhu L, Jorgensen JR, Suzuki SW, Emr SD. Recruitment and organization of ESCRT-0 and ubiquitinated cargo via condensation. SCIENCE ADVANCES 2022; 8:eabm5149. [PMID: 35363519 PMCID: PMC10938570 DOI: 10.1126/sciadv.abm5149] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
The general mechanisms by which ESCRTs (Endosomal Sorting Complexes Required for Transport) are specifically recruited to various membranes, and how ESCRT subunits are spatially organized remain central questions in cell biology. At the endosome and lysosomes, ubiquitination of membrane proteins triggers ESCRT-mediated substrate recognition and degradation. Using the yeast lysosome/vacuole, we define the principles by which substrate engagement by ESCRTs occurs at this organelle. We find that multivalent interactions between ESCRT-0 and polyubiquitin are critical for substrate recognition at yeast vacuoles, with a lower-valency requirement for cargo engagement at endosomes. Direct recruitment of ESCRT-0 induces dynamic foci on the vacuole membrane and forms fluid condensates in vitro with polyubiquitin. We propose that self-assembly of early ESCRTs induces condensation, an initial step in ESCRT assembly/nucleation at membranes. This property can be tuned specifically at various organelles by modulating the number of binding interactions.
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Affiliation(s)
- Sudeep Banjade
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Lu Zhu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Jeffrey R. Jorgensen
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Sho W. Suzuki
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Scott D. Emr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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17
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Zoncu R, Perera RM. Built to last: lysosome remodeling and repair in health and disease. Trends Cell Biol 2022; 32:597-610. [DOI: 10.1016/j.tcb.2021.12.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 12/21/2022]
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18
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Zhu L, Zhang Q, Cordeiro CD, Banjade S, Sardana R, Mao Y, Emr SD. Adaptor linked K63 di-ubiquitin activates Nedd4/Rsp5 E3 ligase. eLife 2022; 11:77424. [PMID: 35770973 PMCID: PMC9282857 DOI: 10.7554/elife.77424] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Nedd4/Rsp5 family E3 ligases mediate numerous cellular processes, many of which require the E3 ligase to interact with PY motif containing adaptor proteins. Several arrestin-related trafficking adaptors (ARTs) of Rsp5 were self-ubiquitinated for activation, but the regulation mechanism remains elusive. Remarkably, we demonstrate that Art1, Art4, and Art5 undergo K63-linked di-ubiquitination by Rsp5. This modification enhances the plasma membrane recruitment of Rsp5 by Art1 or Art5 upon substrate induction, required for cargo protein ubiquitination. In agreement with these observations, we find that di-ubiquitin strengthens the interaction between the pombe orthologs of Rsp5 and Art1, Pub1, and Any1. Furthermore, we discover that the homologous to E6AP C-terminus (HECT) domain exosite protects the K63-linked di-ubiquitin on the adaptors from cleavage by the deubiquitination enzyme Ubp2. Together, our study uncovers a novel ubiquitination modification implemented by Rsp5 adaptor proteins, underscoring the regulatory mechanism of how adaptor proteins control the recruitment, and activity of Rsp5 for the turnover of membrane proteins.
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Affiliation(s)
- Lu Zhu
- Weill Institute of Cell and Molecular Biology, Cornell UniversityIthacaUnited States,Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Qing Zhang
- Weill Institute of Cell and Molecular Biology, Cornell UniversityIthacaUnited States,Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Ciro D Cordeiro
- Weill Institute of Cell and Molecular Biology, Cornell UniversityIthacaUnited States,Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Sudeep Banjade
- Weill Institute of Cell and Molecular Biology, Cornell UniversityIthacaUnited States,Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Richa Sardana
- Weill Institute of Cell and Molecular Biology, Cornell UniversityIthacaUnited States,Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Yuxin Mao
- Weill Institute of Cell and Molecular Biology, Cornell UniversityIthacaUnited States,Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Scott D Emr
- Weill Institute of Cell and Molecular Biology, Cornell UniversityIthacaUnited States,Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
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19
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den Brave F, Gupta A, Becker T. Protein Quality Control at the Mitochondrial Surface. Front Cell Dev Biol 2021; 9:795685. [PMID: 34926473 PMCID: PMC8678412 DOI: 10.3389/fcell.2021.795685] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022] Open
Abstract
Mitochondria contain two membranes, the outer and inner membrane. The outer membrane fulfills crucial functions for the communication of mitochondria with the cellular environment like exchange of lipids via organelle contact sites, the transport of metabolites and the formation of a signaling platform in apoptosis and innate immunity. The translocase of the outer membrane (TOM complex) forms the entry gate for the vast majority of precursor proteins that are produced on cytosolic ribosomes. Surveillance of the functionality of outer membrane proteins is critical for mitochondrial functions and biogenesis. Quality control mechanisms remove defective and mistargeted proteins from the outer membrane as well as precursor proteins that clog the TOM complex. Selective degradation of single proteins is also an important mode to regulate mitochondrial dynamics and initiation of mitophagy pathways. Whereas inner mitochondrial compartments are equipped with specific proteases, the ubiquitin-proteasome system is a central player in protein surveillance on the mitochondrial surface. In this review, we summarize our current knowledge about the molecular mechanisms that govern quality control of proteins at the outer mitochondrial membrane.
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Affiliation(s)
- Fabian den Brave
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Arushi Gupta
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
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20
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Tasnin MN, Ito K, Katsuta H, Takuma T, Sharmin T, Ushimaru T. The PI3 Kinase Complex II-PI3P-Vps27 Axis on Vacuolar Membranes is Critical for Microautophagy Induction and Nutrient Stress Adaptation. J Mol Biol 2021; 434:167360. [PMID: 34798133 DOI: 10.1016/j.jmb.2021.167360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 12/27/2022]
Abstract
Phosphatidylinositol 3-phosphate (PI3P), a scaffold of membrane-associated proteins required for diverse cellular events, is produced by Vps34-containing phosphatidylinositol 3-kinase (PI3K). PI3K complex I (PI3KCI)-generated PI3P is required for macroautophagy, whereas PI3K complex II (PI3KCII)-generated PI3P is required for endosomal sorting complex required for transport (ESCRT)-mediated multi-vesicular body (MVB) formation in late endosomes. ESCRT also promotes vacuolar membrane remodeling in microautophagy after nutrient starvation and inactivation of target of rapamycin complex 1 (TORC1) protein kinase in budding yeast. Whereas PI3KCI and macroautophagy are critical for the nutrient starvation response, the physiological roles of PI3KCII and microautophagy during starvation are largely unknown. Here, we showed that PI3KCII-produced PI3P on vacuolar membranes is required for microautophagy induction and survival in nutrient-stressed conditions. PI3KCII is required for Vps27 (an ESCRT-0 component) recruitment and ESCRT-0 complex formation on vacuolar surfaces after TORC1 inactivation. Forced recruitment of Vps27 onto vacuolar membranes rescued the defect in microautophagy induction in PI3KCII-deficient cells, indicating that a critical role of PI3P on microautophagy induction is Vps27 recruitment onto vacuolar surfaces. Finally, vacuolar membrane-associated Vps27 was able to recover survival during nutrient starvation in cells lacking PI3KCII or Vps27. This study revealed that the PI3KCII-PI3P-Vps27 axis on vacuolar membranes is critical for ESCRT-mediated microautophagy induction and nutrient stress adaptation.
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Affiliation(s)
- Most Naoshia Tasnin
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Kisara Ito
- Department of Bioscience, Faculty of Science, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Haruko Katsuta
- Course of Biological Science, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Tsuneyuki Takuma
- Course of Biological Science, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Tasnuva Sharmin
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Takashi Ushimaru
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan; Department of Bioscience, Faculty of Science, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan; Course of Biological Science, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan.
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21
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Vtc5 Is Localized to the Vacuole Membrane by the Conserved AP-3 Complex to Regulate Polyphosphate Synthesis in Budding Yeast. mBio 2021; 12:e0099421. [PMID: 34544285 PMCID: PMC8510523 DOI: 10.1128/mbio.00994-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Polyphosphates (polyP) are energy-rich polymers of inorganic phosphates assembled into chains ranging from 3 residues to thousands of residues in length. They are thought to exist in all cells on earth and play roles in an eclectic mix of functions ranging from phosphate homeostasis to cell signaling, infection control, and blood clotting. In the budding yeast Saccharomyces cerevisiae, polyP chains are synthesized by the vacuole-bound vacuolar transporter chaperone (VTC) complex, which synthesizes polyP while simultaneously translocating it into the vacuole lumen, where it is stored at high concentrations. VTC’s activity is promoted by an accessory subunit called Vtc5. In this work, we found that the conserved AP-3 complex is required for proper Vtc5 localization to the vacuole membrane. In human cells, previous work has demonstrated that mutation of AP-3 subunits gives rise to Hermansky-Pudlak syndrome, a rare disease with molecular phenotypes that include decreased polyP accumulation in platelet dense granules. In yeast AP-3 mutants, we found that Vtc5 is rerouted to the vacuole lumen by the endosomal sorting complex required for transport (ESCRT), where it is degraded by the vacuolar protease Pep4. Cells lacking functional AP-3 have decreased levels of polyP, demonstrating that membrane localization of Vtc5 is required for its VTC stimulatory activity in vivo. Our work provides insight into the molecular trafficking of a critical regulator of polyP metabolism in yeast. We speculate that AP-3 may also be responsible for the delivery of polyP regulatory proteins to platelet dense granules in higher eukaryotes.
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22
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Kozu F, Shirahama-Noda K, Araki Y, Kira S, Niwa H, Noda T. Isoflurane induces Art2-Rsp5-dependent endocytosis of Bap2 in yeast. FEBS Open Bio 2021; 11:3090-3100. [PMID: 34536986 PMCID: PMC8564346 DOI: 10.1002/2211-5463.13302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/02/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
Although general anesthesia is indispensable during modern surgical procedures, the mechanism by which inhalation anesthetics act on the synaptic membrane at the molecular and cellular level is largely unknown. In this study, we used yeast cells to examine the effect of isoflurane, an inhalation anesthetic, on membrane proteins. Bap2, an amino acid transporter localized on the plasma membrane, was endocytosed when yeast cells were treated with isoflurane. Depletion of RSP5, an E3 ligase, prevented this endocytosis and Bap2 was ubiquitinated in response to isoflurane, indicating an ubiquitin‐dependent process. Screening all the Rsp5 binding adaptors showed that Art2 plays a central role in this process. These results suggest that isoflurane affects Bap2 via an Art2‐Rsp5‐dependent ubiquitination system.
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Affiliation(s)
- Fumi Kozu
- Center of Frontier Oral Science, Graduate School of Dentistry, Osaka University, Suita, Japan.,Department of dental anesthesiology, Graduate School of Dentistry, Osaka University, Suita, Japan
| | - Kanae Shirahama-Noda
- Center of Frontier Oral Science, Graduate School of Dentistry, Osaka University, Suita, Japan
| | - Yasuhiro Araki
- Center of Frontier Oral Science, Graduate School of Dentistry, Osaka University, Suita, Japan
| | - Shintaro Kira
- Center of Frontier Oral Science, Graduate School of Dentistry, Osaka University, Suita, Japan
| | - Hitoshi Niwa
- Department of dental anesthesiology, Graduate School of Dentistry, Osaka University, Suita, Japan
| | - Takeshi Noda
- Center of Frontier Oral Science, Graduate School of Dentistry, Osaka University, Suita, Japan
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23
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Wang Y, Fang S, Chen G, Ganti R, Chernova TA, Zhou L, Duong D, Kiyokawa H, Li M, Zhao B, Shcherbik N, Chernoff YO, Yin J. Regulation of the endocytosis and prion-chaperoning machineries by yeast E3 ubiquitin ligase Rsp5 as revealed by orthogonal ubiquitin transfer. Cell Chem Biol 2021; 28:1283-1297.e8. [PMID: 33667410 PMCID: PMC8380759 DOI: 10.1016/j.chembiol.2021.02.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/22/2020] [Accepted: 02/03/2021] [Indexed: 10/22/2022]
Abstract
Attachment of the ubiquitin (UB) peptide to proteins via the E1-E2-E3 enzymatic machinery regulates diverse biological pathways, yet identification of the substrates of E3 UB ligases remains a challenge. We overcame this challenge by constructing an "orthogonal UB transfer" (OUT) cascade with yeast E3 Rsp5 to enable the exclusive delivery of an engineered UB (xUB) to Rsp5 and its substrate proteins. The OUT screen uncovered new Rsp5 substrates in yeast, such as Pal1 and Pal2, which are partners of endocytic protein Ede1, and chaperones Hsp70-Ssb, Hsp82, and Hsp104 that counteract protein misfolding and control self-perpetuating amyloid aggregates (prions), resembling those involved in human amyloid diseases. We showed that prion formation and effect of Hsp104 on prion propagation are modulated by Rsp5. Overall, our work demonstrates the capacity of OUT to deconvolute the complex E3-substrate relationships in crucial biological processes such as endocytosis and protein assembly disorders through protein ubiquitination.
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Affiliation(s)
- Yiyang Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA; Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou 510632, Guangdong, China
| | - Shuai Fang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA; Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Geng Chen
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA; Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, Guangdong, China
| | - Rakhee Ganti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Li Zhou
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Duc Duong
- Integrated Proteomics Core, Emory University, Atlanta, GA 30322, USA
| | - Hiroaki Kiyokawa
- Department of Pharmacology, Northwestern University, Chicago, IL 60611, USA
| | - Ming Li
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48019, USA
| | - Bo Zhao
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.
| | - Natalia Shcherbik
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA.
| | - Yury O Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia.
| | - Jun Yin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
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24
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Panda B, Sharma Y, Gupta S, Mohanty S. Mesenchymal Stem Cell-Derived Exosomes as an Emerging Paradigm for Regenerative Therapy and Nano-Medicine: A Comprehensive Review. Life (Basel) 2021; 11:life11080784. [PMID: 34440528 PMCID: PMC8399916 DOI: 10.3390/life11080784] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 01/08/2023] Open
Abstract
Mesenchymal Stem Cells are potent therapeutic candidates in the field of regenerative medicine, owing to their immunomodulatory and differentiation potential. However, several complications come with their translational application like viability, duration, and degree of expansion, long-term storage, and high maintenance cost. Therefore, drawbacks of cell-based therapy can be overcome by a novel therapeutic modality emerging in translational research and application, i.e., exosomes. These small vesicles derived from mesenchymal stem cells are emerging as new avenues in the field of nano-medicine. These nano-vesicles have caught the attention of researchers with their potency as regenerative medicine both in nanotherapeutics and drug delivery systems. In this review, we discuss the current knowledge in the biology and handling of exosomes, with their limitations and future applications. Additionally, we highlight current perspectives that primarily focus on their effect on various diseases and their potential as a drug delivery vehicle.
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25
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Abstract
Lysosomes (vacuoles in yeast) are master regulators of metabolism and protein turnover, but how they degrade their own resident proteins is unclear. Recently, multiple models have been proposed explaining yeast vacuole protein sorting, but the role of the ESCRT pathway was unclear. In this JCB issue, work from Yang et al. (https://doi.org/10.1083/jcb.202012104) highlights how the ESCRT pathway localizes to the vacuole surface to execute protein sorting of its resident proteins.
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Affiliation(s)
- W Mike Henne
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
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26
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Zhang W, Yang X, Chen L, Liu YY, Venkatarangan V, Reist L, Hanson P, Xu H, Wang Y, Li M. A conserved ubiquitin- and ESCRT-dependent pathway internalizes human lysosomal membrane proteins for degradation. PLoS Biol 2021; 19:e3001361. [PMID: 34297722 PMCID: PMC8337054 DOI: 10.1371/journal.pbio.3001361] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/04/2021] [Accepted: 07/09/2021] [Indexed: 12/15/2022] Open
Abstract
The lysosome is an essential organelle to recycle cellular materials and maintain nutrient homeostasis, but the mechanism to down-regulate its membrane proteins is poorly understood. In this study, we performed a cycloheximide (CHX) chase assay to measure the half-lives of approximately 30 human lysosomal membrane proteins (LMPs) and identified RNF152 and LAPTM4A as short-lived membrane proteins. The degradation of both proteins is ubiquitin dependent. RNF152 is a transmembrane E3 ligase that ubiquitinates itself, whereas LAPTM4A uses its carboxyl-terminal PY motifs to recruit NEDD4-1 for ubiquitination. After ubiquitination, they are internalized into the lysosome lumen by the endosomal sorting complexes required for transport (ESCRT) machinery for degradation. Strikingly, when ectopically expressed in budding yeast, human RNF152 is still degraded by the vacuole (yeast lysosome) in an ESCRT-dependent manner. Thus, our study uncovered a conserved mechanism to down-regulate lysosome membrane proteins.
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Affiliation(s)
- Weichao Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Xi Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Liang Chen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yun-Yu Liu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Varsha Venkatarangan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lucas Reist
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Phyllis Hanson
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Haoxing Xu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yanzhuang Wang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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27
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Lemus L, Matić Z, Gal L, Fadel A, Schuldiner M, Goder V. Post-ER degradation of misfolded GPI-anchored proteins is linked with microautophagy. Curr Biol 2021; 31:4025-4037.e5. [PMID: 34314677 DOI: 10.1016/j.cub.2021.06.078] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/07/2021] [Accepted: 06/25/2021] [Indexed: 01/08/2023]
Abstract
Glycosylphosphatidylinositol-anchored proteins (GPI-APs) are membrane-conjugated cell-surface proteins with diverse structural, developmental, and signaling functions and clinical relevance. Typically, after biosynthesis and attachment to the preassembled GPI anchor, GPI-APs rapidly leave the endoplasmic reticulum (ER) and rely on post-ER quality control. Terminally misfolded GPI-APs end up inside the vacuole/lysosome for degradation, but their trafficking itinerary to this organelle and the processes linked to their uptake by the vacuole/lysosome remain uncharacterized. In a yeast mutant that is lacking Pep4, a key vacuolar protease, several misfolded model GPI-APs accumulated in the vacuolar membrane. In the same mutant, macroautophagy and the multi-vesicular body (MVB) pathway were intact, hinting at a hitherto-unknown trafficking pathway for the degradation of misfolded GPI-APs. To unravel it, we used a genome-wide screen coupled to high-throughput fluorescence microscopy and followed the fate of the misfolded GPI-AP: Gas1∗. We found that components of the early secretory and endocytic pathways are involved in its targeting to the vacuole and that vacuolar transporter chaperones (VTCs), with roles in microautophagy, negatively affect the vacuolar uptake of Gas1∗. In support, we demonstrate that Gas1∗ internalizes from vacuolar membranes into membrane-bound intravacuolar vesicles prior to degradation. Our data link post-ER degradation with microautophagy.
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Affiliation(s)
- Leticia Lemus
- Department of Genetics, University of Seville, Ave Reina Mercedes, 6, 41012 Seville, Spain.
| | - Zrinka Matić
- Department of Genetics, University of Seville, Ave Reina Mercedes, 6, 41012 Seville, Spain
| | - Lihi Gal
- Department of Molecular Genetics, Meyer Bldg. Room 122, Weizmann Institute of Sciences, 76100 Rehovot, Israel
| | - Amir Fadel
- Department of Molecular Genetics, Meyer Bldg. Room 122, Weizmann Institute of Sciences, 76100 Rehovot, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Meyer Bldg. Room 122, Weizmann Institute of Sciences, 76100 Rehovot, Israel
| | - Veit Goder
- Department of Genetics, University of Seville, Ave Reina Mercedes, 6, 41012 Seville, Spain.
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28
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Rudnik S, Damme M. The lysosomal membrane-export of metabolites and beyond. FEBS J 2021; 288:4168-4182. [PMID: 33067905 DOI: 10.1111/febs.15602] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/01/2020] [Accepted: 10/15/2020] [Indexed: 01/01/2023]
Abstract
Lysosomes are degradative organelles in eukaryotic cells mediating the hydrolytic catabolism of various macromolecules to small basic building blocks. These low-molecular-weight metabolites are transported across the lysosomal membrane and reused in the cytoplasm and other organelles for biosynthetic pathways. Even though in the past 20 years our understanding of the lysosomal membrane regarding various transporters, other integral and peripheral membrane proteins, the lipid composition, but also its turnover has dramatically improved, there are still many unresolved questions concerning key aspects of the function of the lysosomal membrane. These include a possible function of lysosomes as a cellular storage compartment, yet unidentified transporters mediating the export such as various amino acids, mechanisms mediating the transport of lysosomal membrane proteins from the Golgi apparatus to lysosomes, and the turnover of lysosomal membrane proteins. Here, we review the current knowledge about the lysosomal membrane and identify some of the open questions that need to be solved in the future for a comprehensive and complete understanding of how lysosomes communicate with other organelles, cellular processes, and pathways.
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Affiliation(s)
- Sönke Rudnik
- Institut für Biochemie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Markus Damme
- Institut für Biochemie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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29
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He CW, Cui XF, Ma SJ, Xu Q, Ran YP, Chen WZ, Mu JX, Li H, Zhu J, Gong Q, Xie Z. Membrane recruitment of Atg8 by Hfl1 facilitates turnover of vacuolar membrane proteins in yeast cells approaching stationary phase. BMC Biol 2021; 19:117. [PMID: 34088313 PMCID: PMC8176713 DOI: 10.1186/s12915-021-01048-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/07/2021] [Indexed: 12/03/2022] Open
Abstract
Background The vacuole/lysosome is the final destination of autophagic pathways, but can also itself be degraded in whole or in part by selective macroautophagic or microautophagic processes. Diverse molecular mechanisms are involved in these processes, the characterization of which has lagged behind those of ATG-dependent macroautophagy and ESCRT-dependent endosomal multivesicular body pathways. Results Here we show that as yeast cells gradually exhaust available nutrients and approach stationary phase, multiple vacuolar integral membrane proteins with unrelated functions are degraded in the vacuolar lumen. This degradation depends on the ESCRT machinery, but does not strictly require ubiquitination of cargos or trafficking of cargos out of the vacuole. It is also temporally and mechanistically distinct from NPC-dependent microlipophagy. The turnover is facilitated by Atg8, an exception among autophagy proteins, and an Atg8-interacting vacuolar membrane protein, Hfl1. Lack of Atg8 or Hfl1 led to the accumulation of enlarged lumenal membrane structures in the vacuole. We further show that a key function of Hfl1 is the membrane recruitment of Atg8. In the presence of Hfl1, lipidation of Atg8 is not required for efficient cargo turnover. The need for Hfl1 can be partially bypassed by blocking Atg8 delipidation. Conclusions Our data reveal a vacuolar membrane protein degradation process with a unique dependence on vacuole-associated Atg8 downstream of ESCRTs, and we identify a specific role of Hfl1, a protein conserved from yeast to plants and animals, in membrane targeting of Atg8. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01048-7.
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Affiliation(s)
- Cheng-Wen He
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xue-Fei Cui
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shao-Jie Ma
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Present address: Department of Genetics, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Qin Xu
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yan-Peng Ran
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei-Zhi Chen
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun-Xi Mu
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hui Li
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jing Zhu
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qingqiu Gong
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhiping Xie
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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30
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Yang X, Reist L, Chomchai DA, Chen L, Arines FM, Li M. ESCRT, not intralumenal fragments, sorts ubiquitinated vacuole membrane proteins for degradation. THE JOURNAL OF CELL BIOLOGY 2021; 220:212199. [PMID: 34047770 PMCID: PMC8167898 DOI: 10.1083/jcb.202012104] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/19/2021] [Accepted: 05/13/2021] [Indexed: 01/05/2023]
Abstract
The lysosome (or vacuole in fungi and plants) is an essential organelle for nutrient sensing and cellular homeostasis. In response to environmental stresses such as starvation, the yeast vacuole can adjust its membrane composition by selectively internalizing membrane proteins into the lumen for degradation. Regarding the selective internalization mechanism, two competing models have been proposed. One model suggests that the ESCRT machinery is responsible for the sorting. In contrast, the ESCRT-independent intralumenal fragment (ILF) pathway proposes that the fragment generated by homotypic vacuole fusion is responsible for the sorting. Here, we applied a microfluidics-based imaging method to capture the complete degradation process in vivo. Combining live-cell imaging with a synchronized ubiquitination system, we demonstrated that ILF cargoes are not degraded through intralumenal fragments. Instead, ESCRTs function on the vacuole membrane to sort them into the lumen for degradation. We further discussed challenges in reconstituting vacuole membrane protein degradation.
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Affiliation(s)
- Xi Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Lucas Reist
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Dominic A Chomchai
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Liang Chen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Felichi Mae Arines
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
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31
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Hassanzadeh A, Rahman HS, Markov A, Endjun JJ, Zekiy AO, Chartrand MS, Beheshtkhoo N, Kouhbanani MAJ, Marofi F, Nikoo M, Jarahian M. Mesenchymal stem/stromal cell-derived exosomes in regenerative medicine and cancer; overview of development, challenges, and opportunities. Stem Cell Res Ther 2021; 12:297. [PMID: 34020704 PMCID: PMC8138094 DOI: 10.1186/s13287-021-02378-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 05/10/2021] [Indexed: 12/13/2022] Open
Abstract
Recently, mesenchymal stem/stromal cells (MSCs) and their widespread biomedical applications have attracted great consideration from the scientific community around the world. However, reports have shown that the main populations of the transplanted MSCs are trapped in the liver, spleen, and lung upon administration, highlighting the importance of the development of cell-free therapies. Concerning rising evidence suggesting that the beneficial effects of MSC therapy are closely linked to MSC-released components, predominantly MSC-derived exosomes, the development of an MSC-based cell-free approach is of paramount importance. The exosomes are nano-sized (30100nm) lipid bilayer membrane vesicles, which are typically released by MSCs and are found in different body fluids. They include various bioactive molecules, such as messenger RNA (mRNA), microRNAs, proteins, and bioactive lipids, thus showing pronounced therapeutic competence for tissues recovery through the maintenance of their endogenous stem cells, the enhancement of regenerative phenotypic traits, inhibition of apoptosis concomitant with immune modulation, and stimulation of the angiogenesis. Conversely, the specific roles of MSC exosomes in the treatment of various tumors remain challenging. The development and clinical application of novel MSC-based cell-free strategies can be supported by better understanding their mechanisms, classifying the subpopulation of exosomes, enhancing the conditions of cell culture and isolation, and increasing the production of exosomes along with engineering exosomes to deliver drugs and therapeutic molecules to the target sites. In the current review, we deliver a brief overview of MSC-derived exosome biogenesis, composition, and isolation methods and discuss recent investigation regarding the therapeutic potential of MSC exosomes in regenerative medicine accompanied by their double-edged sword role in cancer.
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Affiliation(s)
- Ali Hassanzadeh
- Department of Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Heshu Sulaiman Rahman
- Department of Physiology, College of Medicine, University of Suleimanyah, Sulaymaniyah, Iraq
| | | | - Judi Januadi Endjun
- Medical Faculty, UPN Veteran, Jakarta, Indonesia.,Gatot Soebroto Indonesia Army Hospital, Jakarta, Indonesia
| | | | | | - Nasrin Beheshtkhoo
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Amin Jadidi Kouhbanani
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Faroogh Marofi
- Immunology Research Center (IRC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Marzieh Nikoo
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mostafa Jarahian
- Toxicology and Chemotherapy Unit (G401), German Cancer Research Center, 69120, Heidelberg, Germany.
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32
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Arines FM, Hamlin AJ, Yang X, Liu YYJ, Li M. A selective transmembrane recognition mechanism by a membrane-anchored ubiquitin ligase adaptor. J Cell Biol 2021; 220:211632. [PMID: 33351099 PMCID: PMC7759299 DOI: 10.1083/jcb.202001116] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 09/10/2020] [Accepted: 10/30/2020] [Indexed: 12/30/2022] Open
Abstract
While it is well-known that E3 ubiquitin ligases can selectively ubiquitinate membrane proteins in response to specific environmental cues, the underlying mechanisms for the selectivity are poorly understood. In particular, the role of transmembrane regions, if any, in target recognition remains an open question. Here, we describe how Ssh4, a yeast E3 ligase adaptor, recognizes the PQ-loop lysine transporter Ypq1 only after lysine starvation. We show evidence of an interaction between two transmembrane helices of Ypq1 (TM5 and TM7) and the single transmembrane helix of Ssh4. This interaction is regulated by the conserved PQ motif. Strikingly, recent structural studies of the PQ-loop family have suggested that TM5 and TM7 undergo major conformational changes during substrate transport, implying that transport-associated conformational changes may determine the selectivity. These findings thus provide critical information concerning the regulatory mechanism through which transmembrane domains can be specifically recognized in response to changing environmental conditions.
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Affiliation(s)
- Felichi Mae Arines
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Aaron Jeremy Hamlin
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Xi Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Yun-Yu Jennifer Liu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
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33
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Zhu L, Sardana R, Jin DK, Emr SD. Calcineurin-dependent regulation of endocytosis by a plasma membrane ubiquitin ligase adaptor, Rcr1. J Cell Biol 2021; 219:151785. [PMID: 32421152 PMCID: PMC7401822 DOI: 10.1083/jcb.201909158] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/16/2020] [Accepted: 04/28/2020] [Indexed: 02/04/2023] Open
Abstract
Rsp5, the Nedd4 family member in yeast, is an E3 ubiquitin ligase involved in numerous cellular processes, many of which require Rsp5 to interact with PY-motif containing adaptor proteins. Here, we show that two paralogous transmembrane Rsp5 adaptors, Rcr1 and Rcr2, are sorted to distinct cellular locations: Rcr1 is a plasma membrane (PM) protein, whereas Rcr2 is sorted to the vacuole. Rcr2 is delivered to the vacuole using ubiquitin as a sorting signal. Rcr1 is delivered to the PM by the exomer complex using a newly uncovered PM sorting motif. Further, we show that Rcr1, but not Rcr2, is up-regulated via the calcineurin/Crz1 signaling pathway. Upon exogenous calcium treatment, Rcr1 ubiquitinates and down-regulates the chitin synthase Chs3. We propose that the PM-anchored Rsp5/Rcr1 ubiquitin ligase-adaptor complex can provide an acute response to degrade unwanted proteins under stress conditions, thereby maintaining cell integrity.
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Affiliation(s)
- Lu Zhu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Richa Sardana
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Daniel K Jin
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Scott D Emr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
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34
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Shen W, Zhang Z, Ma J, Lu D, Lyu L. The Ubiquitin Proteasome System and Skin Fibrosis. Mol Diagn Ther 2021; 25:29-40. [PMID: 33433895 DOI: 10.1007/s40291-020-00509-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2020] [Indexed: 12/15/2022]
Abstract
The ubiquitin proteasome system (UPS) is a highly conserved way to regulate protein turnover in cells. The UPS hydrolyzes and destroys variant or misfolded proteins and finely regulates proteins involved in differentiation, apoptosis, and other biological processes. This system is a key regulatory factor in the proliferation, differentiation, and collagen secretion of skin fibroblasts. E3 ubiquitin protein ligases Parkin and NEDD4 regulate multiple signaling pathways in keloid. Tumor necrosis factor (TNF) receptor-associated factor 4 (TRAF4) binding with deubiquitinase USP10 can induce p53 destabilization and promote keloid-derived fibroblast proliferation. The UPS participates in the occurrence and development of hypertrophic scars by regulating the transforming growth factor (TGF)-β/Smad signaling pathway. An initial study suggests that TNFα-induced protein 3 (TNFAIP3) polymorphisms may be significantly associated with scleroderma susceptibility in individuals of Caucasian descent. Sumoylation and multiple ubiquitin ligases, including Smurfs, UFD2, and KLHL42, play vital roles in scleroderma by targeting the TGF-β/Smad signaling pathway. In the future, drugs targeting E3 ligases and deubiquitinating enzymes have great potential for the treatment of skin fibrosis.
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Affiliation(s)
- Wanlu Shen
- Science and Technology Achievement Incubation Center, Kunming Medical University, 1168 West Chunrong Road, Yuhua Avenue, Chenggong District, Kunming, 650500, Yunnan, China
| | - Zhigang Zhang
- Science and Technology Achievement Incubation Center, Kunming Medical University, 1168 West Chunrong Road, Yuhua Avenue, Chenggong District, Kunming, 650500, Yunnan, China
| | - Jiaqing Ma
- School of Basic Medical Sciences, Kunming Medical University, Kunming, China
| | - Di Lu
- Science and Technology Achievement Incubation Center, Kunming Medical University, 1168 West Chunrong Road, Yuhua Avenue, Chenggong District, Kunming, 650500, Yunnan, China
| | - Lechun Lyu
- Science and Technology Achievement Incubation Center, Kunming Medical University, 1168 West Chunrong Road, Yuhua Avenue, Chenggong District, Kunming, 650500, Yunnan, China.
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35
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Abstract
Elimination of membrane proteins often requires recognition of their transmembrane domains (TMDs) in the lipid bilayer. In this issue, Arines et al. (2020. J. Cell Biol.https://doi.org/10.1083/jcb.202001116) show that in Saccharomyces cerevisiae, the vacuole-associated Rsp5 ubiquitin ligase uses a TMD in substrate adaptor Ssh4 to recognize membrane helices in Ypq1, which targets this lysine transporter for lysosomal degradation during lysine starvation.
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Affiliation(s)
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
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36
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Kakhlon O, Escriba PV, Akman HO, Weil M. Editorial: Using Small Molecules to Treat Macromolecule Storage Disorders. Front Cell Dev Biol 2020; 8:623613. [PMID: 33330518 PMCID: PMC7729068 DOI: 10.3389/fcell.2020.623613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 11/12/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Or Kakhlon
- Department of Neurology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Pablo V Escriba
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Hasan O Akman
- Department of Neurology, Columbia University Medical Center, New York, NY, United States
| | - Miguel Weil
- Laboratory for Neurodegenerative Diseases and Personalized Medicine, The Shmunis Schools of Biomedicine and Cancer Research, The George S. Wise Faculty for Life Sciences, Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
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37
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Steinfeld N, Lahiri V, Morrison A, Metur SP, Klionsky DJ, Weisman LS. Elevating PI3P drives select downstream membrane trafficking pathways. Mol Biol Cell 2020; 32:143-156. [PMID: 33237833 PMCID: PMC8120694 DOI: 10.1091/mbc.e20-03-0191] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Phosphoinositide signaling lipids are essential for several cellular processes. The requirement for a phosphoinositide is conventionally studied by depleting the corresponding lipid kinase. However, there are very few reports on the impact of elevating phosphoinositides. That phosphoinositides are dynamically elevated in response to stimuli suggests that, in addition to being required, phosphoinositides drive downstream pathways. To test this hypothesis, we elevated the levels of phosphatidylinositol-3-phosphate (PI3P) by generating hyperactive alleles of the yeast phosphatidylinositol 3-kinase, Vps34. We find that hyperactive Vps34 drives certain pathways, including phosphatidylinositol-3,5-bisphosphate synthesis and retrograde transport from the vacuole. This demonstrates that PI3P is rate limiting in some pathways. Interestingly, hyperactive Vps34 does not affect endosomal sorting complexes required for transport (ESCRT) function. Thus, elevating PI3P does not always increase the rate of PI3P-dependent pathways. Elevating PI3P can also delay a pathway. Elevating PI3P slowed late steps in autophagy, in part by delaying the disassembly of autophagy proteins from mature autophagosomes as well as delaying fusion of autophagosomes with the vacuole. This latter defect is likely due to a more general defect in vacuole fusion, as assessed by changes in vacuole morphology. These studies suggest that stimulus-induced elevation of phosphoinositides provides a way for these stimuli to selectively regulate downstream processes.
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Affiliation(s)
- Noah Steinfeld
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109.,Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Vikramjit Lahiri
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109.,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Anna Morrison
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
| | - Shree Padma Metur
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109.,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Daniel J Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109.,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Lois S Weisman
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109.,Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109.,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
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38
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Yao Y, Hong S, Ikeda T, Mori H, MacDougald OA, Nada S, Okada M, Inoki K. Amino Acids Enhance Polyubiquitination of Rheb and Its Binding to mTORC1 by Blocking Lysosomal ATXN3 Deubiquitinase Activity. Mol Cell 2020; 80:437-451.e6. [PMID: 33157014 PMCID: PMC7665239 DOI: 10.1016/j.molcel.2020.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/22/2020] [Accepted: 10/02/2020] [Indexed: 01/02/2023]
Abstract
Amino-acid-induced lysosomal mechanistic target of rapamycin complex 1 (mTORC1) localization through the Rag GTPases is a critical step for its activation by Rheb GTPase. However, how the mTORC1 interacts with Rheb on the lysosome remains elusive. We report that amino acids enhance the polyubiquitination of Rheb (Ub-Rheb), which shows a strong binding preference for mTORC1 and supports its activation, while the Ub-Rheb is subjected to subsequent degradation. Mechanistically, we identified ATXN3 as a Ub-Rheb deubiquitinase whose lysosomal localization is blocked by active Rag heterodimer in response to amino acid stimulation. Consistently, cells lacking functional Rag heterodimer on the lysosome accumulate Ub-Rheb, and blockade of its degradation instigates robust lysosomal mTORC1 localization and its activation without the Ragulator-Rag system. Thus, polyubiquitination of Rheb is an important post-translational modification, which facilitates the binding of mTORC1 to Rheb on the lysosome and is another crosstalk between the amino acid and growth factor signaling for mTORC1 activation.
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Affiliation(s)
- Yao Yao
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216, USA
| | - Sungki Hong
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216, USA
| | - Takayuki Ikeda
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216, USA; Department of Biochemistry, Kanazawa Medical University School of Medicine, 1-1 Daigaku, Uchinada, Kahoku-gun, Ishikawa 920-0293, Japan
| | - Hiroyuki Mori
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, 1137 E. Catherine St., Ann Arbor, MI 48109-5622, USA
| | - Ormond A MacDougald
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, 1137 E. Catherine St., Ann Arbor, MI 48109-5622, USA; Department of Internal Medicine, University of Michigan Medical School, 1500 East Medical Center Drive, Ann Arbor, MI 48109-5368, USA
| | - Shigeyuki Nada
- Department of Oncogene Research, the Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masato Okada
- Department of Oncogene Research, the Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ken Inoki
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216, USA; Department of Molecular and Integrative Physiology, University of Michigan Medical School, 1137 E. Catherine St., Ann Arbor, MI 48109-5622, USA; Department of Internal Medicine, University of Michigan Medical School, 1500 East Medical Center Drive, Ann Arbor, MI 48109-5368, USA.
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39
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Yang X, Zhang W, Wen X, Bulinski PJ, Chomchai DA, Arines FM, Liu YY, Sprenger S, Teis D, Klionsky DJ, Li M. TORC1 regulates vacuole membrane composition through ubiquitin- and ESCRT-dependent microautophagy. J Cell Biol 2020; 219:133713. [PMID: 32045480 PMCID: PMC7055007 DOI: 10.1083/jcb.201902127] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 11/22/2019] [Accepted: 01/07/2020] [Indexed: 01/12/2023] Open
Abstract
Cellular adaptation in response to nutrient limitation requires the induction of autophagy and lysosome biogenesis for the efficient recycling of macromolecules. Here, we discovered that starvation and TORC1 inactivation not only lead to the up-regulation of autophagy and vacuole proteins involved in recycling but also result in the down-regulation of many vacuole membrane proteins to supply amino acids as part of a vacuole remodeling process. Down-regulation of vacuole membrane proteins is initiated by ubiquitination, which is accomplished by the coordination of multiple E3 ubiquitin ligases, including Rsp5, the Dsc complex, and a newly characterized E3 ligase, Pib1. The Dsc complex is negatively regulated by TORC1 through the Rim15-Ume6 signaling cascade. After ubiquitination, vacuole membrane proteins are sorted into the lumen for degradation by ESCRT-dependent microautophagy. Thus, our study uncovered a complex relationship between TORC1 inactivation and vacuole biogenesis.
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Affiliation(s)
- Xi Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Weichao Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Xin Wen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI.,Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | - Patrick J Bulinski
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Dominic A Chomchai
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Felichi Mae Arines
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Yun-Yu Liu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Simon Sprenger
- Institute for Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - David Teis
- Institute for Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Daniel J Klionsky
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI.,Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
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40
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Abstract
The flavivirus genus encompasses more than 75 unique viruses, including dengue virus which accounts for almost 390 million global infections annually. Flavivirus infection can result in a myriad of symptoms ranging from mild rash and flu-like symptoms, to severe encephalitis and even hemorrhagic fever. Efforts to combat the impact of these viruses have been hindered due to limited antiviral drug and vaccine development. However, the advancement of knowledge in the structural biology of flaviviruses over the last 25 years has produced unique perspectives for the identification of potential therapeutic targets. With particular emphasis on the assembly and maturation stages of the flavivirus life cycle, it is the goal of this review to comparatively analyze the structural similarities between flaviviruses to provide avenues for new research and innovation.
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Affiliation(s)
- Conrrad M R Nicholls
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Madhumati Sevvana
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Richard J Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States; Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN, United States.
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41
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Lee C, Lamech L, Johns E, Overholtzer M. Selective Lysosome Membrane Turnover Is Induced by Nutrient Starvation. Dev Cell 2020; 55:289-297.e4. [PMID: 32916093 DOI: 10.1016/j.devcel.2020.08.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 07/02/2020] [Accepted: 08/17/2020] [Indexed: 12/20/2022]
Abstract
Lysosome function is essential for cellular homeostasis, but quality-control mechanisms that maintain healthy lysosomes remain poorly characterized. Here, we developed a method to measure lysosome turnover and use this to identify a selective mechanism of membrane degradation that involves lipidation of the autophagy protein LC3 onto lysosomal membranes and the formation of intraluminal vesicles through microautophagy. This mechanism is induced in response to metabolic stress resulting from glucose starvation or by treatment with pharmacological agents that induce osmotic stress on lysosomes. Cells lacking ATG5, an essential component of the LC3 lipidation machinery, show reduced ability to regulate lysosome size and degradative capacity in response to activation of this mechanism. These findings identify a selective mechanism of lysosome membrane turnover that is induced by stress and uncover a function for LC3 lipidation in regulating lysosome size and activity through microautophagy.
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Affiliation(s)
- Chan Lee
- Cell Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; BCMB Allied Program, Weill Cornell Medical College, New York, NY 10065, USA
| | - Lilian Lamech
- Cell Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Eleanor Johns
- Cell Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael Overholtzer
- Cell Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA; BCMB Allied Program, Weill Cornell Medical College, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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42
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Nitrogen coordinated import and export of arginine across the yeast vacuolar membrane. PLoS Genet 2020; 16:e1008966. [PMID: 32776922 PMCID: PMC7440668 DOI: 10.1371/journal.pgen.1008966] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 08/20/2020] [Accepted: 06/30/2020] [Indexed: 11/19/2022] Open
Abstract
The vacuole of the yeast Saccharomyces cerevisiae plays an important role in nutrient storage. Arginine, in particular, accumulates in the vacuole of nitrogen-replete cells and is mobilized to the cytosol under nitrogen starvation. The arginine import and export systems involved remain poorly characterized, however. Furthermore, how their activity is coordinated by nitrogen remains unknown. Here we characterize Vsb1 as a novel vacuolar membrane protein of the APC (amino acid-polyamine-organocation) transporter superfamily which, in nitrogen-replete cells, is essential to active uptake and storage of arginine into the vacuole. A shift to nitrogen starvation causes apparent inhibition of Vsb1-dependent activity and mobilization of stored vacuolar arginine to the cytosol. We further show that this arginine export involves Ypq2, a vacuolar protein homologous to the human lysosomal cationic amino acid exporter PQLC2 and whose activity is detected only in nitrogen-starved cells. Our study unravels the main arginine import and export systems of the yeast vacuole and suggests that they are inversely regulated by nitrogen. The lysosome-like vacuole of the yeast Saccharomyces cerevisiae is an important storage compartment for diverse nutrients, including the cationic amino acid arginine, which accumulates at high concentrations in this organelle in nitrogen-replete cells. When these cells are transferred to a nitrogen-free medium, vacuolar arginine is mobilized to the cytosol, where it is used as an alternative nitrogen source to sustain growth. Although this phenomenon has been observed since the 1980s, the identity of the vacuolar transporters involved in the accumulation and the mobilization of arginine is not well established, and whether these processes are regulated according to nutritional cues remains unknown. In this study, we exploited in vitro and in vivo uptake assays in vacuoles to identify and characterize Vsb1 and Ypq2 as vacuolar membrane proteins mediating import and export of arginine, respectively. We further provide evidence that Vsb1 and Ypq2 are inversely regulated according to the nitrogen status of the cell. Our study sheds new light on the poorly studied topic of the diversity and metabolic control of vacuolar transporters. It also raises novel questions about the molecular mechanisms underlying their coordinated regulation and, by extension, the regulation of lysosomal transporters in human cells.
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43
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The Role of Deubiquitinating Enzymes in the Various Forms of Autophagy. Int J Mol Sci 2020; 21:ijms21124196. [PMID: 32545524 PMCID: PMC7352190 DOI: 10.3390/ijms21124196] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/20/2022] Open
Abstract
Deubiquitinating enzymes (DUBs) have an essential role in several cell biological processes via removing the various ubiquitin patterns as posttranslational modification forms from the target proteins. These enzymes also contribute to the normal cytoplasmic ubiquitin pool during the recycling of this molecule. Autophagy, a summary name of the lysosome dependent self-degradative processes, is necessary for maintaining normal cellular homeostatic equilibrium. Numerous forms of autophagy are known depending on how the cellular self-material is delivered into the lysosomal lumen. In this review we focus on the colorful role of DUBs in autophagic processes and discuss the mechanistic contribution of these molecules to normal cellular homeostasis via the possible regulation forms of autophagic mechanisms.
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44
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Higuchi-Sanabria R, Shen K, Kelet N, Frankino PA, Durieux J, Bar-Ziv R, Sing CN, Garcia EJ, Homentcovschi S, Sanchez M, Wu R, Tronnes SU, Joe L, Webster B, Ahilon-Jeronimo A, Monshietehadi S, Dallarda S, Pender C, Pon LA, Zoncu R, Dillin A. Lysosomal recycling of amino acids affects ER quality control. SCIENCE ADVANCES 2020; 6:eaaz9805. [PMID: 32637599 PMCID: PMC7319768 DOI: 10.1126/sciadv.aaz9805] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
Recent work has highlighted the fact that lysosomes are a critical signaling hub of metabolic processes, providing fundamental building blocks crucial for anabolic functions. How lysosomal functions affect other cellular compartments is not fully understood. Here, we find that lysosomal recycling of the amino acids lysine and arginine is essential for proper ER quality control through the UPRER. Specifically, loss of the lysine and arginine amino acid transporter LAAT-1 results in increased sensitivity to proteotoxic stress in the ER and decreased animal physiology. We find that these LAAT-1-dependent effects are linked to glycine metabolism and transport and that the loss of function of the glycine transporter SKAT-1 also increases sensitivity to ER stress. Direct lysine and arginine supplementation, or glycine supplementation alone, can ameliorate increased ER stress sensitivity found in laat-1 mutants. These data implicate a crucial role in recycling lysine, arginine, and glycine in communication between the lysosome and ER.
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Affiliation(s)
- Ryo Higuchi-Sanabria
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Koning Shen
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Naame Kelet
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Phillip A. Frankino
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Jenni Durieux
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Raz Bar-Ziv
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Cierra N. Sing
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Enrique J. Garcia
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Stefan Homentcovschi
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Melissa Sanchez
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Rui Wu
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Sarah U. Tronnes
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Larry Joe
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Brant Webster
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Alex Ahilon-Jeronimo
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Samira Monshietehadi
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Sofia Dallarda
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Corinne Pender
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Liza A. Pon
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Roberto Zoncu
- Department of Biochemistry, Biophysics, and Structural Biology, University of California, Berkeley, Berkeley, CA 94720-3370, USA
| | - Andrew Dillin
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720-3370, USA
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45
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Current Knowledge and Future Perspectives on Mesenchymal Stem Cell-Derived Exosomes as a New Therapeutic Agent. Int J Mol Sci 2020; 21:ijms21030727. [PMID: 31979113 PMCID: PMC7036914 DOI: 10.3390/ijms21030727] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/14/2020] [Accepted: 01/20/2020] [Indexed: 12/13/2022] Open
Abstract
Mesenchymal stem cells (MSCs) are on the cusp of regenerative medicine due to their differentiation capacity, favorable culture conditions, ability to be manipulated in vitro, and strong immunomodulatory activity. Recent studies indicate that the pleiotropic effects of MSCs, especially their immunomodulatory potential, can be largely attributed to paracrine factors. Exosomes, vesicles that are 30-150 nanometers in diameter that function in cell-cell communication, are one of the key paracrine effectors. MSC-derived exosomes are enriched with therapeutic miRNAs, mRNAs, cytokines, lipids, and growth factors. Emerging evidences support the compelling possibility of using MSC-derived exosomes as a new form of therapy for treating several different kinds of disease such as heart, kidney, immune diseases, neural injuries, and neurodegenerative disease. This review provides a summary of current knowledge and discusses engineering of MSC-derived exosomes for their use in translational medicine.
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46
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Abstract
We review the mechanisms responsible for amino acid homeostasis in Saccharomyces cerevisiae and other fungi. Amino acid homeostasis is essential for cell growth and survival. Hence, the de novo synthesis reactions, metabolic conversions, and transport of amino acids are tightly regulated. Regulation varies from nitrogen pool sensing to control by individual amino acids and takes place at the gene (transcription), protein (posttranslational modification and allostery), and vesicle (trafficking and endocytosis) levels. The pools of amino acids are controlled via import, export, and compartmentalization. In yeast, the majority of the amino acid transporters belong to the APC (amino acid-polyamine-organocation) superfamily, and the proteins couple the uphill transport of amino acids to the electrochemical proton gradient. Although high-resolution structures of yeast amino acid transporters are not available, homology models have been successfully exploited to determine and engineer the catalytic and regulatory functions of the proteins. This has led to a further understanding of the underlying mechanisms of amino acid sensing and subsequent downregulation of transport. Advances in optical microscopy have revealed a new level of regulation of yeast amino acid transporters, which involves membrane domain partitioning. The significance and the interrelationships of the latest discoveries on amino acid homeostasis are put in context.
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47
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Schmidt O, Weyer Y, Baumann V, Widerin MA, Eising S, Angelova M, Schleiffer A, Kremser L, Lindner H, Peter M, Fröhlich F, Teis D. Endosome and Golgi-associated degradation (EGAD) of membrane proteins regulates sphingolipid metabolism. EMBO J 2019; 38:e101433. [PMID: 31368600 PMCID: PMC6669922 DOI: 10.15252/embj.2018101433] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 05/08/2019] [Accepted: 05/08/2019] [Indexed: 12/13/2022] Open
Abstract
Cellular homeostasis requires the ubiquitin-dependent degradation of membrane proteins. This was assumed to be mediated exclusively either by endoplasmic reticulum-associated degradation (ERAD) or by endosomal sorting complexes required for transport (ESCRT)-dependent lysosomal degradation. We identified in Saccharomyces cerevisiae an additional pathway that selectively extracts membrane proteins at Golgi and endosomes for degradation by cytosolic proteasomes. One endogenous substrate of this endosome and Golgi-associated degradation pathway (EGAD) is the ER-resident membrane protein Orm2, a negative regulator of sphingolipid biosynthesis. Orm2 degradation is initiated by phosphorylation, which triggers its ER export. Once on Golgi and endosomes, Orm2 is poly-ubiquitinated by the membrane-embedded "Defective in SREBP cleavage" (Dsc) ubiquitin ligase complex. Cdc48/VCP then extracts ubiquitinated Orm2 from membranes, which is tightly coupled to the proteasomal degradation of Orm2. Thereby, EGAD prevents the accumulation of Orm2 at the ER and in post-ER compartments and promotes the controlled de-repression of sphingolipid biosynthesis. Thus, the selective degradation of membrane proteins by EGAD contributes to proteostasis and lipid homeostasis in eukaryotic cells.
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Affiliation(s)
- Oliver Schmidt
- Division of Cell BiologyBiocenterMedical University of InnsbruckInnsbruckAustria
| | - Yannick Weyer
- Division of Cell BiologyBiocenterMedical University of InnsbruckInnsbruckAustria
| | - Verena Baumann
- Division of Cell BiologyBiocenterMedical University of InnsbruckInnsbruckAustria
- Present address:
MFPLUniversity of ViennaViennaAustria
| | - Michael A Widerin
- Division of Cell BiologyBiocenterMedical University of InnsbruckInnsbruckAustria
| | - Sebastian Eising
- Department of Biology/ChemistryUniversity of OsnabrückOsnabrückGermany
| | - Mihaela Angelova
- INSERMLaboratory of Integrative Cancer ImmunologySorbonne UniversitéSorbonne Paris CitéUniversité Paris DescartesCentre de Recherche des CordeliersUniversité Paris DiderotParisFrance
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
| | - Leopold Kremser
- Division of Clinical Biochemistry, Protein Micro‐Analysis FacilityBiocenterMedical University of InnsbruckInnsbruckAustria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Protein Micro‐Analysis FacilityBiocenterMedical University of InnsbruckInnsbruckAustria
| | | | - Florian Fröhlich
- Department of Biology/ChemistryUniversity of OsnabrückOsnabrückGermany
| | - David Teis
- Division of Cell BiologyBiocenterMedical University of InnsbruckInnsbruckAustria
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48
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Goodrum JM, Lever AR, Coody TK, Gottschling DE, Hughes AL. Rsp5 and Mdm30 reshape the mitochondrial network in response to age-induced vacuole stress. Mol Biol Cell 2019; 30:2141-2154. [PMID: 31141470 PMCID: PMC6743467 DOI: 10.1091/mbc.e19-02-0094] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Mitochondrial decline is a hallmark of aging, and cells are equipped with many systems to regulate mitochondrial structure and function in response to stress and metabolic alterations. Here, using budding yeast, we identify a proteolytic pathway that contributes to alterations in mitochondrial structure in aged cells through control of the mitochondrial fusion GTPase Fzo1. We show that mitochondrial fragmentation in old cells correlates with reduced abundance of Fzo1, which is triggered by functional alterations in the vacuole, a known early event in aging. Fzo1 degradation is mediated by a proteolytic cascade consisting of the E3 ubiquitin ligases SCFMdm30 and Rsp5, and the Cdc48 cofactor Doa1. Fzo1 proteolysis is activated by metabolic stress that arises from vacuole impairment, and loss of Fzo1 degradation severely impairs mitochondrial structure and function. Together, these studies identify a new mechanism for stress-responsive regulation of mitochondrial structure that is activated during cellular aging.
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Affiliation(s)
- Jenna M Goodrum
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Austin R Lever
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Troy K Coody
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | | | - Adam L Hughes
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
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49
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Flavivirus Replication Organelle Biogenesis in the Endoplasmic Reticulum: Comparison with Other Single-Stranded Positive-Sense RNA Viruses. Int J Mol Sci 2019; 20:ijms20092336. [PMID: 31083507 PMCID: PMC6539296 DOI: 10.3390/ijms20092336] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/04/2019] [Accepted: 05/09/2019] [Indexed: 12/20/2022] Open
Abstract
Some single-stranded positive-sense RNA [ssRNA(+)] viruses, including Flavivirus, generate specific organelle-like structures in the host endoplasmic reticulum (ER). These structures are called virus replication organelles and consist of two distinct subdomains, the vesicle packets (VPs) and the convoluted membranes (CMs). The VPs are clusters of small vesicle compartments and are considered to be the site of viral genome replication. The CMs are electron-dense amorphous structures observed in proximity to the VPs, but the exact roles of CMs are mostly unknown. Several recent studies have revealed that flaviviruses recruit several host factors that are usually used for the biogenesis of other conventional organelles and usurp their function to generate virus replication organelles. In the current review, we summarize recent studies focusing on the role of host factors in the formation of virus replication organelles and discuss how these intricate membrane structures are organized.
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50
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Guiney EL, Zhu L, Sardana R, Emr SD, Baile MG. Methods for studying the regulation of membrane traffic by ubiquitin and the ESCRT pathway. Methods Enzymol 2019; 619:269-291. [PMID: 30910024 DOI: 10.1016/bs.mie.2018.12.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Covalent modification of proteins with ubiquitin dynamically regulates their function and fate. The ubiquitination of most plasma membrane proteins initiates endocytosis and ESCRT-mediated sorting to the lysosomal lumen for degradation. Powerful genetic approaches in the budding yeast Saccharomyces cerevisiae have been particularly instrumental in the discovery and elucidation of these molecular mechanisms, which are conserved in all eukaryotes. Here we provide two detailed protocols and tools for studying ubiquitination-dependent membrane trafficking mechanisms in yeast. The first utilizes fusions between a protein of interest and an auxotrophic marker to screen for mutants that affect ubiquitin-mediated endocytosis. The second method artificially ubiquitinates a protein of interest, allowing downstream trafficking steps to be studied independently from the regulatory signals that initiate endocytosis.
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Affiliation(s)
- Evan L Guiney
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Lu Zhu
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Richa Sardana
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Scott D Emr
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States.
| | - Matthew G Baile
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
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