1
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Hazan Ben-Menachem R, Pines O, Saada A. Mitochondrial derived vesicles- Quo Vadis? FEBS J 2024. [PMID: 38414203 DOI: 10.1111/febs.17103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 02/29/2024]
Abstract
Mitochondria are dynamic, intracellular organelles with a separate genome originating from prokaryotes. They perform numerous functions essential for cellular metabolism and energy production. Mitochondrial-derived vesicles (MDVs) are single or double membrane-enclosed vesicles, formed and released from the mitochondrial sub-compartments into the cytosol, in response to various triggers. MDVs interact with other organelles such as lysosomes and peroxisomes or may be incorporated and excreted via extracellular vesicles (EVs). MDVs selectively incorporate diverse protein and lipid cargoes and are involved in various functions such as mitochondrial quality control, immunomodulation, energy complementation, and compartmentalization and transport. This review aims to provide a summary of the current knowledge of MDVs biogenesis, release, cargoes, and roles.
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Affiliation(s)
- Reut Hazan Ben-Menachem
- Department of Molecular Genetics and Microbiology, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Ophry Pines
- Department of Molecular Genetics and Microbiology, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Ann Saada
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Israel
- Department of Medical Laboratory Sciences Hadassah Academic College, Jerusalem, Israel
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2
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Zhang Y, Karmon O, Das K, Wiener R, Lehming N, Pines O. Ubiquitination Occurs in the Mitochondrial Matrix by Eclipsed Targeted Components of the Ubiquitination Machinery. Cells 2022; 11:cells11244109. [PMID: 36552873 PMCID: PMC9777009 DOI: 10.3390/cells11244109] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Ubiquitination is a critical type of post-translational modification in eukaryotic cells. It is involved in regulating nearly all cellular processes in the cytosol and nucleus. Mitochondria, known as the metabolism heart of the cell, are organelles that evolved from bacteria. Using the subcellular compartment-dependent α-complementation, we detect multiple components of ubiquitination machinery as being eclipsed distributed to yeast mitochondria. Ubiquitin conjugates and mono-ubiquitin can be detected in lysates of isolated mitochondria from cells expressing HA-Ub and treated with trypsin. By expressing MTS (mitochondrial targeting sequence) targeted HA-tagged ubiquitin, we demonstrate that certain ubiquitination events specifically occur in yeast mitochondria and are independent of proteasome activity. Importantly, we show that the E2 Rad6 affects the pattern of protein ubiquitination in mitochondria and provides an in vivo assay for its activity in the matrix of the organelle. This study shows that ubiquitination occurs in the mitochondrial matrix by eclipsed targeted components of the ubiquitin machinery, providing a new perspective on mitochondrial and ubiquitination research.
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Affiliation(s)
- Yu Zhang
- NUS-HUJ-CREATE Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 138602, Singapore
| | - Ofri Karmon
- NUS-HUJ-CREATE Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 138602, Singapore
| | - Koyeli Das
- Department of Molecular Genetics and Microbiology, IMRIC, Faculty of Medicine, Hebrew University, Jerusalem 9112001, Israel
| | - Reuven Wiener
- Department of Biochemistry and Molecular Biology, IMRIC, Faculty of Medicine, Hebrew University, Jerusalem 9112001, Israel
| | - Norbert Lehming
- NUS-HUJ-CREATE Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 138602, Singapore
| | - Ophry Pines
- NUS-HUJ-CREATE Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 138602, Singapore
- Department of Molecular Genetics and Microbiology, IMRIC, Faculty of Medicine, Hebrew University, Jerusalem 9112001, Israel
- Correspondence:
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3
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Jin K, Xia H, Liu Y, Li J, Du G, Lv X, Liu L. Compartmentalization and transporter engineering strategies for terpenoid synthesis. Microb Cell Fact 2022; 21:92. [PMID: 35599322 PMCID: PMC9125818 DOI: 10.1186/s12934-022-01819-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/12/2022] [Indexed: 12/18/2022] Open
Abstract
Microbial cell factories for terpenoid synthesis form a less expensive and more environment-friendly approach than chemical synthesis and extraction, and are thus being regarded as mainstream research recently. Organelle compartmentalization for terpenoid synthesis has received much attention from researchers owing to the diverse physiochemical characteristics of organelles. In this review, we first systematically summarized various compartmentalization strategies utilized in terpenoid production, mainly plant terpenoids, which can provide catalytic reactions with sufficient intermediates and a suitable environment, while bypassing competing metabolic pathways. In addition, because of the limited storage capacity of cells, strategies used for the expansion of specific organelle membranes were discussed. Next, transporter engineering strategies to overcome the cytotoxic effects of terpenoid accumulation were analyzed. Finally, we discussed the future perspectives of compartmentalization and transporter engineering strategies, with the hope of providing theoretical guidance for designing and constructing cell factories for the purpose of terpenoid production.
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Affiliation(s)
- Ke Jin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Hongzhi Xia
- Richen Bioengineering Co., Ltd, Nantong, 226000, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China.
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China.
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4
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Capera J, Navarro-Pérez M, Moen AS, Szabó I, Felipe A. The Mitochondrial Routing of the Kv1.3 Channel. Front Oncol 2022; 12:865686. [PMID: 35402277 PMCID: PMC8990977 DOI: 10.3389/fonc.2022.865686] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/02/2022] [Indexed: 12/19/2022] Open
Abstract
Voltage-gated potassium channels control neuronal excitability and cardiac action potentials. In addition, these proteins are involved in a myriad of cellular processes. The potassium channel Kv1.3 plays an essential role in the immune response mediated by leukocytes. Kv1.3 is functional both at the plasma membrane and the inner mitochondrial membrane. Plasma membrane Kv1.3 mediates cellular activation and proliferation, whereas mitochondrial Kv1.3 participates in cell survival and apoptosis. Therefore, this protein emerges as an important target in cancer therapies. Several forward-traffic motifs target the channel to the plasma membrane in a COPII-dependent manner. However, the mitochondrial import pathway for Kv1.3 is largely unknown. Here, we deciphered the mitochondrial routing of the mitoKv1.3 channel. Kv1.3 uses the TIM23 complex to translocate to the inner mitochondrial membrane. This mechanism is unconventional because the channel is a multimembrane spanning protein without a defined N-terminal presequence. We found that transmembrane domains cooperatively mediate Kv1.3 mitochondrial targeting and identified the cytosolic HSP70/HSP90 chaperone complex as a key regulator of the process. Our results provide insights into the mechanisms mediating the localization of Kv1.3 to mitochondrial membranes, further extending the knowledge of ion channel biogenesis and turnover in mitochondria.
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Affiliation(s)
- Jesusa Capera
- Molecular Physiology Laboratory, Dpt. de Bioquímica i Biomedicina Molecular, Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain.,Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - María Navarro-Pérez
- Molecular Physiology Laboratory, Dpt. de Bioquímica i Biomedicina Molecular, Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Anne Stine Moen
- Molecular Physiology Laboratory, Dpt. de Bioquímica i Biomedicina Molecular, Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Ildiko Szabó
- Department of Biology, University of Padova, Padova, Italy
| | - Antonio Felipe
- Molecular Physiology Laboratory, Dpt. de Bioquímica i Biomedicina Molecular, Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
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5
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Hemmerle M, Senger B, di Rago JP, Kucharczyk R, Becker HD. Visualizing Mitochondrial Importability of a Protein Using the Yeast Bi-Genomic Mitochondrial-Split-GFP Strain and an Ordinary Fluorescence Microscope. Methods Mol Biol 2022; 2497:255-267. [PMID: 35771447 DOI: 10.1007/978-1-0716-2309-1_16] [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: 01/14/2023]
Abstract
Proving with certainty that a GFP-tagged protein is imported inside mitochondria by visualizing its fluorescence emission with an epifluorescence microscope is currently impossible using regular GFP-tagging. This is particularly true for proteins dual localized in the cytosol and mitochondria, which have been estimated to represent up to one third of the established mitoproteomes. These proteins are usually composed of a surpassingly abundant pool of the cytosolic isoform compared to the mitochondrial isoform. As a consequence, when tagged with a regular GFP, the fluorescence emission of the cytosolic isoform will inevitably eclipse that of the mitochondrial one and prevent the detection of the mitochondrial echoform. To overcome this technical limit, we engineered a yeast strain expressing a new type of GFP called Bi-Genomic Mitochondrial-Split-GFP (BiG Mito-Split-GFP). In this strain, one moiety of the GFP is encoded by the mitochondrial DNA while the second moiety of the GFP can be tagged to any nuclear-encoded protein (suspected to be dual localized or bona fide mitochondrial). By doing so, only mitochondrial proteins or echoforms of dual localized proteins, regardless of their organismal origin, trigger GFP reconstitution that can be visualized by regular fluorescence microscopy. The strength of the BiG Mito-Split-GFP system is that proof of the mitochondrial localization of a given protein rests on a simple and effortless microscopy observation.
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Affiliation(s)
- Marine Hemmerle
- Université de Strasbourg, CNRS, Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, Strasbourg Cedex, France
| | - Bruno Senger
- Université de Strasbourg, CNRS, Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, Strasbourg Cedex, France
| | - Jean-Paul di Rago
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, Bordeaux cedex, France
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Hubert D Becker
- Université de Strasbourg, CNRS, Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, Strasbourg Cedex, France.
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6
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Bruni F, Giancaspero TA, Oreb M, Tolomeo M, Leone P, Boles E, Roberti M, Caselle M, Barile M. Subcellular Localization of Fad1p in Saccharomyces cerevisiae: A Choice at Post-Transcriptional Level? Life (Basel) 2021; 11:967. [PMID: 34575116 PMCID: PMC8470081 DOI: 10.3390/life11090967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/06/2021] [Accepted: 09/13/2021] [Indexed: 11/24/2022] Open
Abstract
FAD synthase is the last enzyme in the pathway that converts riboflavin into FAD. In Saccharomyces cerevisiae, the gene encoding for FAD synthase is FAD1, from which a sole protein product (Fad1p) is expected to be generated. In this work, we showed that a natural Fad1p exists in yeast mitochondria and that, in its recombinant form, the protein is able, per se, to both enter mitochondria and to be destined to cytosol. Thus, we propose that FAD1 generates two echoforms-that is, two identical proteins addressed to different subcellular compartments. To shed light on the mechanism underlying the subcellular destination of Fad1p, the 3' region of FAD1 mRNA was analyzed by 3'RACE experiments, which revealed the existence of (at least) two FAD1 transcripts with different 3'UTRs, the short one being 128 bp and the long one being 759 bp. Bioinformatic analysis on these 3'UTRs allowed us to predict the existence of a cis-acting mitochondrial localization motif, present in both the transcripts and, presumably, involved in protein targeting based on the 3'UTR context. Here, we propose that the long FAD1 transcript might be responsible for the generation of mitochondrial Fad1p echoform.
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Affiliation(s)
- Francesco Bruni
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (F.B.); (T.A.G.); (M.T.); (P.L.); (M.R.)
| | - Teresa Anna Giancaspero
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (F.B.); (T.A.G.); (M.T.); (P.L.); (M.R.)
| | - Mislav Oreb
- Institute of Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; (M.O.); (E.B.)
| | - Maria Tolomeo
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (F.B.); (T.A.G.); (M.T.); (P.L.); (M.R.)
| | - Piero Leone
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (F.B.); (T.A.G.); (M.T.); (P.L.); (M.R.)
| | - Eckhard Boles
- Institute of Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; (M.O.); (E.B.)
| | - Marina Roberti
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (F.B.); (T.A.G.); (M.T.); (P.L.); (M.R.)
| | - Michele Caselle
- Physics Department, University of Turin and INFN, Via P. Giuria 1, 10125 Turin, Italy;
| | - Maria Barile
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (F.B.); (T.A.G.); (M.T.); (P.L.); (M.R.)
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7
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Dekker FA, Rüdiger SGD. The Mitochondrial Hsp90 TRAP1 and Alzheimer's Disease. Front Mol Biosci 2021; 8:697913. [PMID: 34222342 PMCID: PMC8249562 DOI: 10.3389/fmolb.2021.697913] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/02/2021] [Indexed: 12/31/2022] Open
Abstract
Alzheimer’s Disease (AD) is the most common form of dementia, characterised by intra- and extracellular protein aggregation. In AD, the cellular protein quality control (PQC) system is derailed and fails to prevent the formation of these aggregates. Especially the mitochondrial paralogue of the conserved Hsp90 chaperone class, tumour necrosis factor receptor-associated protein 1 (TRAP1), is strongly downregulated in AD, more than other major PQC factors. Here, we review molecular mechanism and cellular function of TRAP1 and subsequently discuss possible links to AD. TRAP1 is an interesting paradigm for the Hsp90 family, as it chaperones proteins with vital cellular function, despite not being regulated by any of the co-chaperones that drive its cytosolic paralogues. TRAP1 encloses late folding intermediates in a non-active state. Thereby, it is involved in the assembly of the electron transport chain, and it favours the switch from oxidative phosphorylation to glycolysis. Another key function is that it ensures mitochondrial integrity by regulating the mitochondrial pore opening through Cyclophilin D. While it is still unclear whether TRAP1 itself is a driver or a passenger in AD, it might be a guide to identify key factors initiating neurodegeneration.
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Affiliation(s)
- Françoise A Dekker
- Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands.,Science for Life, Utrecht University, Utrecht, Netherlands
| | - Stefan G D Rüdiger
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands.,Science for Life, Utrecht University, Utrecht, Netherlands
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8
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Lin J, Chen K, Chen W, Yao Y, Ni S, Ye M, Zhuang G, Hu M, Gao J, Gao C, Liu Y, Yang M, Zhang Z, Zhang X, Huang J, Chen F, Sun L, Zhang X, Yu S, Chen Y, Jiang Y, Wang S, Yang X, Liu K, Zhou HM, Ji Z, Deng H, Haque ME, Li J, Mi LZ, Li Y, Yang Y. Paradoxical Mitophagy Regulation by PINK1 and TUFm. Mol Cell 2020; 80:607-620.e12. [PMID: 33113344 DOI: 10.1016/j.molcel.2020.10.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/25/2020] [Accepted: 10/06/2020] [Indexed: 01/19/2023]
Abstract
Aberrant mitophagy has been implicated in a broad spectrum of disorders. PINK1, Parkin, and ubiquitin have pivotal roles in priming mitophagy. However, the entire regulatory landscape and the precise control mechanisms of mitophagy remain to be elucidated. Here, we uncover fundamental mitophagy regulation involving PINK1 and a non-canonical role of the mitochondrial Tu translation elongation factor (TUFm). The mitochondrion-cytosol dual-localized TUFm interacts with PINK1 biochemically and genetically, which is an evolutionarily conserved Parkin-independent route toward mitophagy. A PINK1-dependent TUFm phosphoswitch at Ser222 determines conversion from activating to suppressing mitophagy. PINK1 modulates differential translocation of TUFm because p-S222-TUFm is restricted predominantly to the cytosol, where it inhibits mitophagy by impeding Atg5-Atg12 formation. The self-antagonizing feature of PINK1/TUFm is critical for the robustness of mitophagy regulation, achieved by the unique kinetic parameters of p-S222-TUFm, p-S65-ubiquitin, and their common kinase PINK1. Our findings provide new mechanistic insights into mitophagy and mitophagy-associated disorders.
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Affiliation(s)
- Jingjing Lin
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Kai Chen
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Wenfeng Chen
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Yizhou Yao
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Shiwei Ni
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Meina Ye
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Guifeng Zhuang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Minhuang Hu
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Jun Gao
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Caixi Gao
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Yan Liu
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Mingjuan Yang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Zhenkun Zhang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Xiaohui Zhang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Jiexiang Huang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Fei Chen
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Ling Sun
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Xi Zhang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Suhong Yu
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Yuling Chen
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yating Jiang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Shujuan Wang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Xiaozhen Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Ke Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Hai-Meng Zhou
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Zhejiang Jiaxing 314006, China
| | - Zhiliang Ji
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - M Emdadul Haque
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, PO Box 17666, United Arab Emirates
| | - Junxiang Li
- AgeCode R&D Center, Yangtze Delta Region Institute of Tsinghua University, Zhejiang Jiaxing 314006, China
| | - Li-Zhi Mi
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Yuexi Li
- Huadong Research Institute for Medicine and Biotechniques, 293 East Zhongshan Road, Nanjing 210002, China.
| | - Yufeng Yang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian 350108, China.
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9
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Bader G, Enkler L, Araiso Y, Hemmerle M, Binko K, Baranowska E, De Craene JO, Ruer-Laventie J, Pieters J, Tribouillard-Tanvier D, Senger B, di Rago JP, Friant S, Kucharczyk R, Becker HD. Assigning mitochondrial localization of dual localized proteins using a yeast Bi-Genomic Mitochondrial-Split-GFP. eLife 2020; 9:56649. [PMID: 32657755 PMCID: PMC7358010 DOI: 10.7554/elife.56649] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/11/2020] [Indexed: 12/31/2022] Open
Abstract
A single nuclear gene can be translated into a dual localized protein that distributes between the cytosol and mitochondria. Accumulating evidences show that mitoproteomes contain lots of these dual localized proteins termed echoforms. Unraveling the existence of mitochondrial echoforms using current GFP (Green Fluorescent Protein) fusion microscopy approaches is extremely difficult because the GFP signal of the cytosolic echoform will almost inevitably mask that of the mitochondrial echoform. We therefore engineered a yeast strain expressing a new type of Split-GFP that we termed Bi-Genomic Mitochondrial-Split-GFP (BiG Mito-Split-GFP). Because one moiety of the GFP is translated from the mitochondrial machinery while the other is fused to the nuclear-encoded protein of interest translated in the cytosol, the self-reassembly of this Bi-Genomic-encoded Split-GFP is confined to mitochondria. We could authenticate the mitochondrial importability of any protein or echoform from yeast, but also from other organisms such as the human Argonaute 2 mitochondrial echoform.
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Affiliation(s)
- Gaétan Bader
- Université de Strasbourg, CNRS UMR7156, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Ludovic Enkler
- Université de Strasbourg, CNRS UMR7156, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Yuhei Araiso
- Université de Strasbourg, CNRS UMR7156, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Marine Hemmerle
- Université de Strasbourg, CNRS UMR7156, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Krystyna Binko
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Emilia Baranowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Johan-Owen De Craene
- Université de Strasbourg, CNRS UMR7156, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | | | - Jean Pieters
- Biozentrum, University of Basel, Basel, Switzerland
| | | | - Bruno Senger
- Université de Strasbourg, CNRS UMR7156, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Jean-Paul di Rago
- Institut de Biochimie et Génétique Cellulaires, CNRS UMR5095, Université de Bordeaux, Bordeaux, France
| | - Sylvie Friant
- Université de Strasbourg, CNRS UMR7156, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Hubert Dominique Becker
- Université de Strasbourg, CNRS UMR7156, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
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10
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Krupinska K, Blanco NE, Oetke S, Zottini M. Genome communication in plants mediated by organelle-n-ucleus-located proteins. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190397. [PMID: 32362260 PMCID: PMC7209962 DOI: 10.1098/rstb.2019.0397] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
An increasing number of eukaryotic proteins have been shown to have a dual localization in the DNA-containing organelles, mitochondria and plastids, and/or the nucleus. Regulation of dual targeting and relocation of proteins from organelles to the nucleus offer the most direct means for communication between organelles as well as organelles and nucleus. Most of the mitochondrial proteins of animals have functions in DNA repair and gene expression by modelling of nucleoid architecture and/or chromatin. In plants, such proteins can affect replication and early development. Most plastid proteins with a confirmed or predicted second location in the nucleus are associated with the prokaryotic core RNA polymerase and are required for chloroplast development and light responses. Few plastid–nucleus-located proteins are involved in pathogen defence and cell cycle control. For three proteins, it has been clearly shown that they are first targeted to the organelle and then relocated to the nucleus, i.e. the nucleoid-associated proteins HEMERA and Whirly1 and the stroma-located defence protein NRIP1. Relocation to the nucleus can be experimentally demonstrated by plastid transformation leading to the synthesis of proteins with a tag that enables their detection in the nucleus or by fusions with fluoroproteins in different experimental set-ups. This article is part of the theme issue ‘Retrograde signalling from endosymbiotic organelles’.
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Affiliation(s)
- Karin Krupinska
- Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany
| | - Nicolás E Blanco
- Centre of Photosynthetic and Biochemical Studies, Faculty of Biochemical Science and Pharmacy, National University of Rosario (CEFOBI/UNR-CONICET), Rosario, Argentina
| | - Svenja Oetke
- Institute of Botany, Christian-Albrechts-University of Kiel, Olshausenstraße 40, 24098 Kiel, Germany
| | - Michela Zottini
- Department of Biology, University of Padova, Via U. Bassi 58B, 35131 Padova, Italy
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11
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Pfanner N, Warscheid B, Wiedemann N. Mitochondrial proteins: from biogenesis to functional networks. Nat Rev Mol Cell Biol 2020; 20:267-284. [PMID: 30626975 DOI: 10.1038/s41580-018-0092-0] [Citation(s) in RCA: 555] [Impact Index Per Article: 138.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mitochondria are essential for the viability of eukaryotic cells as they perform crucial functions in bioenergetics, metabolism and signalling and have been associated with numerous diseases. Recent functional and proteomic studies have revealed the remarkable complexity of mitochondrial protein organization. Protein machineries with diverse functions such as protein translocation, respiration, metabolite transport, protein quality control and the control of membrane architecture interact with each other in dynamic networks. In this Review, we discuss the emerging role of the mitochondrial protein import machinery as a key organizer of these mitochondrial protein networks. The preprotein translocases that reside on the mitochondrial membranes not only function during organelle biogenesis to deliver newly synthesized proteins to their final mitochondrial destination but also cooperate with numerous other mitochondrial protein complexes that perform a wide range of functions. Moreover, these protein networks form membrane contact sites, for example, with the endoplasmic reticulum, that are key for integration of mitochondria with cellular function, and defects in protein import can lead to diseases.
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Affiliation(s)
- Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - Bettina Warscheid
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.,Institute of Biology II, Biochemistry - Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
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12
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Chin HL, Goh DLM, Wang FS, Tay SKH, Heng CK, Donnini C, Baruffini E, Pines O. A combination of two novel VARS2 variants causes a mitochondrial disorder associated with failure to thrive and pulmonary hypertension. J Mol Med (Berl) 2019; 97:1557-1566. [PMID: 31529142 DOI: 10.1007/s00109-019-01834-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 07/29/2019] [Accepted: 08/13/2019] [Indexed: 01/30/2023]
Abstract
The VARS2 gene encodes a mitochondrial valyl-transfer RNA synthetase which is used in mitochondrial translation. To date, several patients with VARS2 pathogenic variants have been described in the literature. These patients have features of lactic acidosis with encephalomyopathy. We present a case of an infant with lactic acidosis, failure to thrive, and severe primary pulmonary hypertension who was found to be a compound heterozygote for two novel VARS2 variants (c.1940C>T, p.(Thr647Met) and c.2318G>A, p.(Arg773Gln)). The patient was treated with vitamin supplements and a carbohydrate-restricted diet. The lactic acidosis and failure to thrive resolved, and he showed good growth and development. Functional studies and molecular analysis employed a yeast model system and the VAS1 gene (yeast homolog of VARS2). VAS1 genes harboring either one of two mutations corresponding to the two novel variants in the VARS2 gene, exhibited partially reduced function in haploid yeast strains. A combination of both VAS1 variant alleles in a diploid yeast cell exhibited a more significant decrease in oxidative metabolism-dependent growth and in the oxygen consumption rate (reminiscent of the patient who carries two mutant VARS2 alleles). Our results demonstrate the pathogenicity of the biallellic novel VARS2 variants. KEY MESSAGES: • A case of an infant who is a compound heterozygote for two novel VARS2 variants. • This infant displayed lactic acidosis, failure to thrive, and pulmonary hypertension. • Treatment of the patient with a carbohydrate-restricted diet resulted in good growth and development. • Studies with the homologous yeast VAS1 gene showed reduced function of corresponding single mutant in haploid yeast strains. • A combination of both VAS1 variant alleles in diploid yeast exhibited a more significant decrease in function, thereby confirming the pathogenicity of the biallellic novel VARS2 variants.
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Affiliation(s)
- Hui-Lin Chin
- Khoo Teck Puat-National University Children's Medical Institute, National University Health Systems (NUHS), Singapore, Singapore. .,Department of Pediatrics, Yong Loo Lin School of Medicine, National University Hospital, National University of Singapore, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore.
| | - Denise Li-Meng Goh
- Khoo Teck Puat-National University Children's Medical Institute, National University Health Systems (NUHS), Singapore, Singapore.,Department of Pediatrics, Yong Loo Lin School of Medicine, National University Hospital, National University of Singapore, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
| | - Furene Sijia Wang
- Khoo Teck Puat-National University Children's Medical Institute, National University Health Systems (NUHS), Singapore, Singapore.,Department of Pediatrics, Yong Loo Lin School of Medicine, National University Hospital, National University of Singapore, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
| | - Stacey Kiat Hong Tay
- Khoo Teck Puat-National University Children's Medical Institute, National University Health Systems (NUHS), Singapore, Singapore.,Department of Pediatrics, Yong Loo Lin School of Medicine, National University Hospital, National University of Singapore, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
| | - Chew Kiat Heng
- Khoo Teck Puat-National University Children's Medical Institute, National University Health Systems (NUHS), Singapore, Singapore.,Department of Pediatrics, Yong Loo Lin School of Medicine, National University Hospital, National University of Singapore, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
| | - Claudia Donnini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy.
| | - Ophry Pines
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.,NUS-HUJ-CREATE Program and the Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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13
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Weill U, Yofe I, Sass E, Stynen B, Davidi D, Natarajan J, Ben-Menachem R, Avihou Z, Goldman O, Harpaz N, Chuartzman S, Kniazev K, Knoblach B, Laborenz J, Boos F, Kowarzyk J, Ben-Dor S, Zalckvar E, Herrmann JM, Rachubinski RA, Pines O, Rapaport D, Michnick SW, Levy ED, Schuldiner M. Genome-wide SWAp-Tag yeast libraries for proteome exploration. Nat Methods 2018; 15:617-622. [PMID: 29988094 PMCID: PMC6076999 DOI: 10.1038/s41592-018-0044-9] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/10/2018] [Indexed: 12/31/2022]
Abstract
Yeast libraries revolutionized the systematic study of cell biology. To extensively increase the number of such libraries and the type of information that can be gleaned from them, we previously devised the SWAp-Tag (SWAT) approach that enables rapid, easy and efficient creation of yeast strain collections. Here we present the construction and investigation of a full genome library of ~5500 strains carrying the SWAT NOP1promoter-GFP module at the N terminus of proteins, as well as its use in creating six additional libraries that either restore the native regulation, create an overexpression library with a Cherry tag or enable protein complementation assays from two fragments of an enzyme or fluorophore. We show methods to utilize these SWAT collections to systematically characterize the yeast proteome on multiple levels spanning protein abundance, localization, topology and interactions. Our findings demonstrate how diverse full-genome SWAT libraries facilitate obtaining insights into numerous aspects of the proteome.
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Affiliation(s)
- Uri Weill
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ido Yofe
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ehud Sass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Bram Stynen
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
| | - Dan Davidi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Janani Natarajan
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Reut Ben-Menachem
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zohar Avihou
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Omer Goldman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Nofar Harpaz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Silvia Chuartzman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Kiril Kniazev
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, AB, Canada
| | - Janina Laborenz
- Department of Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Felix Boos
- Department of Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jacqueline Kowarzyk
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Johannes M Herrmann
- Department of Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | | | - Ophry Pines
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Stephen W Michnick
- Département de Biochimie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
| | - Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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