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Santonoceto G, Jurkiewicz A, Szczesny RJ. RNA degradation in human mitochondria: the journey is not finished. Hum Mol Genet 2024; 33:R26-R33. [PMID: 38779774 DOI: 10.1093/hmg/ddae043] [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: 01/04/2024] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 05/25/2024] Open
Abstract
Mitochondria are vital organelles present in almost all eukaryotic cells. Although most of the mitochondrial proteins are nuclear-encoded, mitochondria contain their own genome, whose proper expression is necessary for mitochondrial function. Transcription of the human mitochondrial genome results in the synthesis of long polycistronic transcripts that are subsequently processed by endonucleases to release individual RNA molecules, including precursors of sense protein-encoding mRNA (mt-mRNA) and a vast amount of antisense noncoding RNAs. Because of mitochondrial DNA (mtDNA) organization, the regulation of individual gene expression at the transcriptional level is limited. Although transcription of most protein-coding mitochondrial genes occurs with the same frequency, steady-state levels of mature transcripts are different. Therefore, post-transcriptional processes are important for regulating mt-mRNA levels. The mitochondrial degradosome is a complex composed of the RNA helicase SUV3 (also known as SUPV3L1) and polynucleotide phosphorylase (PNPase, PNPT1). It is the best-characterized RNA-degrading machinery in human mitochondria, which is primarily responsible for the decay of mitochondrial antisense RNA. The mechanism of mitochondrial sense RNA decay is less understood. This review aims to provide a general picture of mitochondrial genome expression, with a particular focus on mitochondrial RNA (mtRNA) degradation.
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Affiliation(s)
- Giulia Santonoceto
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland
| | - Aneta Jurkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland
| | - Roman J Szczesny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, Warsaw 02-106, Poland
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2
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Han K, Zheng H, Yan D, Zhou H, Jia Z, Zhai Y, Wu J, Lu Y, Wu G, Rao S, Chen J, Peng J, Qi R, Yan F. Pepper mild mottle virus coat protein interacts with pepper chloroplast outer envelope membrane protein OMP24 to inhibit antiviral immunity in plants. HORTICULTURE RESEARCH 2023; 10:uhad046. [PMID: 37180740 PMCID: PMC10170409 DOI: 10.1093/hr/uhad046] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/07/2023] [Indexed: 05/16/2023]
Abstract
Pepper mild mottle virus (PMMoV) is a devastating viral pathogen of pepper (Capsicum annuum) but it is unclear whether and how peppers protect against PMMoV infection. The expression of the chloroplast outer membrane protein 24 (OMP24) of C. annuum was upregulated under PMMoV infection and it interacted with PMMoV coat protein (CP). Silencing of OMP24 in either C. annuum or Nicotiana benthamiana facilitated PMMoV infection, whereas overexpression of N. benthamiana OMP24 in transgenic plants inhibited PMMoV infection. Both C. annuum OMP24 (CaOMP24) and N. benthamiana OMP24 (NbOMP24) localized to the chloroplast and have a moderately hydrophobic transmembrane domain that is necessary for their localization. Overexpression of CaOMP24 induced stromules, perinuclear chloroplast clustering, and accumulation of reactive oxygen species (ROS), the typical defense responses of chloroplasts transferring the retrograde signaling to the nucleus to regulate resistance genes. The expression of PR1 and PR2 was also upregulated significantly in plants overexpressing OMP24. Self-interaction of OMP24 was demonstrated and was required for OMP24-mediated plant defense. Interaction with PMMoV CP interfered with the self-interaction of OMP24 and impaired OMP24-induced stromules, perinuclear chloroplast clustering and ROS accumulation. The results demonstrate the defense function of OMP24 in pepper during viral infection and suggest a possible mechanism by which PMMoV CP modulates the plant defense to facilitate viral infection.
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Affiliation(s)
- Kelei Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China
| | - Hongying Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Dankan Yan
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China
| | - Huijie Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Zhaoxing Jia
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yushan Zhai
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jian Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yuwen Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Guanwei Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Shaofei Rao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | | | - Rende Qi
- Corresponding author. E-mail: , ,
| | - Fei Yan
- Corresponding author. E-mail: , ,
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3
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Nguyen TTM, Munkhzul C, Kim J, Kyoung Y, Vianney M, Shin S, Ju S, Pham-Bui HA, Kim J, Kim JS, Lee M. In vivo profiling of the Zucchini proximal proteome in the Drosophila ovary. Development 2023; 150:286990. [PMID: 36762624 DOI: 10.1242/dev.201220] [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: 08/23/2022] [Accepted: 01/24/2023] [Indexed: 02/11/2023]
Abstract
PIWI-interacting RNAs (piRNAs) are small RNAs that play a conserved role in genome defense. The piRNA processing pathway is dependent on the sequestration of RNA precursors and protein factors in specific subcellular compartments. Therefore, a highly resolved spatial proteomics approach can help identify the local interactions and elucidate the unknown aspects of piRNA biogenesis. Herein, we performed TurboID proximity labeling to investigate the interactome of Zucchini (Zuc), a key factor of piRNA biogenesis in germline cells and somatic follicle cells of the Drosophila ovary. Quantitative mass spectrometry analysis of biotinylated proteins defined the Zuc-proximal proteome, including the well-known partners of Zuc. Many of these were enriched in the outer mitochondrial membrane (OMM), where Zuc was specifically localized. The proximal proteome of Zuc showed a distinct set of proteins compared with that of Tom20, a representative OMM protein, indicating that chaperone function-related and endomembrane system/vesicle transport proteins are previously unreported interacting partners of Zuc. The functional relevance of several candidates in piRNA biogenesis was validated by derepression of transposable elements after knockdown. Our results present potential Zuc-interacting proteins, suggesting unrecognized biological processes.
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Affiliation(s)
- Thi Thanh My Nguyen
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea
| | - Choijamts Munkhzul
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan 31151, Korea
| | - Jeesoo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Yeonju Kyoung
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Michele Vianney
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan 31151, Korea
| | - Sanghee Shin
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Seonmin Ju
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Hoang-Anh Pham-Bui
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan 31151, Korea
| | - Junhyung Kim
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan 31151, Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Mihye Lee
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan 31151, Korea
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4
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Sandoz J, Cigrang M, Zachayus A, Catez P, Donnio LM, Elly C, Nieminuszczy J, Berico P, Braun C, Alekseev S, Egly JM, Niedzwiedz W, Giglia-Mari G, Compe E, Coin F. Active mRNA degradation by EXD2 nuclease elicits recovery of transcription after genotoxic stress. Nat Commun 2023; 14:341. [PMID: 36670096 PMCID: PMC9859823 DOI: 10.1038/s41467-023-35922-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 01/06/2023] [Indexed: 01/22/2023] Open
Abstract
The transcriptional response to genotoxic stress involves gene expression arrest, followed by recovery of mRNA synthesis (RRS) after DNA repair. We find that the lack of the EXD2 nuclease impairs RRS and decreases cell survival after UV irradiation, without affecting DNA repair. Overexpression of wild-type, but not nuclease-dead EXD2, restores RRS and cell survival. We observe that UV irradiation triggers the relocation of EXD2 from mitochondria to the nucleus. There, EXD2 is recruited to chromatin where it transiently interacts with RNA Polymerase II (RNAPII) to promote the degradation of nascent mRNAs synthesized at the time of genotoxic attack. Reconstitution of the EXD2-RNAPII partnership on a transcribed DNA template in vitro shows that EXD2 primarily interacts with an elongation-blocked RNAPII and efficiently digests mRNA. Overall, our data highlight a crucial step in the transcriptional response to genotoxic attack in which EXD2 interacts with elongation-stalled RNAPII on chromatin to potentially degrade the associated nascent mRNA, allowing transcription restart after DNA repair.
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Affiliation(s)
- Jérémy Sandoz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Max Cigrang
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Amélie Zachayus
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Philippe Catez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Lise-Marie Donnio
- Institut NeuroMyogène (INMG) - Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, Lyon, France
| | - Clèmence Elly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | | | - Pietro Berico
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Cathy Braun
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Sergey Alekseev
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | | | - Giuseppina Giglia-Mari
- Institut NeuroMyogène (INMG) - Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U1315, Lyon, France
| | - Emmanuel Compe
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Frédéric Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Equipe Labellisée Ligue contre le Cancer, 2022, Strasbourg, France.
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.
- Université de Strasbourg, Strasbourg, France.
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5
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Jia X, Li Y, Wang T, Bi L, Guo L, Chen Z, Zhang X, Ye S, Chen J, Yang B, Sun B. Discrete RNA-DNA hybrid cleavage by the EXD2 exonuclease pinpoints two rate-limiting steps. EMBO J 2023; 42:e111703. [PMID: 36326837 PMCID: PMC9811613 DOI: 10.15252/embj.2022111703] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
EXD2 is a recently identified exonuclease that cleaves RNA and DNA in double-stranded (ds) forms. It thus serves as a model system for investigating the similarities and discrepancies between exoribonuclease and exodeoxyribonuclease activities and for understanding the nucleic acid (NA) unwinding-degradation coordination of an exonuclease. Here, using a single-molecule fluorescence resonance energy transfer (smFRET) approach, we show that despite stable binding to both substrates, EXD2 barely cleaves dsDNA and yet displays both exoribonuclease and exodeoxyribonuclease activities toward RNA-DNA hybrids with a cleavage preference for RNA. Unexpectedly, EXD2-mediated hybrid cleavage proceeds in a discrete stepwise pattern, wherein a sudden 4-bp duplex unwinding increment and the subsequent dwell constitute a complete hydrolysis cycle. The relatively weak exodeoxyribonuclease activity of EXD2 partially originates from frequent hybrid rewinding. Importantly, kinetic analysis and comparison of the dwell times under varied conditions reveal two rate-limiting steps of hybrid unwinding and nucleotide excision. Overall, our findings help better understand the cellular functions of EXD2, and the cyclic coupling between duplex unwinding and exonucleolytic degradation may be generalizable to other exonucleases.
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Affiliation(s)
- Xinshuo Jia
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Yanan Li
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Teng Wang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Lulu Bi
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Lijuan Guo
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Ziting Chen
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Xia Zhang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Shasha Ye
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Present address:
ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhouChina
| | - Jia Chen
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Bei Yang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghaiChina
| | - Bo Sun
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
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6
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Qin W, Myers SA, Carey DK, Carr SA, Ting AY. Spatiotemporally-resolved mapping of RNA binding proteins via functional proximity labeling reveals a mitochondrial mRNA anchor promoting stress recovery. Nat Commun 2021; 12:4980. [PMID: 34404792 PMCID: PMC8370977 DOI: 10.1038/s41467-021-25259-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
Proximity labeling (PL) with genetically-targeted promiscuous enzymes has emerged as a powerful tool for unbiased proteome discovery. By combining the spatiotemporal specificity of PL with methods for functional protein enrichment, we show that it is possible to map specific protein subclasses within distinct compartments of living cells. In particular, we develop a method to enrich subcompartment-specific RNA binding proteins (RBPs) by combining peroxidase-catalyzed PL with organic-aqueous phase separation of crosslinked protein-RNA complexes (“APEX-PS”). We use APEX-PS to generate datasets of nuclear, nucleolar, and outer mitochondrial membrane (OMM) RBPs, which can be mined for novel functions. For example, we find that the OMM RBP SYNJ2BP retains specific nuclear-encoded mitochondrial mRNAs at the OMM during translation stress, facilitating their local translation and import of protein products into the mitochondrion during stress recovery. Functional PL in general, and APEX-PS in particular, represent versatile approaches for the discovery of proteins with novel function in specific subcellular compartments. Proximity labeling is used to map and discover proteins in specific subcellular compartments. Here the authors combine APEX-mediated proximity labeling with organic-aqueous phase separation to identify nuclear, nucleolar, and outer mitochondrial membrane RNA binding proteins.
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Affiliation(s)
- Wei Qin
- Departments of Biology, Genetics, and Chemistry, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Samuel A Myers
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alice Y Ting
- Departments of Biology, Genetics, and Chemistry, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
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7
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Antonicka H, Lin ZY, Janer A, Aaltonen MJ, Weraarpachai W, Gingras AC, Shoubridge EA. A High-Density Human Mitochondrial Proximity Interaction Network. Cell Metab 2020; 32:479-497.e9. [PMID: 32877691 DOI: 10.1016/j.cmet.2020.07.017] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/24/2020] [Accepted: 07/28/2020] [Indexed: 12/17/2022]
Abstract
We used BioID, a proximity-dependent biotinylation assay with 100 mitochondrial baits from all mitochondrial sub-compartments, to create a high-resolution human mitochondrial proximity interaction network. We identified 1,465 proteins, producing 15,626 unique high-confidence proximity interactions. Of these, 528 proteins were previously annotated as mitochondrial, nearly half of the mitochondrial proteome defined by Mitocarta 2.0. Bait-bait analysis showed a clear separation of mitochondrial compartments, and correlation analysis among preys across all baits allowed us to identify functional clusters involved in diverse mitochondrial functions and to assign uncharacterized proteins to specific modules. We demonstrate that this analysis can assign isoforms of the same mitochondrial protein to different mitochondrial sub-compartments and show that some proteins may have multiple cellular locations. Outer membrane baits showed specific proximity interactions with cytosolic proteins and proteins in other organellar membranes, suggesting specialization of proteins responsible for contact site formation between mitochondria and individual organelles.
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Affiliation(s)
- Hana Antonicka
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
| | - Alexandre Janer
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Mari J Aaltonen
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Woranontee Weraarpachai
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada; Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Eric A Shoubridge
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada.
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8
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Cho KF, Branon TC, Rajeev S, Svinkina T, Udeshi ND, Thoudam T, Kwak C, Rhee HW, Lee IK, Carr SA, Ting AY. Split-TurboID enables contact-dependent proximity labeling in cells. Proc Natl Acad Sci U S A 2020; 117:12143-12154. [PMID: 32424107 PMCID: PMC7275672 DOI: 10.1073/pnas.1919528117] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proximity labeling catalyzed by promiscuous enzymes, such as TurboID, have enabled the proteomic analysis of subcellular regions difficult or impossible to access by conventional fractionation-based approaches. Yet some cellular regions, such as organelle contact sites, remain out of reach for current PL methods. To address this limitation, we split the enzyme TurboID into two inactive fragments that recombine when driven together by a protein-protein interaction or membrane-membrane apposition. At endoplasmic reticulum-mitochondria contact sites, reconstituted TurboID catalyzed spatially restricted biotinylation, enabling the enrichment and identification of >100 endogenous proteins, including many not previously linked to endoplasmic reticulum-mitochondria contacts. We validated eight candidates by biochemical fractionation and overexpression imaging. Overall, split-TurboID is a versatile tool for conditional and spatially specific proximity labeling in cells.
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Affiliation(s)
- Kelvin F Cho
- Cancer Biology Program, Stanford University, Stanford, CA 94305
| | - Tess C Branon
- Department of Genetics, Stanford University, Stanford, CA 94305
- Department of Biology, Stanford University, Stanford, CA 94305
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Sanjana Rajeev
- Department of Genetics, Stanford University, Stanford, CA 94305
| | | | | | - Themis Thoudam
- Research Institute of Aging and Metabolism, Kyungpook National University, 37224 Daegu, South Korea
| | - Chulhwan Kwak
- Department of Chemistry, Seoul National University, 08826 Seoul, South Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology, 44919 Ulsan, South Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, 08826 Seoul, South Korea
- School of Biological Sciences, Seoul National University, 08826 Seoul, South Korea
| | - In-Kyu Lee
- Research Institute of Aging and Metabolism, Kyungpook National University, 37224 Daegu, South Korea
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, 41944 Daegu, South Korea
- Leading-edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University, 41944 Daegu, South Korea
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Alice Y Ting
- Department of Genetics, Stanford University, Stanford, CA 94305;
- Department of Biology, Stanford University, Stanford, CA 94305
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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Park J, Lee SY, Jeong H, Kang MG, Van Haute L, Minczuk M, Seo JK, Jun Y, Myung K, Rhee HW, Lee C. The structure of human EXD2 reveals a chimeric 3' to 5' exonuclease domain that discriminates substrates via metal coordination. Nucleic Acids Res 2020; 47:7078-7093. [PMID: 31127291 PMCID: PMC6648332 DOI: 10.1093/nar/gkz454] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/07/2019] [Accepted: 05/10/2019] [Indexed: 12/24/2022] Open
Abstract
EXD2 (3′-5′ exonuclease domain-containing protein 2) is an essential protein with a conserved DEDDy superfamily 3′-5′ exonuclease domain. Recent research suggests that EXD2 has two potential functions: as a component of the DNA double-strand break repair machinery and as a ribonuclease for the regulation of mitochondrial translation. Herein, electron microscope imaging analysis and proximity labeling revealed that EXD2 is anchored to the mitochondrial outer membrane through a conserved N-terminal transmembrane domain, while the C-terminal region is cytosolic. Crystal structures of the exonuclease domain in complex with Mn2+/Mg2+ revealed a domain-swapped dimer in which the central α5−α7 helices are mutually crossed over, resulting in chimeric active sites. Additionally, the C-terminal segments absent in other DnaQ family exonucleases enclose the central chimeric active sites. Combined structural and biochemical analyses demonstrated that the unusual dimeric organization stabilizes the active site, facilitates discrimination between DNA and RNA substrates based on divalent cation coordination and generates a positively charged groove that binds substrates.
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Affiliation(s)
- Jumi Park
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea.,Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Song-Yi Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea.,Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Hanbin Jeong
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea.,Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Myeong-Gyun Kang
- Department of Chemistry, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Lindsey Van Haute
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Jeong Kon Seo
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Youngsoo Jun
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea.,Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Kyungjae Myung
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea.,Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Changwook Lee
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea.,Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea.,Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
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10
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van Esveld SL, Cansız-Arda Ş, Hensen F, van der Lee R, Huynen MA, Spelbrink JN. A Combined Mass Spectrometry and Data Integration Approach to Predict the Mitochondrial Poly(A) RNA Interacting Proteome. Front Cell Dev Biol 2019; 7:283. [PMID: 31803741 PMCID: PMC6873792 DOI: 10.3389/fcell.2019.00283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/01/2019] [Indexed: 01/03/2023] Open
Abstract
In order to synthesize the 13 oxidative phosphorylation proteins encoded by mammalian mtDNA, a large assortment of nuclear encoded proteins is required. These include mitoribosomal proteins and various RNA processing, modification and degradation enzymes. RNA crosslinking has been successfully applied to identify whole-cell poly(A) RNA-binding proteomes, but this method has not been adapted to identify mitochondrial poly(A) RNA-binding proteomes. Here we developed and compared two related methods that specifically enrich for mitochondrial poly(A) RNA-binding proteins and analyzed bound proteins using mass spectrometry. To obtain a catalog of the mitochondrial poly(A) RNA interacting proteome, we used Bayesian data integration to combine these two mitochondrial-enriched datasets as well as published whole-cell datasets of RNA-binding proteins with various online resources, such as mitochondrial localization from MitoCarta 2.0 and co-expression analyses. Our integrated analyses ranked the complete human proteome for the likelihood of mtRNA interaction. We show that at a specific, inclusive cut-off of the corrected false discovery rate (cFDR) of 69%, we improve the number of predicted proteins from 185 to 211 with our mass spectrometry data as input for the prediction instead of the published whole-cell datasets. The chosen cut-off determines the cFDR: the less proteins included, the lower the cFDR will be. For the top 100 proteins, inclusion of our data instead of the published whole-cell datasets improve the cFDR from 54% to 31%. We show that the mass spectrometry method most specific for mitochondrial RNA-binding proteins involves ex vivo 4-thiouridine labeling followed by mitochondrial isolation with subsequent in organello UV-crosslinking.
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Affiliation(s)
- Selma L. van Esveld
- Radboud Center for Mitochondrial Medicine, Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Şirin Cansız-Arda
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Fenna Hensen
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Robin van der Lee
- Radboud Center for Mitochondrial Medicine, Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Martijn A. Huynen
- Radboud Center for Mitochondrial Medicine, Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Johannes N. Spelbrink
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, Netherlands
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11
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Fazal FM, Han S, Parker KR, Kaewsapsak P, Xu J, Boettiger AN, Chang HY, Ting AY. Atlas of Subcellular RNA Localization Revealed by APEX-Seq. Cell 2019; 178:473-490.e26. [PMID: 31230715 PMCID: PMC6786773 DOI: 10.1016/j.cell.2019.05.027] [Citation(s) in RCA: 354] [Impact Index Per Article: 70.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/31/2018] [Accepted: 05/14/2019] [Indexed: 01/25/2023]
Abstract
We introduce APEX-seq, a method for RNA sequencing based on direct proximity labeling of RNA using the peroxidase enzyme APEX2. APEX-seq in nine distinct subcellular locales produced a nanometer-resolution spatial map of the human transcriptome as a resource, revealing extensive patterns of localization for diverse RNA classes and transcript isoforms. We uncover a radial organization of the nuclear transcriptome, which is gated at the inner surface of the nuclear pore for cytoplasmic export of processed transcripts. We identify two distinct pathways of messenger RNA localization to mitochondria, each associated with specific sets of transcripts for building complementary macromolecular machines within the organelle. APEX-seq should be widely applicable to many systems, enabling comprehensive investigations of the spatial transcriptome.
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Affiliation(s)
- Furqan M Fazal
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shuo Han
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Kevin R Parker
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pornchai Kaewsapsak
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jin Xu
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alistair N Boettiger
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Alice Y Ting
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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