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Sharma S, Fazal FM. Localization of RNAs to the mitochondria-mechanisms and functions. RNA (NEW YORK, N.Y.) 2024; 30:597-608. [PMID: 38448244 PMCID: PMC11098466 DOI: 10.1261/rna.079999.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/08/2024]
Abstract
The mammalian mitochondrial proteome comprises over 1000 proteins, with the majority translated from nuclear-encoded messenger RNAs (mRNAs). Mounting evidence suggests many of these mRNAs are localized to the outer mitochondrial membrane (OMM) in a pre- or cotranslational state. Upon reaching the mitochondrial surface, these mRNAs are locally translated to produce proteins that are cotranslationally imported into mitochondria. Here, we summarize various mechanisms cells use to localize RNAs, including transfer RNAs (tRNAs), to the OMM and recent technological advancements in the field to study these processes. While most early studies in the field were carried out in yeast, recent studies reveal RNA localization to the OMM and their regulation in higher organisms. Various factors regulate this localization process, including RNA sequence elements, RNA-binding proteins (RBPs), cytoskeletal motors, and translation machinery. In this review, we also highlight the role of RNA structures and modifications in mitochondrial RNA localization and discuss how these features can alter the binding properties of RNAs. Finally, in addition to RNAs related to mitochondrial function, RNAs involved in other cellular processes can also localize to the OMM, including those implicated in the innate immune response and piRNA biogenesis. As impairment of messenger RNA (mRNA) localization and regulation compromise mitochondrial function, future studies will undoubtedly expand our understanding of how RNAs localize to the OMM and investigate the consequences of their mislocalization in disorders, particularly neurodegenerative diseases, muscular dystrophies, and cancers.
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Affiliation(s)
- Surbhi Sharma
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, USA
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas 77030, USA
| | - Furqan M Fazal
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, USA
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas 77030, USA
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Cui M, Yamano K, Yamamoto K, Yamamoto-Imoto H, Minami S, Yamamoto T, Matsui S, Kaminishi T, Shima T, Ogura M, Tsuchiya M, Nishino K, Layden BT, Kato H, Ogawa H, Oki S, Okada Y, Isaka Y, Kosako H, Matsuda N, Yoshimori T, Nakamura S. HKDC1, a target of TFEB, is essential to maintain both mitochondrial and lysosomal homeostasis, preventing cellular senescence. Proc Natl Acad Sci U S A 2024; 121:e2306454120. [PMID: 38170752 PMCID: PMC10786298 DOI: 10.1073/pnas.2306454120] [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: 04/23/2023] [Accepted: 11/15/2023] [Indexed: 01/05/2024] Open
Abstract
Mitochondrial and lysosomal functions are intimately linked and are critical for cellular homeostasis, as evidenced by the fact that cellular senescence, aging, and multiple prominent diseases are associated with concomitant dysfunction of both organelles. However, it is not well understood how the two important organelles are regulated. Transcription factor EB (TFEB) is the master regulator of lysosomal function and is also implicated in regulating mitochondrial function; however, the mechanism underlying the maintenance of both organelles remains to be fully elucidated. Here, by comprehensive transcriptome analysis and subsequent chromatin immunoprecipitation-qPCR, we identified hexokinase domain containing 1 (HKDC1), which is known to function in the glycolysis pathway as a direct TFEB target. Moreover, HKDC1 was upregulated in both mitochondrial and lysosomal stress in a TFEB-dependent manner, and its function was critical for the maintenance of both organelles under stress conditions. Mechanistically, the TFEB-HKDC1 axis was essential for PINK1 (PTEN-induced kinase 1)/Parkin-dependent mitophagy via its initial step, PINK1 stabilization. In addition, the functions of HKDC1 and voltage-dependent anion channels, with which HKDC1 interacts, were essential for the clearance of damaged lysosomes and maintaining mitochondria-lysosome contact. Interestingly, HKDC1 regulated mitophagy and lysosomal repair independently of its prospective function in glycolysis. Furthermore, loss function of HKDC1 accelerated DNA damage-induced cellular senescence with the accumulation of hyperfused mitochondria and damaged lysosomes. Our results show that HKDC1, a factor downstream of TFEB, maintains both mitochondrial and lysosomal homeostasis, which is critical to prevent cellular senescence.
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Affiliation(s)
- Mengying Cui
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
| | - Koji Yamano
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo156-8506, Japan
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo113-8510, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
| | - Hitomi Yamamoto-Imoto
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
| | - Satoshi Minami
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
- Department of Nephrology, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
| | - Takeshi Yamamoto
- Department of Nephrology, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
| | - Sho Matsui
- Department of Nephrology, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
| | - Tatsuya Kaminishi
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka565-0871, Japan
| | - Takayuki Shima
- Department of Biochemistry, Nara Medical University, Kashihara, Nara634-8521, Japan
| | - Monami Ogura
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Megumi Tsuchiya
- Laboratory of Nuclear Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Kohei Nishino
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima770-8503, Japan
| | - Brian T. Layden
- Division of Endocrinology, Diabetes, and Metabolism, University of Illinois Chicago, Chicago, IL60612
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL60612
| | - Hisakazu Kato
- Department of Medical Biochemistry, Graduate School of Medicine/Frontier Bioscience, Osaka University, Suita, Osaka565-0871, Japan
| | - Hidesato Ogawa
- Laboratory of Nuclear Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Shinya Oki
- Department of Drug Discovery Medicine, Graduate School of Medicine, Kyoto University, Kyoto606-8501, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka565-0871, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center, World Premier International Research Center (WPI-IFReC), Osaka University, Suita, Osaka565-0871, Japan
| | - Yoshitaka Isaka
- Department of Nephrology, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima770-8503, Japan
| | - Noriyuki Matsuda
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo156-8506, Japan
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo113-8510, Japan
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Osaka565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka565-0871, Japan
- Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Shuhei Nakamura
- Department of Biochemistry, Nara Medical University, Kashihara, Nara634-8521, Japan
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Busch JD, Fielden LF, Pfanner N, Wiedemann N. Mitochondrial protein transport: Versatility of translocases and mechanisms. Mol Cell 2023; 83:890-910. [PMID: 36931257 DOI: 10.1016/j.molcel.2023.02.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 03/17/2023]
Abstract
Biogenesis of mitochondria requires the import of approximately 1,000 different precursor proteins into and across the mitochondrial membranes. Mitochondria exhibit a wide variety of mechanisms and machineries for the translocation and sorting of precursor proteins. Five major import pathways that transport proteins to their functional intramitochondrial destination have been elucidated; these pathways range from the classical amino-terminal presequence-directed pathway to pathways using internal or even carboxy-terminal targeting signals in the precursors. Recent studies have provided important insights into the structural organization of membrane-embedded preprotein translocases of mitochondria. A comparison of the different translocases reveals the existence of at least three fundamentally different mechanisms: two-pore-translocase, β-barrel switching, and transport cavities open to the lipid bilayer. In addition, translocases are physically engaged in dynamic interactions with respiratory chain complexes, metabolite transporters, quality control factors, and machineries controlling membrane morphology. Thus, mitochondrial preprotein translocases are integrated into multi-functional networks of mitochondrial and cellular machineries.
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Affiliation(s)
- Jakob D Busch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Laura F Fielden
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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