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Rubalcava-Gracia D, Bubb K, Levander F, Burr SP, August AV, Chinnery PF, Koolmeister C, Larsson NG. LRPPRC and SLIRP synergize to maintain sufficient and orderly mammalian mitochondrial translation. Nucleic Acids Res 2024:gkae662. [PMID: 39087558 DOI: 10.1093/nar/gkae662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 07/15/2024] [Accepted: 07/18/2024] [Indexed: 08/02/2024] Open
Abstract
In mammals, the leucine-rich pentatricopeptide repeat protein (LRPPRC) and the stem-loop interacting RNA-binding protein (SLIRP) form a complex in the mitochondrial matrix that is required throughout the life cycle of most mitochondrial mRNAs. Although pathogenic mutations in the LRPPRC and SLIRP genes cause devastating human mitochondrial diseases, the in vivo function of the corresponding proteins is incompletely understood. We show here that loss of SLIRP in mice causes a decrease of complex I levels whereas other OXPHOS complexes are unaffected. We generated knock-in mice to study the in vivo interdependency of SLIRP and LRPPRC by mutating specific amino acids necessary for protein complex formation. When protein complex formation is disrupted, LRPPRC is partially degraded and SLIRP disappears. Livers from Lrpprc knock-in mice had impaired mitochondrial translation except for a marked increase in the synthesis of ATP8. Furthermore, the introduction of a heteroplasmic pathogenic mtDNA mutation (m.C5024T of the tRNAAla gene) into Slirp knockout mice causes an additive effect on mitochondrial translation leading to embryonic lethality and reduced growth of mouse embryonic fibroblasts. To summarize, we report that the LRPPRC/SLIRP protein complex is critical for maintaining normal complex I levels and that it also coordinates mitochondrial translation in a tissue-specific manner.
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Affiliation(s)
- Diana Rubalcava-Gracia
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kristina Bubb
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Levander
- Department en Immunotechnology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Stephen P Burr
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit,University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Amelie V August
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit,University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Camilla Koolmeister
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nils-Göran Larsson
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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2
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Tan M, Zhao Y, Ren L, Li C, Cai J, He B. Methionine Improves Boar Sperm Quality by Promoting Mitochondrial Translation during Liquid Storage. Animals (Basel) 2024; 14:2227. [PMID: 39123753 PMCID: PMC11310967 DOI: 10.3390/ani14152227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/26/2024] [Accepted: 07/27/2024] [Indexed: 08/12/2024] Open
Abstract
Boar sperm quality serves as an important indicator of reproductive efficiency, playing a direct role in enhancing the output of livestock production. It has been demonstrated that mitochondrial protein translation is present in sperm and plays a crucial role in regulating sperm motility, capacitation and in vitro fertilization rate. The present study aimed to determine whether methionine supplementation enhances mitochondrial translation in boar sperm, thereby improving sperm quality. The results showed a significant elevation in the abundance of mitochondrial methionyl-tRNA formyltransferase (MTFMT), a crucial enzyme for mitochondrial protein translation, and mitochondrial DNA-encoded cytochrome c oxidase subunit 1 (COX1) in boar sperm exhibiting high motility. Both amino acids and methionine supplementation significantly enhanced boar sperm motility during storage. Moreover, methionine supplementation mitigates the loss of acrosomal integrity, enhances the expression of COX1, and boosts mitochondrial activity. Furthermore, the positive impact of methionine was negated in the presence of the mitochondrial translation inhibitor chloramphenicol. Together, these findings suggest that boar sperm may utilize methionine as a protein translation substrate to enhance sperm motility by stimulating mitochondrial protein translation. The supplementation of methionine may enhance the quality of boar sperm, thereby providing guidance for the optimization of diluent formulations for liquid storage and the identification of physiological regulators that regulate sperm motility.
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Affiliation(s)
- Meiling Tan
- Key Laboratory of Animal Physiology & Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (M.T.); (Y.Z.); (L.R.); (C.L.); (J.C.)
| | - Yuting Zhao
- Key Laboratory of Animal Physiology & Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (M.T.); (Y.Z.); (L.R.); (C.L.); (J.C.)
| | - Li Ren
- Key Laboratory of Animal Physiology & Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (M.T.); (Y.Z.); (L.R.); (C.L.); (J.C.)
| | - Chenxuan Li
- Key Laboratory of Animal Physiology & Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (M.T.); (Y.Z.); (L.R.); (C.L.); (J.C.)
| | - Jiangxue Cai
- Key Laboratory of Animal Physiology & Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (M.T.); (Y.Z.); (L.R.); (C.L.); (J.C.)
| | - Bin He
- Key Laboratory of Animal Physiology & Biochemistry, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (M.T.); (Y.Z.); (L.R.); (C.L.); (J.C.)
- MOE Joint International Research Laboratory of Animal Health & Food Safety, Nanjing Agricultural University, Nanjing 210095, China
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3
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Hasegawa K, Tamaki M, Sakamaki Y, Wakino S. Nmnat1 Deficiency Causes Mitoribosome Excess in Diabetic Nephropathy Mediated by Transcriptional Repressor HIC1. Int J Mol Sci 2024; 25:6384. [PMID: 38928090 PMCID: PMC11204038 DOI: 10.3390/ijms25126384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/31/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Nicotinamide adenine dinucleotide (NAD) is involved in renal physiology and is synthesized by nicotinamide mononucleotide adenylyltransferase (NMNAT). NMNAT exists as three isoforms, namely, NMNAT1, NMNAT2, and NMNAT3, encoded by Nmnat1, Nmnat2, and Nmnat3, respectively. In diabetic nephropathy (DN), NAD levels decrease, aggravating renal fibrosis. Conversely, sodium-glucose cotransporter-2 inhibitors increase NAD levels, mitigating renal fibrosis. In this regard, renal NAD synthesis has recently gained attention. However, the renal role of Nmnat in DN remains uncertain. Therefore, we investigated the role of Nmnat by establishing genetically engineered mice. Among the three isoforms, NMNAT1 levels were markedly reduced in the proximal tubules (PTs) of db/db mice. We examined the phenotypic changes in PT-specific Nmnat1 conditional knockout (CKO) mice. In CKO mice, Nmnat1 expression in PTs was downregulated when the tubules exhibited albuminuria, peritubular type IV collagen deposition, and mitochondrial ribosome (mitoribosome) excess. In CKO mice, Nmnat1 deficiency-induced mitoribosome excess hindered mitoribosomal translation of mitochondrial inner membrane-associated oxidative phosphorylation complex I (CI), CIII, CIV, and CV proteins and mitoribosomal dysfunction. Furthermore, the expression of hypermethylated in cancer 1, a transcription repressor, was downregulated in CKO mice, causing mitoribosome excess. Nmnat1 overexpression preserved mitoribosomal function, suggesting its protective role in DN.
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Affiliation(s)
- Kazuhiro Hasegawa
- Department of Nephrology, Tokushima University Graduate School of Biomedical Sciences, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan; (M.T.); (S.W.)
| | - Masanori Tamaki
- Department of Nephrology, Tokushima University Graduate School of Biomedical Sciences, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan; (M.T.); (S.W.)
| | - Yusuke Sakamaki
- Department of Internal Medicine, Tokyo Dental College Ichikawa General Hospital, Chiba 272-8583, Japan;
| | - Shu Wakino
- Department of Nephrology, Tokushima University Graduate School of Biomedical Sciences, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan; (M.T.); (S.W.)
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4
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Hughes LA, Rackham O, Filipovska A. Illuminating mitochondrial translation through mouse models. Hum Mol Genet 2024; 33:R61-R79. [PMID: 38779771 PMCID: PMC11112386 DOI: 10.1093/hmg/ddae020] [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: 11/10/2023] [Revised: 01/22/2024] [Accepted: 01/31/2024] [Indexed: 05/25/2024] Open
Abstract
Mitochondria are hubs of metabolic activity with a major role in ATP conversion by oxidative phosphorylation (OXPHOS). The mammalian mitochondrial genome encodes 11 mRNAs encoding 13 OXPHOS proteins along with 2 rRNAs and 22 tRNAs, that facilitate their translation on mitoribosomes. Maintaining the internal production of core OXPHOS subunits requires modulation of the mitochondrial capacity to match the cellular requirements and correct insertion of particularly hydrophobic proteins into the inner mitochondrial membrane. The mitochondrial translation system is essential for energy production and defects result in severe, phenotypically diverse diseases, including mitochondrial diseases that typically affect postmitotic tissues with high metabolic demands. Understanding the complex mechanisms that underlie the pathologies of diseases involving impaired mitochondrial translation is key to tailoring specific treatments and effectively targeting the affected organs. Disease mutations have provided a fundamental, yet limited, understanding of mitochondrial protein synthesis, since effective modification of the mitochondrial genome has proven challenging. However, advances in next generation sequencing, cryoelectron microscopy, and multi-omic technologies have revealed unexpected and unusual features of the mitochondrial protein synthesis machinery in the last decade. Genome editing tools have generated unique models that have accelerated our mechanistic understanding of mitochondrial translation and its physiological importance. Here we review the most recent mouse models of disease pathogenesis caused by defects in mitochondrial protein synthesis and discuss their value for preclinical research and therapeutic development.
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Affiliation(s)
- Laetitia A Hughes
- Telethon Kids Institute, Northern Entrance, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands, WA 6009, Australia
- Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, 35 Stirling Highway, Crawley, WA 6009, The University of Western Australia, Crawley, WA 6009, Australia
| | - Oliver Rackham
- Telethon Kids Institute, Northern Entrance, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands, WA 6009, Australia
- Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, 35 Stirling Highway, Crawley, WA 6009, The University of Western Australia, Crawley, WA 6009, Australia
- Curtin Medical School, Curtin University, Kent Street, Bentley, WA 6102, Australia
- Curtin Health Innovation Research Institute, Curtin University, Kent Street, Bentley, WA 6102, Australia
| | - Aleksandra Filipovska
- Telethon Kids Institute, Northern Entrance, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands, WA 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, 35 Stirling Highway, Crawley, WA 6009, The University of Western Australia, Crawley, WA 6009, Australia
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 19 Innovation Walk, Clayton, Clayton, VIC 3168, Australia
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5
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Wang Y, Jin T, Huang Y. Sls1 and Mtf2 mediate the assembly of the Mrh5C complex required for activation of cox1 mRNA translation. J Biol Chem 2024; 300:107176. [PMID: 38499152 PMCID: PMC11015131 DOI: 10.1016/j.jbc.2024.107176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/06/2024] [Accepted: 03/09/2024] [Indexed: 03/20/2024] Open
Abstract
Mitochondrial translation depends on mRNA-specific activators. In Schizosaccharomyces pombe, DEAD-box protein Mrh5, pentatricopeptide repeat (PPR) protein Ppr4, Mtf2, and Sls1 form a stable complex (designated Mrh5C) required for translation of mitochondrial DNA (mtDNA)-encoded cox1 mRNA, the largest subunit of the cytochrome c oxidase complex. However, how Mrh5C is formed and what role Mrh5C plays in cox1 mRNA translation have not been reported. To address these questions, we investigated the role of individual Mrh5C subunits in the assembly and function of Mrh5C. Our results revealed that Mtf2 and Sls1 form a subcomplex that serves as a scaffold to bring Mrh5 and Ppr4 together. Mrh5C binds to the small subunit of the mitoribosome (mtSSU), but each subunit could not bind to the mtSSU independently. Importantly, Mrh5C is required for the association of cox1 mRNA with the mtSSU. Finally, we investigated the importance of the signature DEAD-box in Mrh5. We found that the DEAD-box of Mrh5 is required for the association of Mrh5C and cox1 mRNA with the mtSSU. Unexpectedly, this motif is also required for the interaction of Mrh5 with other Mrh5C subunits. Altogether, our results suggest that Mrh5 and Ppr4 cooperate in activating the translation of cox1 mRNA. Our results also suggest that Mrh5C activates the translation of cox1 mRNA by promoting the recruitment of cox1 mRNA to the mtSSU.
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Affiliation(s)
- Yirong Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Nanjing Normal University, Nanjing, China
| | - Ting Jin
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Nanjing Normal University, Nanjing, China
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Nanjing Normal University, Nanjing, China.
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6
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Lee RG, Rudler DL, Raven SA, Peng L, Chopin A, Moh ESX, McCubbin T, Siira SJ, Fagan SV, DeBono NJ, Stentenbach M, Browne J, Rackham FF, Li J, Simpson KJ, Marcellin E, Packer NH, Reid GE, Padman BS, Rackham O, Filipovska A. Quantitative subcellular reconstruction reveals a lipid mediated inter-organelle biogenesis network. Nat Cell Biol 2024; 26:57-71. [PMID: 38129691 DOI: 10.1038/s41556-023-01297-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 10/18/2023] [Indexed: 12/23/2023]
Abstract
The structures and functions of organelles in cells depend on each other but have not been systematically explored. We established stable knockout cell lines of peroxisomal, Golgi and endoplasmic reticulum genes identified in a whole-genome CRISPR knockout screen for inducers of mitochondrial biogenesis stress, showing that defects in peroxisome, Golgi and endoplasmic reticulum metabolism disrupt mitochondrial structure and function. Our quantitative total-organelle profiling approach for focussed ion beam scanning electron microscopy revealed in unprecedented detail that specific organelle dysfunctions precipitate multi-organelle biogenesis defects, impair mitochondrial morphology and reduce respiration. Multi-omics profiling showed a unified proteome response and global shifts in lipid and glycoprotein homeostasis that are elicited when organelle biogenesis is compromised, and that the resulting mitochondrial dysfunction can be rescued with precursors for ether-glycerophospholipid metabolic pathways. This work defines metabolic and morphological interactions between organelles and how their perturbation can cause disease.
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Affiliation(s)
- Richard G Lee
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Danielle L Rudler
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Samuel A Raven
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
- Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, Australia
| | - Liuyu Peng
- School of Chemistry, The University of Melbourne, Parkville, Victoria, Australia
| | - Anaëlle Chopin
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Edward S X Moh
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Tim McCubbin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Queensland, Australia
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Queensland, Australia
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Samuel V Fagan
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Nicholas J DeBono
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Maike Stentenbach
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Jasmin Browne
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Filip F Rackham
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Ji Li
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Kaylene J Simpson
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, Victoria, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Queensland, Australia
- ARC Centre of Excellence in Synthetic Biology, The University of Queensland, Queensland, Australia
| | - Nicolle H Packer
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Gavin E Reid
- School of Chemistry, The University of Melbourne, Parkville, Victoria, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, Victoria, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Benjamin S Padman
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, Western Australia, Australia
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Western Australia, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
- Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, Australia
| | - Aleksandra Filipovska
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia, Australia.
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, Western Australia, Australia.
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Richman TR, Ermer JA, Baker J, Siira SJ, Kile BT, Linden MD, Rackham O, Filipovska A. Mitochondrial gene expression is required for platelet function and blood clotting. Cell Rep 2023; 42:113312. [PMID: 37889747 DOI: 10.1016/j.celrep.2023.113312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/20/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Platelets are anucleate blood cells that contain mitochondria and regulate blood clotting in response to injury. Mitochondria contain their own gene expression machinery that relies on nuclear-encoded factors for the biogenesis of the oxidative phosphorylation system to produce energy required for thrombosis. The autonomy of the mitochondrial gene expression machinery from the nucleus is unclear, and platelets provide a valuable model to understand its importance in anucleate cells. Here, we conditionally delete Elac2, Ptcd1, or Mtif3 in platelets, which are essential for mitochondrial gene expression at the level of RNA processing, stability, or translation, respectively. Loss of ELAC2, PTCD1, or MTIF3 leads to increased megakaryocyte ploidy, elevated circulating levels of reticulated platelets, thrombocytopenia, and consequent extended bleeding time. Impaired mitochondrial gene expression reduces agonist-induced platelet activation. Transcriptomic and proteomic analyses show that mitochondrial gene expression is required for fibrinolysis, hemostasis, and blood coagulation in response to injury.
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Affiliation(s)
- Tara R Richman
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia; ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA 6009, Australia; Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA 6009, Australia; Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, Australia
| | - Judith A Ermer
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia; ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA 6009, Australia; Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Jessica Baker
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia; ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA 6009, Australia; Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA 6009, Australia; Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, Australia
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia; ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA 6009, Australia; Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA 6009, Australia; Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, Australia
| | - Benjamin T Kile
- Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Matthew D Linden
- Pathology and Laboratory Science, The University of Western Australia, Perth, WA, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia; ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA 6009, Australia; Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, Australia; Curtin Medical School, Curtin University, Bentley, WA 6102, Australia; Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
| | - Aleksandra Filipovska
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA 6009, Australia; Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, Australia.
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8
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Baleva MV, Piunova UE, Chicherin IV, Levitskii SA, Kamenski PA. Diversity and Evolution of Mitochondrial Translation Apparatus. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1832-1843. [PMID: 38105202 DOI: 10.1134/s0006297923110135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 12/19/2023]
Abstract
The evolution of mitochondria has proceeded independently in different eukaryotic lines, which is reflected in the diversity of mitochondrial genomes and mechanisms of their expression in eukaryotic species. Mitochondria have lost most of bacterial ancestor genes by transferring them to the nucleus or eliminating them. However, mitochondria of almost all eukaryotic cells still retain relatively small genomes, as well as their replication, transcription, and translation apparatuses. The dependence on the nuclear genome, specific features of mitochondrial transcripts, and synthesis of highly hydrophobic membrane proteins in the mitochondria have led to significant changes in the translation apparatus inherited from the bacterial ancestor, which retained the basic structure necessary for protein synthesis but became more specialized and labile. In this review, we discuss specific properties of translation initiation in the mitochondria and how the evolution of mitochondria affected the functions of main factors initiating protein biosynthesis in these organelles.
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Affiliation(s)
- Mariya V Baleva
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Ulyana E Piunova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Ivan V Chicherin
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Sergey A Levitskii
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Piotr A Kamenski
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
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9
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Khawaja A, Cipullo M, Krüger A, Rorbach J. Insights into mitoribosomal biogenesis from recent structural studies. Trends Biochem Sci 2023; 48:629-641. [PMID: 37169615 DOI: 10.1016/j.tibs.2023.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 05/13/2023]
Abstract
The mitochondrial ribosome (mitoribosome) is a multicomponent machine that has unique structural features. Biogenesis of the human mitoribosome includes correct maturation and folding of the mitochondria-encoded RNA components (12S and 16S mt-rRNAs, and mt-tRNAVal) and their assembly together with 82 nucleus-encoded mitoribosomal proteins. This complex process requires the coordinated action of multiple assembly factors. Recent advances in single-particle cryo-electron microscopy (cryo-EM) have provided detailed insights into the specific functions of several mitoribosome assembly factors and have defined their timing. In this review we summarize mitoribosomal small (mtSSU) and large subunit (mtLSU) biogenesis based on structural findings, and we discuss potential crosstalk between mtSSU and mtLSU assembly pathways as well as coordination between mitoribosome biogenesis and other processes involved in mitochondrial gene expression.
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Affiliation(s)
- Anas Khawaja
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65 Solna, Sweden; Max Planck Institute Biology of Ageing, Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65 Solna, Sweden; Max Planck Institute Biology of Ageing, Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Annika Krüger
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65 Solna, Sweden; Max Planck Institute Biology of Ageing, Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65 Solna, Sweden; Max Planck Institute Biology of Ageing, Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.
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10
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Donati G, Nicoli P, Verrecchia A, Vallelonga V, Croci O, Rodighiero S, Audano M, Cassina L, Ghsein A, Binelli G, Boletta A, Mitro N, Amati B. Oxidative stress enhances the therapeutic action of a respiratory inhibitor in MYC-driven lymphoma. EMBO Mol Med 2023:e16910. [PMID: 37158102 DOI: 10.15252/emmm.202216910] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 04/13/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023] Open
Abstract
MYC is a key oncogenic driver in multiple tumor types, but concomitantly endows cancer cells with a series of vulnerabilities that provide opportunities for targeted pharmacological intervention. For example, drugs that suppress mitochondrial respiration selectively kill MYC-overexpressing cells. Here, we unravel the mechanistic basis for this synthetic lethal interaction and exploit it to improve the anticancer effects of the respiratory complex I inhibitor IACS-010759. In a B-lymphoid cell line, ectopic MYC activity and treatment with IACS-010759 added up to induce oxidative stress, with consequent depletion of reduced glutathione and lethal disruption of redox homeostasis. This effect could be enhanced either with inhibitors of NADPH production through the pentose phosphate pathway, or with ascorbate (vitamin C), known to act as a pro-oxidant at high doses. In these conditions, ascorbate synergized with IACS-010759 to kill MYC-overexpressing cells in vitro and reinforced its therapeutic action against human B-cell lymphoma xenografts. Hence, complex I inhibition and high-dose ascorbate might improve the outcome of patients affected by high-grade lymphomas and potentially other MYC-driven cancers.
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Affiliation(s)
- Giulio Donati
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Paola Nicoli
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | | | | | - Ottavio Croci
- Center for Genomic Science of IIT@SEMM, Milan, Italy
| | | | - Matteo Audano
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Laura Cassina
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Aya Ghsein
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Giorgio Binelli
- Dipartimento di Biotecnologie e Scienze della Vita, Università dell'Insubria, Varese, Italy
| | | | - Nico Mitro
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Bruno Amati
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
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11
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Saurer M, Leibundgut M, Nadimpalli HP, Scaiola A, Schönhut T, Lee RG, Siira SJ, Rackham O, Dreos R, Lenarčič T, Kummer E, Gatfield D, Filipovska A, Ban N. Molecular basis of translation termination at noncanonical stop codons in human mitochondria. Science 2023; 380:531-536. [PMID: 37141370 DOI: 10.1126/science.adf9890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the standard genetic code, including the reassignment of two arginine codons to stop codons. The protein required for translation termination at these noncanonical stop codons to release the newly synthesized polypeptides is not currently known. In this study, we used gene editing and ribosomal profiling in combination with cryo-electron microscopy to establish that mitochondrial release factor 1 (mtRF1) detects noncanonical stop codons in human mitochondria by a previously unknown mechanism of codon recognition. We discovered that binding of mtRF1 to the decoding center of the ribosome stabilizes a highly unusual conformation in the messenger RNA in which the ribosomal RNA participates in specific recognition of the noncanonical stop codons.
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Affiliation(s)
- Martin Saurer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Alain Scaiola
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Tanja Schönhut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Richard G Lee
- Harry Perkins Institute of Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, The University of Western Australia, Nedlands, Western Australia 6009, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, Western Australia, Australia
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, The University of Western Australia, Nedlands, Western Australia 6009, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, The University of Western Australia, Nedlands, Western Australia 6009, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, Western Australia, Australia
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia 6102, Australia
| | - René Dreos
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Tea Lenarčič
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Eva Kummer
- Novo Nordisk Foundation Center for Protein Research, Protein Structure and Function Program, Blegdamsvej 3B, 2200 København N, Denmark
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, The University of Western Australia, Nedlands, Western Australia 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, The University of Western Australia, Nedlands, Western Australia 6009, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, Western Australia, Australia
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
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12
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Stentenbach M, Ermer JA, Rudler DL, Perks KL, Raven SA, Lee RG, McCubbin T, Marcellin E, Siira SJ, Rackham O, Filipovska A. Multi-omic profiling reveals an RNA processing rheostat that predisposes to prostate cancer. EMBO Mol Med 2023:e17463. [PMID: 37093546 DOI: 10.15252/emmm.202317463] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 04/25/2023] Open
Abstract
Prostate cancer is the most commonly diagnosed malignancy and the third leading cause of cancer deaths. GWAS have identified variants associated with prostate cancer susceptibility; however, mechanistic and functional validation of these mutations is lacking. We used CRISPR-Cas9 genome editing to introduce a missense variant identified in the ELAC2 gene, which encodes a dually localised nuclear and mitochondrial RNA processing enzyme, into the mouse Elac2 gene as well as to generate a prostate-specific knockout of Elac2. These mutations caused enlargement and inflammation of the prostate and nodule formation. The Elac2 variant or knockout mice on the background of the transgenic adenocarcinoma of the mouse prostate (TRAMP) model show that Elac2 mutation with a secondary genetic insult exacerbated the onset and progression of prostate cancer. Multiomic profiling revealed defects in energy metabolism that activated proinflammatory and tumorigenic pathways as a consequence of impaired noncoding RNA processing and reduced protein synthesis. Our physiologically relevant models show that the ELAC2 variant is a predisposing factor for prostate cancer and identify changes that underlie the pathogenesis of this cancer.
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Affiliation(s)
- Maike Stentenbach
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Judith A Ermer
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Danielle L Rudler
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Kara L Perks
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Samuel A Raven
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Richard G Lee
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Tim McCubbin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Curtin Medical School, Curtin University, Bentley, WA, Australia
- Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA, Australia
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13
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Hughes LA, Rudler DL, Siira SJ, McCubbin T, Raven SA, Browne JM, Ermer JA, Rientjes J, Rodger J, Marcellin E, Rackham O, Filipovska A. Copy number variation in tRNA isodecoder genes impairs mammalian development and balanced translation. Nat Commun 2023; 14:2210. [PMID: 37072429 PMCID: PMC10113395 DOI: 10.1038/s41467-023-37843-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/29/2023] [Indexed: 04/20/2023] Open
Abstract
The number of tRNA isodecoders has increased dramatically in mammals, but the specific molecular and physiological reasons for this expansion remain elusive. To address this fundamental question we used CRISPR editing to knockout the seven-membered phenylalanine tRNA gene family in mice, both individually and combinatorially. Using ATAC-Seq, RNA-seq, ribo-profiling and proteomics we observed distinct molecular consequences of single tRNA deletions. We show that tRNA-Phe-1-1 is required for neuronal function and its loss is partially compensated by increased expression of other tRNAs but results in mistranslation. In contrast, the other tRNA-Phe isodecoder genes buffer the loss of each of the remaining six tRNA-Phe genes. In the tRNA-Phe gene family, the expression of at least six tRNA-Phe alleles is required for embryonic viability and tRNA-Phe-1-1 is most important for development and survival. Our results reveal that the multi-copy configuration of tRNA genes is required to buffer translation and viability in mammals.
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Affiliation(s)
- Laetitia A Hughes
- Harry Perkins Institute of Medical Research, Perth, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Danielle L Rudler
- Harry Perkins Institute of Medical Research, Perth, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research, Perth, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Tim McCubbin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Samuel A Raven
- Harry Perkins Institute of Medical Research, Perth, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Jasmin M Browne
- Harry Perkins Institute of Medical Research, Perth, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Judith A Ermer
- Harry Perkins Institute of Medical Research, Perth, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Jeanette Rientjes
- Monash Genome Modification Platform, Monash University, 35 Rainforest Walk, Clayton, VIC, 3800, Australia
| | - Jennifer Rodger
- School of Biological Sciences (Physiology), The University of Western Australia, Crawley, WA, 6009, Australia
- Perron Institute for Neurological and Translational Sciences, Nedlands, WA, 6009, Australia
| | - Esteban Marcellin
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, 4072, QLD, Australia
- Queensland Metabolomics and Proteomics (Q-MAP), The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, Perth, WA, Australia.
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia.
- Curtin Medical School, Curtin University, Bentley, WA, 6102, Australia.
- Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, 6102, Australia.
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, Australia.
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, Perth, WA, Australia.
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia.
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia.
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, Australia.
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14
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Huang M, Coral D, Ardalani H, Spegel P, Saadat A, Claussnitzer M, Mulder H, Franks PW, Kalamajski S. Identification of a weight loss-associated causal eQTL in MTIF3 and the effects of MTIF3 deficiency on human adipocyte function. eLife 2023; 12:84168. [PMID: 36876906 PMCID: PMC10023155 DOI: 10.7554/elife.84168] [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: 10/12/2022] [Accepted: 03/05/2023] [Indexed: 03/07/2023] Open
Abstract
Genetic variation at the MTIF3 (Mitochondrial Translational Initiation Factor 3) locus has been robustly associated with obesity in humans, but the functional basis behind this association is not known. Here, we applied luciferase reporter assay to map potential functional variants in the haplotype block tagged by rs1885988 and used CRISPR-Cas9 to edit the potential functional variants to confirm the regulatory effects on MTIF3 expression. We further conducted functional studies on MTIF3-deficient differentiated human white adipocyte cell line (hWAs-iCas9), generated through inducible expression of CRISPR-Cas9 combined with delivery of synthetic MTIF3-targeting guide RNA. We demonstrate that rs67785913-centered DNA fragment (in LD with rs1885988, r2 > 0.8) enhances transcription in a luciferase reporter assay, and CRISPR-Cas9-edited rs67785913 CTCT cells show significantly higher MTIF3 expression than rs67785913 CT cells. Perturbed MTIF3 expression led to reduced mitochondrial respiration and endogenous fatty acid oxidation, as well as altered expression of mitochondrial DNA-encoded genes and proteins, and disturbed mitochondrial OXPHOS complex assembly. Furthermore, after glucose restriction, the MTIF3 knockout cells retained more triglycerides than control cells. This study demonstrates an adipocyte function-specific role of MTIF3, which originates in the maintenance of mitochondrial function, providing potential explanations for why MTIF3 genetic variation at rs67785913 is associated with body corpulence and response to weight loss interventions.
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Affiliation(s)
- Mi Huang
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Clinical Research Centre, Lund UniversityMalmöSweden
| | - Daniel Coral
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Clinical Research Centre, Lund UniversityMalmöSweden
| | - Hamidreza Ardalani
- Department of Chemistry, Centre for Analysis and Synthesis, Lund UniversityLundSweden
| | - Peter Spegel
- Department of Chemistry, Centre for Analysis and Synthesis, Lund UniversityLundSweden
| | - Alham Saadat
- Metabolism Program, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Melina Claussnitzer
- Metabolism Program, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Hindrik Mulder
- Unit of Molecular Metabolism, Department of Clinical Sciences, Clinical Research Centre, Lund UniversityMalmöSweden
| | - Paul W Franks
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Clinical Research Centre, Lund UniversityMalmöSweden
- Department of Nutrition, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Sebastian Kalamajski
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Clinical Research Centre, Lund UniversityMalmöSweden
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15
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Remes C, Khawaja A, Pearce SF, Dinan AM, Gopalakrishna S, Cipullo M, Kyriakidis V, Zhang J, Dopico XC, Yukhnovets O, Atanassov I, Firth AE, Cooperman B, Rorbach J. Translation initiation of leaderless and polycistronic transcripts in mammalian mitochondria. Nucleic Acids Res 2023; 51:891-907. [PMID: 36629253 PMCID: PMC9881170 DOI: 10.1093/nar/gkac1233] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 11/11/2022] [Accepted: 12/09/2022] [Indexed: 01/12/2023] Open
Abstract
The synthesis of mitochondrial OXPHOS complexes is central to cellular metabolism, yet many molecular details of mitochondrial translation remain elusive. It has been commonly held view that translation initiation in human mitochondria proceeded in a manner similar to bacterial systems, with the mitoribosomal small subunit bound to the initiation factors, mtIF2 and mtIF3, along with initiator tRNA and an mRNA. However, unlike in bacteria, most human mitochondrial mRNAs lack 5' leader sequences that can mediate small subunit binding, raising the question of how leaderless mRNAs are recognized by mitoribosomes. By using novel in vitro mitochondrial translation initiation assays, alongside biochemical and genetic characterization of cellular knockouts of mitochondrial translation factors, we describe unique features of translation initiation in human mitochondria. We show that in vitro, leaderless mRNA transcripts can be loaded directly onto assembled 55S mitoribosomes, but not onto the mitoribosomal small subunit (28S), in a manner that requires initiator fMet-tRNAMet binding. In addition, we demonstrate that in human cells and in vitro, mtIF3 activity is not required for translation of leaderless mitochondrial transcripts but is essential for translation of ATP6 in the case of the bicistronic ATP8/ATP6 transcript. Furthermore, we show that mtIF2 is indispensable for mitochondrial protein synthesis. Our results demonstrate an important evolutionary divergence of the mitochondrial translation system and further our fundamental understanding of a process central to eukaryotic metabolism.
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Affiliation(s)
- Cristina Remes
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anas Khawaja
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 17165, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Sarah F Pearce
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 17165, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Adam M Dinan
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Shreekara Gopalakrishna
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 17165, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 17165, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Vasileios Kyriakidis
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 17165, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Jingdian Zhang
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 17165, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor & Cell Biology, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Olessya Yukhnovets
- RWTH Aachen, I. Physikalisches Institut (IA), Aachen, Germany
- Forschungszentrum Jülich, Institute of Complex Systems ICS-5, Jülich, Germany
| | - Ilian Atanassov
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Andrew E Firth
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Barry Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 17165, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
- STIAS: Stellenbosch Institute for Advanced Study at Stellenbosch University, Marais Rd, Stellenbosch 7600, South Africa
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16
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Chrzanowska-Lightowlers ZM, Lightowlers RN. Translation in Mitochondrial Ribosomes. Methods Mol Biol 2023; 2661:53-72. [PMID: 37166631 DOI: 10.1007/978-1-0716-3171-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Mitochondrial protein synthesis is essential for the life of aerobic eukaryotes. Without it, oxidative phosphorylation cannot be coupled. Evolution has shaped a battery of factors and machinery that are key to production of just a handful of critical proteins. In this general concept chapter, we attempt to briefly summarize our current knowledge of the overall process in mitochondria from a variety of species, breaking this down to the four parts of translation: initiation, elongation, termination, and recycling. Where appropriate, we highlight differences between species and emphasize gaps in our understanding. Excitingly, with the current revolution in cryoelectron microscopy and mitochondrial genome editing, it is highly likely that many of these gaps will be resolved in the near future. However, the absence of a faithful in vitro reconstituted system to study mitochondrial translation is still problematic.
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Affiliation(s)
- Zofia M Chrzanowska-Lightowlers
- Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK.
| | - Robert N Lightowlers
- Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK
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17
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Rudler DL, Siira SJ, Rackham O, Filipovska A. Digital RNase Footprinting of RNA-Protein Complexes and Ribosomes in Mitochondria. Methods Mol Biol 2023; 2661:317-328. [PMID: 37166645 DOI: 10.1007/978-1-0716-3171-3_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
RNA-binding proteins and mitochondrial ribosomes have been found to be linchpins of mitochondrial gene expression in health and disease. The expanding repertoire of proteins that bind and regulate the mitochondrial transcriptome has necessitated the development of new tools and methods to examine their molecular functions. Next-generation sequencing technologies have advanced the RNA biology field through application of high-throughput methods to study RNA-protein interactions. Here we describe a digital RNase footprinting method to analyze protein and ribosome interactions with mitochondrially encoded transcripts that provides insight into their mechanisms and minimal binding sites. We provide details on RNase digestion and next-generation sequencing, along with computational analyses and visualization of the binding targets within the mitochondrial transcriptome.
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Affiliation(s)
- Danielle L Rudler
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia
- Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, Australia
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, Australia.
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, Australia.
- Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, Australia.
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Marmolejo-Garza A, Medeiros-Furquim T, Rao R, Eggen BJL, Boddeke E, Dolga AM. Transcriptomic and epigenomic landscapes of Alzheimer's disease evidence mitochondrial-related pathways. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119326. [PMID: 35839870 DOI: 10.1016/j.bbamcr.2022.119326] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 02/06/2023]
Abstract
Alzheimers disease (AD) is the main cause of dementia and it is defined by cognitive decline coupled to extracellular deposit of amyloid-beta protein and intracellular hyperphosphorylation of tau protein. Historically, efforts to target such hallmarks have failed in numerous clinical trials. In addition to these hallmark-targeted approaches, several clinical trials focus on other AD pathological processes, such as inflammation, mitochondrial dysfunction, and oxidative stress. Mitochondria and mitochondrial-related mechanisms have become an attractive target for disease-modifying strategies, as mitochondrial dysfunction prior to clinical onset has been widely described in AD patients and AD animal models. Mitochondrial function relies on both the nuclear and mitochondrial genome. Findings from omics technologies have shed light on AD pathophysiology at different levels (e.g., epigenome, transcriptome and proteome). Most of these studies have focused on the nuclear-encoded components. The first part of this review provides an updated overview of the mechanisms that regulate mitochondrial gene expression and function. The second part of this review focuses on evidence of mitochondrial dysfunction in AD. We have focused on published findings and datasets that study AD. We analyzed published data and provide examples for mitochondrial-related pathways. These pathways are strikingly dysregulated in AD neurons and glia in sex-, cell- and disease stage-specific manners. Analysis of mitochondrial omics data highlights the involvement of mitochondria in AD, providing a rationale for further disease modeling and drug targeting.
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Affiliation(s)
- Alejandro Marmolejo-Garza
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, the Netherlands; Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, Faculty of Medical Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tiago Medeiros-Furquim
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, the Netherlands; Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, Faculty of Medical Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ramya Rao
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, the Netherlands
| | - Bart J L Eggen
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, Faculty of Medical Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Erik Boddeke
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, Faculty of Medical Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N, Denmark.
| | - Amalia M Dolga
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, the Netherlands.
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19
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ANGEL2 phosphatase activity is required for non-canonical mitochondrial RNA processing. Nat Commun 2022; 13:5750. [PMID: 36180430 PMCID: PMC9525292 DOI: 10.1038/s41467-022-33368-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 09/14/2022] [Indexed: 11/18/2022] Open
Abstract
Canonical RNA processing in mammalian mitochondria is defined by tRNAs acting as recognition sites for nucleases to release flanking transcripts. The relevant factors, their structures, and mechanism are well described, but not all mitochondrial transcripts are punctuated by tRNAs, and their mode of processing has remained unsolved. Using Drosophila and mouse models, we demonstrate that non-canonical processing results in the formation of 3′ phosphates, and that phosphatase activity by the carbon catabolite repressor 4 domain-containing family member ANGEL2 is required for their hydrolysis. Furthermore, our data suggest that members of the FAST kinase domain-containing protein family are responsible for these 3′ phosphates. Our results therefore propose a mechanism for non-canonical RNA processing in metazoan mitochondria, by identifying the role of ANGEL2. A subset of mitochondrial transcripts is not flanked by tRNAs and thus does not conform to the canonical mode of processing. Here, Clemente et al. demonstrate that phosphatase activity of ANGEL2 is required for correct processing of these transcripts.
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20
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Itoh Y, Khawaja A, Laptev I, Cipullo M, Atanassov I, Sergiev P, Rorbach J, Amunts A. Mechanism of mitoribosomal small subunit biogenesis and preinitiation. Nature 2022; 606:603-608. [PMID: 35676484 PMCID: PMC9200640 DOI: 10.1038/s41586-022-04795-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/22/2022] [Indexed: 12/27/2022]
Abstract
Mitoribosomes are essential for the synthesis and maintenance of bioenergetic proteins. Here we use cryo-electron microscopy to determine a series of the small mitoribosomal subunit (SSU) intermediates in complex with auxiliary factors, revealing a sequential assembly mechanism. The methyltransferase TFB1M binds to partially unfolded rRNA h45 that is promoted by RBFA, while the mRNA channel is blocked. This enables binding of METTL15 that promotes further rRNA maturation and a large conformational change of RBFA. The new conformation allows initiation factor mtIF3 to already occupy the subunit interface during the assembly. Finally, the mitochondria-specific ribosomal protein mS37 (ref. 1) outcompetes RBFA to complete the assembly with the SSU-mS37-mtIF3 complex2 that proceeds towards mtIF2 binding and translation initiation. Our results explain how the action of step-specific factors modulate the dynamic assembly of the SSU, and adaptation of a unique protein, mS37, links the assembly to initiation to establish the catalytic human mitoribosome.
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Affiliation(s)
- Yuzuru Itoh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Anas Khawaja
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
- Max Planck Institute for Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Ivan Laptev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
- Max Planck Institute for Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Ilian Atanassov
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Cologne, Germany
| | - Petr Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, Russia
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.
- Max Planck Institute for Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.
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21
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Mitochondrial rRNA Methylation by Mettl15 Contributes to the Exercise and Learning Capability in Mice. Int J Mol Sci 2022; 23:ijms23116056. [PMID: 35682734 PMCID: PMC9181494 DOI: 10.3390/ijms23116056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/22/2022] [Accepted: 05/26/2022] [Indexed: 02/01/2023] Open
Abstract
Mitochondrial translation is a unique relic of the symbiotic origin of the organelle. Alterations of its components cause a number of severe human diseases. Hereby we report a study of mice devoid of Mettl15 mitochondrial 12S rRNA methyltransferase, responsible for the formation of m4C839 residue (human numbering). Homozygous Mettl15−/− mice appeared to be viable in contrast to other mitochondrial rRNA methyltransferase knockouts reported earlier. The phenotype of Mettl15−/− mice is much milder than that of other mutants of mitochondrial translation apparatus. In agreement with the results obtained earlier for cell cultures with an inactivated Mettl15 gene, we observed accumulation of the RbfA factor, normally associated with the precursor of the 28S subunit, in the 55S mitochondrial ribosome fraction of knockout mice. A lack of Mettl15 leads to a lower blood glucose level after physical exercise relative to that of the wild-type mice. Mettl15−/− mice demonstrated suboptimal muscle performance and lower levels of Cox3 protein synthesized by mitoribosomes in the oxidative soleus muscles. Additionally, we detected decreased learning capabilities in the Mettl15−/− knockout mice in the tests with both positive and negative reinforcement. Such properties make Mettl15−/− knockout mice a suitable model for mild mitochondriopathies.
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22
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Organization and expression of the mammalian mitochondrial genome. Nat Rev Genet 2022; 23:606-623. [PMID: 35459860 DOI: 10.1038/s41576-022-00480-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 02/07/2023]
Abstract
The mitochondrial genome encodes core subunits of the respiratory chain that drives oxidative phosphorylation and is, therefore, essential for energy conversion. Advances in high-throughput sequencing technologies and cryoelectron microscopy have shed light on the structure and organization of the mitochondrial genome and revealed unique mechanisms of mitochondrial gene regulation. New animal models of impaired mitochondrial protein synthesis have shown how the coordinated regulation of the cytoplasmic and mitochondrial translation machineries ensures the correct assembly of the respiratory chain complexes. These new technologies and disease models are providing a deeper understanding of mitochondrial genome organization and expression and of the diseases caused by impaired energy conversion, including mitochondrial, neurodegenerative, cardiovascular and metabolic diseases. They also provide avenues for the development of treatments for these conditions.
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23
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Li Q, Yang H, Stroup EK, Wang H, Ji Z. Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation. Genome Res 2022; 32:545-557. [PMID: 35193938 PMCID: PMC8896460 DOI: 10.1101/gr.276139.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 01/25/2022] [Indexed: 12/02/2022]
Abstract
We describe a low-input RNase footprinting approach for the rapid quantification of ribosome-protected fragments with as few as 1000 cultured cells. The assay uses a simplified procedure to selectively capture ribosome footprints based on optimized RNase digestion. It simultaneously maps cytosolic and mitochondrial translation with single-nucleotide resolution. We applied it to reveal selective functions of the elongation factor TUFM in mitochondrial translation, as well as synchronized repression of cytosolic translation after TUFM perturbation. We show the assay is applicable to small amounts of primary tissue samples with low protein synthesis rates, including snap-frozen tissues and immune cells from an individual's blood draw. We showed its feasibility to characterize the personalized immuno-translatome. Our analyses revealed that thousands of genes show lower translation efficiency in monocytes compared with lymphocytes, and identified thousands of translated noncanonical open reading frames (ORFs). Altogether, our RNase footprinting approach opens an avenue to assay transcriptome-wide translation using low-input samples from a wide range of physiological conditions.
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Affiliation(s)
- Qianru Li
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Haiwang Yang
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Emily K Stroup
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Hongbin Wang
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Zhe Ji
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA.,Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, Illinois 60628, USA
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24
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mtIF3 is locally translated in axons and regulates mitochondrial translation for axonal growth. BMC Biol 2022; 20:12. [PMID: 34996455 PMCID: PMC8742369 DOI: 10.1186/s12915-021-01215-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Background The establishment and maintenance of functional neural connections relies on appropriate distribution and localization of mitochondria in neurites, as these organelles provide essential energy and metabolites. In particular, mitochondria are transported to axons and support local energy production to maintain energy-demanding neuronal processes including axon branching, growth, and regeneration. Additionally, local protein synthesis is required for structural and functional changes in axons, with nuclear-encoded mitochondrial mRNAs having been found localized in axons. However, it remains unclear whether these mRNAs are locally translated and whether the potential translated mitochondrial proteins are involved in the regulation of mitochondrial functions in axons. Here, we aim to further understand the purpose of such compartmentalization by focusing on the role of mitochondrial initiation factor 3 (mtIF3), whose nuclear-encoded transcripts have been shown to be present in axonal growth cones. Results We demonstrate that brain-derived neurotrophic factor (BDNF) induces local translation of mtIF3 mRNA in axonal growth cones. Subsequently, mtIF3 protein is translocated into axonal mitochondria and promotes mitochondrial translation as assessed by our newly developed bimolecular fluorescence complementation sensor for the assembly of mitochondrial ribosomes. We further show that BDNF-induced axonal growth requires mtIF3-dependent mitochondrial translation in distal axons. Conclusion We describe a previously unknown function of mitochondrial initiation factor 3 (mtIF3) in axonal protein synthesis and development. These findings provide insight into the way neurons adaptively control mitochondrial physiology and axonal development via local mtIF3 translation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01215-w.
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25
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Wang Y, Li J, Lu D, Meng Q, Song N, Zhou H, Xiao X, Sun L, Zhu H. Integrated proteome and phosphoproteome analysis of interscapular brown adipose and subcutaneous white adipose tissues upon high fat diet feeding in mouse. J Proteomics 2022; 255:104500. [DOI: 10.1016/j.jprot.2022.104500] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/10/2022] [Accepted: 01/22/2022] [Indexed: 11/17/2022]
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26
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Nadler F, Lavdovskaia E, Richter-Dennerlein R. Maintaining mitochondrial ribosome function: The role of ribosome rescue and recycling factors. RNA Biol 2021; 19:117-131. [PMID: 34923906 PMCID: PMC8786322 DOI: 10.1080/15476286.2021.2015561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The universally conserved process of protein biosynthesis is crucial for maintaining cellular homoeostasis and in eukaryotes, mitochondrial translation is essential for aerobic energy production. Mitochondrial ribosomes (mitoribosomes) are highly specialized to synthesize 13 core subunits of the oxidative phosphorylation (OXPHOS) complexes. Although the mitochondrial translation machinery traces its origin from a bacterial ancestor, it has acquired substantial differences within this endosymbiotic environment. The cycle of mitoribosome function proceeds through the conserved canonical steps of initiation, elongation, termination and mitoribosome recycling. However, when mitoribosomes operate in the context of limited translation factors or on aberrant mRNAs, they can become stalled and activation of rescue mechanisms is required. This review summarizes recent advances in the understanding of protein biosynthesis in mitochondria, focusing especially on the mechanistic and physiological details of translation termination, and mitoribosome recycling and rescue.
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Affiliation(s)
- Franziska Nadler
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany
| | - Elena Lavdovskaia
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany
| | - Ricarda Richter-Dennerlein
- Department of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany
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27
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Molina‐Berenguer M, Vila‐Julià F, Pérez‐Ramos S, Salcedo‐Allende MT, Cámara Y, Torres‐Torronteras J, Martí R. Dysfunctional mitochondrial translation and combined oxidative phosphorylation deficiency in a mouse model of hepatoencephalopathy due to
Gfm1
mutations. FASEB J 2021; 36:e22091. [DOI: 10.1096/fj.202100819rrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Miguel Molina‐Berenguer
- Research Group on Neuromuscular and Mitochondrial Diseases Vall d'Hebron Research Institute Universitat Autònoma de Barcelona Barcelona Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid Spain
| | - Ferran Vila‐Julià
- Research Group on Neuromuscular and Mitochondrial Diseases Vall d'Hebron Research Institute Universitat Autònoma de Barcelona Barcelona Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid Spain
| | - Sandra Pérez‐Ramos
- Research Group on Neuromuscular and Mitochondrial Diseases Vall d'Hebron Research Institute Universitat Autònoma de Barcelona Barcelona Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid Spain
| | - Maria Teresa Salcedo‐Allende
- Pathology Department Vall d'Hebron Research Institute Hospital Universitari Vall d'Hebron Universitat Autònoma de Barcelona Barcelona Spain
| | - Yolanda Cámara
- Research Group on Neuromuscular and Mitochondrial Diseases Vall d'Hebron Research Institute Universitat Autònoma de Barcelona Barcelona Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid Spain
| | - Javier Torres‐Torronteras
- Research Group on Neuromuscular and Mitochondrial Diseases Vall d'Hebron Research Institute Universitat Autònoma de Barcelona Barcelona Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid Spain
| | - Ramon Martí
- Research Group on Neuromuscular and Mitochondrial Diseases Vall d'Hebron Research Institute Universitat Autònoma de Barcelona Barcelona Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER) Instituto de Salud Carlos III Madrid Spain
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28
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Shirokikh NE. Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells. Crit Rev Biochem Mol Biol 2021; 57:261-304. [PMID: 34852690 DOI: 10.1080/10409238.2021.2006599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
During protein biosynthesis, ribosomes bind to messenger (m)RNA, locate its protein-coding information, and translate the nucleotide triplets sequentially as codons into the corresponding sequence of amino acids, forming proteins. Non-coding mRNA features, such as 5' and 3' untranslated regions (UTRs), start sites or stop codons of different efficiency, stretches of slower or faster code and nascent polypeptide interactions can alter the translation rates transcript-wise. Most of the homeostatic and signal response pathways of the cells converge on individual mRNA control, as well as alter the global translation output. Among the multitude of approaches to study translational control, one of the most powerful is to infer the locations of translational complexes on mRNA based on the mRNA fragments protected by these complexes from endonucleolytic hydrolysis, or footprints. Translation complex profiling by high-throughput sequencing of the footprints allows to quantify the transcript-wise, as well as global, alterations of translation, and uncover the underlying control mechanisms by attributing footprint locations and sizes to different configurations of the translational complexes. The accuracy of all footprint profiling approaches critically depends on the fidelity of footprint generation and many methods have emerged to preserve certain or multiple configurations of the translational complexes, often in challenging biological material. In this review, a systematic summary of approaches to stabilize translational complexes on mRNA for footprinting is presented and major findings are discussed. Future directions of translation footprint profiling are outlined, focusing on the fidelity and accuracy of inference of the native in vivo translation complex distribution on mRNA.
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Affiliation(s)
- Nikolay E Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
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29
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Jeong H, Kim Y, Jung YS, Kang DR, Cho YR. Entropy-Based Graph Clustering of PPI Networks for Predicting Overlapping Functional Modules of Proteins. ENTROPY 2021; 23:e23101271. [PMID: 34681995 PMCID: PMC8534328 DOI: 10.3390/e23101271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/25/2021] [Accepted: 09/25/2021] [Indexed: 12/26/2022]
Abstract
Functional modules can be predicted using genome-wide protein-protein interactions (PPIs) from a systematic perspective. Various graph clustering algorithms have been applied to PPI networks for this task. In particular, the detection of overlapping clusters is necessary because a protein is involved in multiple functions under different conditions. graph entropy (GE) is a novel metric to assess the quality of clusters in a large, complex network. In this study, the unweighted and weighted GE algorithm is evaluated to prove the validity of predicting function modules. To measure clustering accuracy, the clustering results are compared to protein complexes and Gene Ontology (GO) annotations as references. We demonstrate that the GE algorithm is more accurate in overlapping clusters than the other competitive methods. Moreover, we confirm the biological feasibility of the proteins that occur most frequently in the set of identified clusters. Finally, novel proteins for the additional annotation of GO terms are revealed.
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Affiliation(s)
- Hoyeon Jeong
- Department of Biostatistics, Wonju College of Medicine, Yonsei University, Wonju-si 26426, Gangwon-do, Korea; (H.J.); (D.R.K.)
- National Health Big Data Clinical Research Institute, Wonju College of Medicine, Yonsei University, Wonju-si 26426, Gangwon-do, Korea
| | - Yoonbee Kim
- Division of Software, Yonsei University Mirae Campus, Wonju-si 26493, Gangwon-do, Korea; (Y.K.); (Y.-S.J.)
| | - Yi-Sue Jung
- Division of Software, Yonsei University Mirae Campus, Wonju-si 26493, Gangwon-do, Korea; (Y.K.); (Y.-S.J.)
| | - Dae Ryong Kang
- Department of Biostatistics, Wonju College of Medicine, Yonsei University, Wonju-si 26426, Gangwon-do, Korea; (H.J.); (D.R.K.)
- National Health Big Data Clinical Research Institute, Wonju College of Medicine, Yonsei University, Wonju-si 26426, Gangwon-do, Korea
| | - Young-Rae Cho
- Division of Software, Yonsei University Mirae Campus, Wonju-si 26493, Gangwon-do, Korea; (Y.K.); (Y.-S.J.)
- Division of Digital Healthcare, Yonsei University Mirae Campus, Wonju-si 26493, Gangwon-do, Korea
- Correspondence: ; Tel.: +82-33-760-2245
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Bharmal MHM, Gega A, Schrader JM. A combination of mRNA features influence the efficiency of leaderless mRNA translation initiation. NAR Genom Bioinform 2021; 3:lqab081. [PMID: 34568822 PMCID: PMC8459731 DOI: 10.1093/nargab/lqab081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/03/2021] [Accepted: 08/27/2021] [Indexed: 12/30/2022] Open
Abstract
Bacterial translation is thought to initiate by base pairing of the 16S rRNA and the Shine-Dalgarno sequence in the mRNA's 5' untranslated region (UTR). However, transcriptomics has revealed that leaderless mRNAs, which completely lack any 5' UTR, are broadly distributed across bacteria and can initiate translation in the absence of the Shine-Dalgarno sequence. To investigate the mechanism of leaderless mRNA translation initiation, synthetic in vivo translation reporters were designed that systematically tested the effects of start codon accessibility, leader length, and start codon identity on leaderless mRNA translation initiation. Using these data, a simple computational model was built based on the combinatorial relationship of these mRNA features that can accurately classify leaderless mRNAs and predict the translation initiation efficiency of leaderless mRNAs. Thus, start codon accessibility, leader length, and start codon identity combine to define leaderless mRNA translation initiation in bacteria.
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Affiliation(s)
| | - Alisa Gega
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Jared M Schrader
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
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31
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Wang F, Zhang D, Zhang D, Li P, Gao Y. Mitochondrial Protein Translation: Emerging Roles and Clinical Significance in Disease. Front Cell Dev Biol 2021; 9:675465. [PMID: 34277617 PMCID: PMC8280776 DOI: 10.3389/fcell.2021.675465] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/09/2021] [Indexed: 12/28/2022] Open
Abstract
Mitochondria are one of the most important organelles in cells. Mitochondria are semi-autonomous organelles with their own genetic system, and can independently replicate, transcribe, and translate mitochondrial DNA. Translation initiation, elongation, termination, and recycling of the ribosome are four stages in the process of mitochondrial protein translation. In this process, mitochondrial protein translation factors and translation activators, mitochondrial RNA, and other regulatory factors regulate mitochondrial protein translation. Mitochondrial protein translation abnormalities are associated with a variety of diseases, including cancer, cardiovascular diseases, and nervous system diseases. Mutation or deletion of various mitochondrial protein translation factors and translation activators leads to abnormal mitochondrial protein translation. Mitochondrial tRNAs and mitochondrial ribosomal proteins are essential players during translation and mutations in genes encoding them represent a large fraction of mitochondrial diseases. Moreover, there is crosstalk between mitochondrial protein translation and cytoplasmic translation, and the imbalance between mitochondrial protein translation and cytoplasmic translation can affect some physiological and pathological processes. This review summarizes the regulation of mitochondrial protein translation factors, mitochondrial ribosomal proteins, mitochondrial tRNAs, and mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) in the mitochondrial protein translation process and its relationship with diseases. The regulation of mitochondrial protein translation and cytoplasmic translation in multiple diseases is also summarized.
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Affiliation(s)
- Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Deyu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.,Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, China
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32
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Richman TR, Ermer JA, Siira SJ, Kuznetsova I, Brosnan CA, Rossetti G, Baker J, Perks KL, Cserne Szappanos H, Viola HM, Gray N, Larance M, Hool LC, Zuryn S, Rackham O, Filipovska A. Mitochondrial mistranslation modulated by metabolic stress causes cardiovascular disease and reduced lifespan. Aging Cell 2021; 20:e13408. [PMID: 34096683 PMCID: PMC8282274 DOI: 10.1111/acel.13408] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/17/2021] [Accepted: 05/08/2021] [Indexed: 12/25/2022] Open
Abstract
Changes in the rate and fidelity of mitochondrial protein synthesis impact the metabolic and physiological roles of mitochondria. Here we explored how environmental stress in the form of a high-fat diet modulates mitochondrial translation and affects lifespan in mutant mice with error-prone (Mrps12ep / ep ) or hyper-accurate (Mrps12ha / ha ) mitochondrial ribosomes. Intriguingly, although both mutations are metabolically beneficial in reducing body weight, decreasing circulating insulin and increasing glucose tolerance during a high-fat diet, they manifest divergent (either deleterious or beneficial) outcomes in a tissue-specific manner. In two distinct organs that are commonly affected by the metabolic disease, the heart and the liver, Mrps12ep / ep mice were protected against heart defects but sensitive towards lipid accumulation in the liver, activating genes involved in steroid and amino acid metabolism. In contrast, enhanced translational accuracy in Mrps12ha / ha mice protected the liver from a high-fat diet through activation of liver proliferation programs, but enhanced the development of severe hypertrophic cardiomyopathy and led to reduced lifespan. These findings reflect the complex transcriptional and cell signalling responses that differ between post-mitotic (heart) and highly proliferative (liver) tissues. We show trade-offs between the rate and fidelity of mitochondrial protein synthesis dictate tissue-specific outcomes due to commonly encountered stressful environmental conditions or aging.
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Affiliation(s)
- Tara R. Richman
- Harry Perkins Institute of Medical Research QEII Medical Centre Nedlands WA Australia
- ARC Centre of Excellence in Synthetic Biology QEII Medical Centre Nedlands WA Australia
- Centre for Medical Research QEII Medical Centre, The University of Western Australia Nedlands WA Australia
| | - Judith A. Ermer
- Harry Perkins Institute of Medical Research QEII Medical Centre Nedlands WA Australia
- ARC Centre of Excellence in Synthetic Biology QEII Medical Centre Nedlands WA Australia
- Centre for Medical Research QEII Medical Centre, The University of Western Australia Nedlands WA Australia
| | - Stefan J. Siira
- Harry Perkins Institute of Medical Research QEII Medical Centre Nedlands WA Australia
- ARC Centre of Excellence in Synthetic Biology QEII Medical Centre Nedlands WA Australia
- Centre for Medical Research QEII Medical Centre, The University of Western Australia Nedlands WA Australia
| | - Irina Kuznetsova
- Harry Perkins Institute of Medical Research QEII Medical Centre Nedlands WA Australia
- ARC Centre of Excellence in Synthetic Biology QEII Medical Centre Nedlands WA Australia
- Centre for Medical Research QEII Medical Centre, The University of Western Australia Nedlands WA Australia
| | - Christopher A. Brosnan
- Clem Jones Centre for Ageing Dementia Research Queensland Brain Institute The University of Queensland Brisbane Qld Australia
| | - Giulia Rossetti
- Harry Perkins Institute of Medical Research QEII Medical Centre Nedlands WA Australia
- ARC Centre of Excellence in Synthetic Biology QEII Medical Centre Nedlands WA Australia
- Centre for Medical Research QEII Medical Centre, The University of Western Australia Nedlands WA Australia
- Telethon Kids Institute Perth Children's Hospital Nedlands WA Australia
| | - Jessica Baker
- Harry Perkins Institute of Medical Research QEII Medical Centre Nedlands WA Australia
- ARC Centre of Excellence in Synthetic Biology QEII Medical Centre Nedlands WA Australia
- Centre for Medical Research QEII Medical Centre, The University of Western Australia Nedlands WA Australia
- Telethon Kids Institute Perth Children's Hospital Nedlands WA Australia
| | - Kara L. Perks
- Harry Perkins Institute of Medical Research QEII Medical Centre Nedlands WA Australia
- ARC Centre of Excellence in Synthetic Biology QEII Medical Centre Nedlands WA Australia
- Centre for Medical Research QEII Medical Centre, The University of Western Australia Nedlands WA Australia
- Telethon Kids Institute Perth Children's Hospital Nedlands WA Australia
- School of Pharmacy and Biomedical Sciences Curtin University Bentley WA Australia
| | | | - Helena M. Viola
- School of Human Sciences The University of Western Australia Nedlands WA Australia
| | - Nicola Gray
- Australian National Phenome Centre Centre for Computational and Systems Medicine Health Futures Institute Murdoch University Perth WA Australia
| | - Mark Larance
- Charles Perkins Centre School of Life and Environmental Sciences University of Sydney Sydney NSW Australia
| | - Livia C. Hool
- School of Human Sciences The University of Western Australia Nedlands WA Australia
- Victor Chang Cardiac Research Institute Sydney NSW Australia
| | - Steven Zuryn
- Clem Jones Centre for Ageing Dementia Research Queensland Brain Institute The University of Queensland Brisbane Qld Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research QEII Medical Centre Nedlands WA Australia
- ARC Centre of Excellence in Synthetic Biology QEII Medical Centre Nedlands WA Australia
- Centre for Medical Research QEII Medical Centre, The University of Western Australia Nedlands WA Australia
- Telethon Kids Institute Perth Children's Hospital Nedlands WA Australia
- School of Pharmacy and Biomedical Sciences Curtin University Bentley WA Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research QEII Medical Centre Nedlands WA Australia
- ARC Centre of Excellence in Synthetic Biology QEII Medical Centre Nedlands WA Australia
- Centre for Medical Research QEII Medical Centre, The University of Western Australia Nedlands WA Australia
- Telethon Kids Institute Perth Children's Hospital Nedlands WA Australia
- Victor Chang Cardiac Research Institute Sydney NSW Australia
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33
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Luo Y, Wang Y, Huang Y. Schizosaccharomyces pombe Ppr10 and Mpa1 together mediate mitochondrial translational initiation. J Biol Chem 2021; 297:100869. [PMID: 34119521 PMCID: PMC8258696 DOI: 10.1016/j.jbc.2021.100869] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 12/26/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are a large family of proteins that act primarily at different posttranscriptional steps of organellar gene expression. We have previously found that the Schizosaccharomyces pombe PPR protein mpal10 interacts with mitochondrial translational activator Mpa1, and both are essential for mitochondrial protein synthesis. However, it is unclear how these two proteins function in mitochondrial protein synthesis in S. pombe. In this study, we further investigated the role of Ppr10 and Mpa1 in mitochondrial protein synthesis. Mitochondrial translational initiation requires two initiation factors, Mti2 and Mti3, which bind to the small subunit of the mitochondrial ribosome (mt-SSU) during the formation of the mitochondrial translational initiation complex. Using sucrose gradient sedimentation analysis, we found that disruption of ppr10, mpa1, or the PPR motifs in Ppr10 impairs the association of Mti2 and Mti3 with the mt-SSU, suggesting that both Ppr10 and Mpa1 may be required for the interaction of Mti2 and Mti3 with the mt-SSU during the assembly of mitochondrial translational initiation complex. Loss of Ppr10 perturbs the association of mitochondrially encoded cytochrome b (cob1) and cytochrome c oxidase subunit 1 (cox1) mRNAs with assembled mitochondrial ribosomes. Proteomic analysis revealed that a fraction of Ppr10 and Mpa1 copurified with a subset of mitoribosomal proteins. The PPR motifs of Ppr10 are necessary for its interaction with Mpa1 and that disruption of these PPR motifs impairs mitochondrial protein synthesis. Our results suggest that Ppr10 and Mpa1 function together to mediate mitochondrial translational initiation.
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Affiliation(s)
- Ying Luo
- Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yirong Wang
- Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China.
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34
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Hu Y, Xu Y, Chen W, Qiu Z. Stomatin-Like Protein-2: A Potential Target to Treat Mitochondrial Cardiomyopathy. Heart Lung Circ 2021; 30:1449-1455. [PMID: 34088631 DOI: 10.1016/j.hlc.2021.05.074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/16/2021] [Accepted: 05/02/2021] [Indexed: 12/27/2022]
Abstract
Stomatin-like protein-2 (SLP-2) is a mitochondrial-associated protein that is abundant in cardiomyocytes. Many reports have shown that SLP-2 plays an important role in mitochondria. The treatment of mitochondrial cardiomyopathy (MCM) needs further improvement, so the relationship between SLP-2 and MCM is worth exploring. This study reviewed some protective mechanisms of SLP-2 on mitochondria. Published studies have shown that SLP-2 protects mitochondria by stabilising the function of optic atrophy 1 (OPA1), promoting mitofusin (Mfn) 2 expression, interacting with prohibitins and cardiolipin, forming SLP-2-PARL-YME1L (SPY) complex, and stabilising respiratory chain complexes, suggesting that SLP-2 is a new potential target for the treatment of MCM. However, the specific mechanism of SLP-2 needs to be confirmed by further research.
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Affiliation(s)
- Yuntao Hu
- Department of Thoracic and Cardiovascular Surgery, Nanjing First Hospital, Nanjing Medical University, Jiangsu, China
| | - Yueyue Xu
- Department of Thoracic and Cardiovascular Surgery, Nanjing First Hospital, Nanjing Medical University, Jiangsu, China
| | - Wen Chen
- Department of Thoracic and Cardiovascular Surgery, Nanjing First Hospital, Nanjing Medical University, Jiangsu, China.
| | - Zhibing Qiu
- Department of Thoracic and Cardiovascular Surgery, Nanjing First Hospital, Nanjing Medical University, Jiangsu, China.
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35
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Kummer E, Schubert KN, Schoenhut T, Scaiola A, Ban N. Structural basis of translation termination, rescue, and recycling in mammalian mitochondria. Mol Cell 2021; 81:2566-2582.e6. [PMID: 33878294 DOI: 10.1016/j.molcel.2021.03.042] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/12/2021] [Accepted: 03/24/2021] [Indexed: 12/26/2022]
Abstract
The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as a screening tool to identify mitochondrial translation termination mechanisms and to describe them in molecular detail. We show how mitochondrial release factor 1a releases the nascent chain from the ribosome when it encounters the canonical stop codons UAA and UAG. Furthermore, we define how the peptidyl-tRNA hydrolase ICT1 acts as a rescue factor on mitoribosomes that have stalled on truncated messages to recover them for protein synthesis. Finally, we present structural models detailing the process of mitochondrial ribosome recycling to explain how a dedicated elongation factor, mitochondrial EFG2 (mtEFG2), has specialized for cooperation with the mitochondrial ribosome recycling factor to dissociate the mitoribosomal subunits at the end of the translation process.
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Affiliation(s)
- Eva Kummer
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland.
| | - Katharina Noel Schubert
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Tanja Schoenhut
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Alain Scaiola
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Nenad Ban
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland.
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36
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Mechanisms and regulation of protein synthesis in mitochondria. Nat Rev Mol Cell Biol 2021; 22:307-325. [PMID: 33594280 DOI: 10.1038/s41580-021-00332-2] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 02/06/2023]
Abstract
Mitochondria are cellular organelles responsible for generation of chemical energy in the process called oxidative phosphorylation. They originate from a bacterial ancestor and maintain their own genome, which is expressed by designated, mitochondrial transcription and translation machineries that differ from those operating for nuclear gene expression. In particular, the mitochondrial protein synthesis machinery is structurally and functionally very different from that governing eukaryotic, cytosolic translation. Despite harbouring their own genetic information, mitochondria are far from being independent of the rest of the cell and, conversely, cellular fitness is closely linked to mitochondrial function. Mitochondria depend heavily on the import of nuclear-encoded proteins for gene expression and function, and hence engage in extensive inter-compartmental crosstalk to regulate their proteome. This connectivity allows mitochondria to adapt to changes in cellular conditions and also mediates responses to stress and mitochondrial dysfunction. With a focus on mammals and yeast, we review fundamental insights that have been made into the biogenesis, architecture and mechanisms of the mitochondrial translation apparatus in the past years owing to the emergence of numerous near-atomic structures and a considerable amount of biochemical work. Moreover, we discuss how cellular mitochondrial protein expression is regulated, including aspects of mRNA and tRNA maturation and stability, roles of auxiliary factors, such as translation regulators, that adapt mitochondrial translation rates, and the importance of inter-compartmental crosstalk with nuclear gene expression and cytosolic translation and how it enables integration of mitochondrial translation into the cellular context.
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37
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Levitskii SA, Baleva MV, Chicherin IV, Krasheninnikov IA, Kamenski PA. Protein Biosynthesis in Mitochondria: Past Simple, Present Perfect, Future Indefinite. BIOCHEMISTRY (MOSCOW) 2021; 85:257-263. [PMID: 32564730 DOI: 10.1134/s0006297920030013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Mitochondria are obligate organelles of most eukaryotic cells that perform many different functions important for cellular homeostasis. The main role of mitochondria is supplying cells with energy in a form of ATP, which is synthesized in a chain of oxidative phosphorylation reactions on the organelle inner membrane. It is commonly believed now that mitochondria have the endosymbiotic origin. In the course of evolution, they have lost most of their genetic material as a result of genome reduction and gene transfer to the nucleus. The majority of mitochondrial proteins are synthesized in the cytosol and then imported to the mitochondria. However, almost all known mitochondria still contain genomes that are maintained and expressed. The processes of protein biosynthesis in the mitochondria - mitochondrial translation - substantially differs from the analogous processes in bacteria and the cytosol of eukaryotic cells. Mitochondrial translation is characterized by a high degree of specialization and specific regulatory mechanisms. In this review, we analyze available information on the common principles of mitochondrial translation with emphasis on the molecular mechanisms of translation initiation in the mitochondria of yeast and mammalian cells.
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Affiliation(s)
- S A Levitskii
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - M V Baleva
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - I V Chicherin
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - I A Krasheninnikov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - P A Kamenski
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia.
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38
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Kuznetsova I, Lugmayr A, Rackham O, Filipovska A. OmicsVolcano: software for intuitive visualization and interactive exploration of high-throughput biological data. STAR Protoc 2021; 2:100279. [PMID: 33532728 PMCID: PMC7821039 DOI: 10.1016/j.xpro.2020.100279] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Advances in omics technologies have generated exponentially larger volumes of biological data; however, their analyses and interpretation are limited to computationally proficient scientists. We created OmicsVolcano, an interactive open-source software tool to enable visualization and exploration of high-throughput biological data, while highlighting features of interest using a volcano plot interface. In contrast to existing tools, our software and user-interface design allow it to be used without requiring any programming skills to generate high-quality and presentation-ready images.
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Affiliation(s)
- Irina Kuznetsova
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA 6009, Australia.,Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Artur Lugmayr
- Umea University, Department of Computing Science, 901 87 Umea, Sweden.,Edith Cowan University, School of Science, AI and Optimization Research Group, Joondalup, WA 6027, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA 6009, Australia.,School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, WA 6102, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia.,Telethon Kids Institute, Perth Children's Hospital, Northern Entrance, 15 Hospital Avenue, Nedlands, WA 6009, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA 6009, Australia.,Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA 6009, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia.,Telethon Kids Institute, Perth Children's Hospital, Northern Entrance, 15 Hospital Avenue, Nedlands, WA 6009, Australia.,School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
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39
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Li Y, Meng Y, Zhu X, Van Wijnen A, Eirin A, Lerman LO. Metabolic Syndrome Is Associated With Altered mRNA and miRNA Content in Human Circulating Extracellular Vesicles. Front Endocrinol (Lausanne) 2021; 12:687586. [PMID: 34456862 PMCID: PMC8387871 DOI: 10.3389/fendo.2021.687586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/23/2021] [Indexed: 12/19/2022] Open
Abstract
As mediators of intercellular communication, circulating extracellular vehicles (EVs) can modulate tissue and cellular pathways by altering transcription profiles in recipient cells, and their content may reflect the status of their parent cells. However, whether their cargo is altered in the metabolic syndrome (Mets) remains unclear. We hypothesized that MetS altered mRNAs and miRNAs packed within circulating-EVs. EVs were collected from plasma of patients with MetS or age-matched Lean controls (n=4 each). RNA sequencing was performed to identify dysregulated mRNAs and miRNAs, and analyze genes targeted by miRNAs, top pathways, and diseases associated with MetS-EVs. MetS patients showed elevated body weight, blood pressure, glucose, insulin, and liver injury markers levels. 1,446 mRNAs were downregulated and 32 upregulated in MetS- compared to Lean-EVs, whereas 40 miRNAs were selectively enriched and 10 downregulated in MetS-EVs. MetS upregulated in EVs genes involved in apoptosis, mitochondrial regulation, transport, and lipoproteins, but downregulated vessel and heart development, protein complex biogenesis, and angiogenesis. MetS also upregulated miRNAs targeting genes implicated in cellular processes, including oxidation-reduction, and downregulated miRNAs capable of modulating catalytic activity, as well as heart, blood vessel, and skeletal development, transcriptional regulation, apoptosis, and cell cycle. Our study, thus, indicates that human subjects with MetS show modified cargo of circulating EVs, which in turn may modulate several critical cellular functions and fate. These EVs may reflect the anomalous status of their parent cells, and potentially serve as important regulators, biomarkers, and targets in the progression and treatment of MetS.
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Affiliation(s)
- Yongxin Li
- Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, United States
| | - Yu Meng
- Central Laboratory, The Fifth Affiliated Hospital of Jinan University, Heyuan, China
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
- *Correspondence: Lilach O. Lerman, ; Yu Meng,
| | - Xiangyang Zhu
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, United States
| | - Andre Van Wijnen
- Departments of Orthopedic Surgery, Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Alfonso Eirin
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, United States
| | - Lilach O. Lerman
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, United States
- *Correspondence: Lilach O. Lerman, ; Yu Meng,
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40
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Rudler DL, Hughes LA, Viola HM, Hool LC, Rackham O, Filipovska A. Fidelity and coordination of mitochondrial protein synthesis in health and disease. J Physiol 2020; 599:3449-3462. [PMID: 32710561 DOI: 10.1113/jp280359] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
The evolutionary acquisition of mitochondria has given rise to the diversity of eukaryotic life. Mitochondria have retained their ancestral α-proteobacterial traits through the maintenance of double membranes and their own circular genome. Their genome varies in size from very large in plants to the smallest in animals and their parasites. The mitochondrial genome encodes essential genes for protein synthesis and has to coordinate its expression with the nuclear genome from which it sources most of the proteins required for mitochondrial biogenesis and function. The mitochondrial protein synthesis machinery is unique because it is encoded by both the nuclear and mitochondrial genomes thereby requiring tight regulation to produce the respiratory complexes that drive oxidative phosphorylation for energy production. The fidelity and coordination of mitochondrial protein synthesis are essential for ATP production. Here we compare and contrast the mitochondrial translation mechanisms in mammals and fungi to bacteria and reveal that their diverse regulation can have unusual impacts on the health and disease of these organisms. We highlight that in mammals the rate of protein synthesis is more important than the fidelity of translation, enabling coordinated biogenesis of the mitochondrial respiratory chain with respiratory chain proteins synthesised by cytoplasmic ribosomes. Changes in mitochondrial protein fidelity can trigger the activation of the diverse cellular signalling networks in fungi and mammals to combat dysfunction in energy conservation. The physiological consequences of altered fidelity of protein synthesis can range from liver regeneration to the onset and development of cardiomyopathy.
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Affiliation(s)
- Danielle L Rudler
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia.,Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia
| | - Laetitia A Hughes
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia.,Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia
| | - Helena M Viola
- School of Human Sciences, University of Western Australia, 35 Stirling Highway, Nedlands, Western Australia, 6009, Australia
| | - Livia C Hool
- School of Human Sciences, University of Western Australia, 35 Stirling Highway, Nedlands, Western Australia, 6009, Australia.,Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia.,School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Western Australia, 6102, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, 6102, Australia.,Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, Western Australia, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia.,ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia.,Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia, 6009, Australia.,Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, Western Australia, Australia.,School of Molecular Sciences, University of Western Australia, Crawley, Western Australia, 6009, Australia
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41
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Khawaja A, Itoh Y, Remes C, Spåhr H, Yukhnovets O, Höfig H, Amunts A, Rorbach J. Distinct pre-initiation steps in human mitochondrial translation. Nat Commun 2020; 11:2932. [PMID: 32522994 PMCID: PMC7287080 DOI: 10.1038/s41467-020-16503-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/07/2020] [Indexed: 11/08/2022] Open
Abstract
Translation initiation in human mitochondria relies upon specialized mitoribosomes and initiation factors, mtIF2 and mtIF3, which have diverged from their bacterial counterparts. Here we report two distinct mitochondrial pre-initiation assembly steps involving those factors. Single-particle cryo-EM revealed that in the first step, interactions between mitochondria-specific protein mS37 and mtIF3 keep the small mitoribosomal subunit in a conformation favorable for a subsequent accommodation of mtIF2 in the second step. Combination with fluorescence cross-correlation spectroscopy analyses suggests that mtIF3 promotes complex assembly without mRNA or initiator tRNA binding, where exclusion is achieved by the N-terminal and C-terminal domains of mtIF3. Finally, the association of large mitoribosomal subunit is required for initiator tRNA and leaderless mRNA recruitment to form a stable initiation complex. These data reveal fundamental aspects of mammalian protein synthesis that are specific to mitochondria.
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Affiliation(s)
- Anas Khawaja
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65, Solna, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Yuzuru Itoh
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65, Solna, Sweden
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden
| | - Cristina Remes
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Cologne, Germany
| | - Henrik Spåhr
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65, Solna, Sweden
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Cologne, Germany
| | - Olessya Yukhnovets
- RWTH Aachen, I. Physikalisches Institut (IA), Aachen, Germany
- Forschungszentrum Jülich, Institute of Complex Systems ICS-5, Jülich, Germany
| | - Henning Höfig
- RWTH Aachen, I. Physikalisches Institut (IA), Aachen, Germany
- Forschungszentrum Jülich, Institute of Complex Systems ICS-5, Jülich, Germany
| | - Alexey Amunts
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65, Solna, Sweden.
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165, Solna, Sweden.
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Biomedicum, 171 65, Solna, Sweden.
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.
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Yeast Mitochondrial Translation Initiation Factor 3 Interacts with Pet111p to Promote COX2 mRNA Translation. Int J Mol Sci 2020; 21:ijms21103414. [PMID: 32408541 PMCID: PMC7279496 DOI: 10.3390/ijms21103414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial genomes code for several core components of respiratory chain complexes. Thus, mitochondrial translation is of great importance for the organelle as well as for the whole cell. In yeast, mitochondrial translation initiation factor 3, Aim23p, is not essential for the organellar protein synthesis; however, its absence leads to a significant quantitative imbalance of the mitochondrial translation products. This fact points to a possible specific action of Aim23p on the biosynthesis of some mitochondrial protein species. In this work, we examined such peculiar effects of Aim23p in relation to yeast mitochondrial COX2 mRNA translation. We show that Aim23p is indispensable to this process. According to our data, this is mediated by Aimp23p interaction with the known specific factor of the COX2 mRNA translation, Pet111p. If there is no Aim23p in the yeast cells, an increased amount of Pet111p ensures proper COX2 mRNA translation. Our results demonstrate the additional non-canonical function of initiation factor 3 in yeast mitochondrial translation.
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Initiation Factor 3 is Dispensable For Mitochondrial Translation in Cultured Human Cells. Sci Rep 2020; 10:7110. [PMID: 32346061 PMCID: PMC7188818 DOI: 10.1038/s41598-020-64139-5] [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: 10/02/2019] [Accepted: 04/13/2020] [Indexed: 11/08/2022] Open
Abstract
The initiation of protein synthesis in bacteria is ruled by three canonical factors: IF1, IF2, and IF3. This system persists in human mitochondria; however, it functions in a rather different way due to specialization and adaptation to the organellar micro-environment. We focused on human mitochondrial IF3, which was earlier studied in vitro, but no knock-out cellular models have been published up to date. In this work, we generated human HeLa cell lines deficient in the MTIF3 gene and analyzed their mitochondrial function. Despite the lack of IF3mt in these cells, they preserved functional mitochondria capable of oxygen consumption and protein synthesis; however, the translation of ATP6 mRNA was selectively decreased which compromised the assembly of ATP synthase. Together with the analogous results obtained earlier for baker's yeast mitochondrial IF3, our findings point to a functional divergence of mitochondrial initiation factors from their bacterial ancestors.
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