1
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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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2
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Bruni F. Human mtDNA-Encoded Long ncRNAs: Knotty Molecules and Complex Functions. Int J Mol Sci 2024; 25:1502. [PMID: 38338781 PMCID: PMC10855489 DOI: 10.3390/ijms25031502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Until a few decades ago, most of our knowledge of RNA transcription products was focused on protein-coding sequences, which were later determined to make up the smallest portion of the mammalian genome. Since 2002, we have learnt a great deal about the intriguing world of non-coding RNAs (ncRNAs), mainly due to the rapid development of bioinformatic tools and next-generation sequencing (NGS) platforms. Moreover, interest in non-human ncRNAs and their functions has increased as a result of these technologies and the accessibility of complete genome sequences of species ranging from Archaea to primates. Despite not producing proteins, ncRNAs constitute a vast family of RNA molecules that serve a number of regulatory roles and are essential for cellular physiology and pathology. This review focuses on a subgroup of human ncRNAs, namely mtDNA-encoded long non-coding RNAs (mt-lncRNAs), which are transcribed from the mitochondrial genome and whose disparate localisations and functions are linked as much to mitochondrial metabolism as to cellular physiology and pathology.
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Affiliation(s)
- Francesco Bruni
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, 70125 Bari, Italy
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3
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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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4
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Dinh N, Bonnefoy N. Schizosaccharomyces pombe as a fundamental model for research on mitochondrial gene expression: Progress, achievements and outlooks. IUBMB Life 2023. [PMID: 38117001 DOI: 10.1002/iub.2801] [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: 09/27/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023]
Abstract
Schizosaccharomyces pombe (fission yeast) is an attractive model for mitochondrial research. The organism resembles human cells in terms of mitochondrial inheritance, mitochondrial transport, sugar metabolism, mitogenome structure and dependence of viability on the mitogenome (the petite-negative phenotype). Transcriptions of these genomes produce only a few polycistronic transcripts, which then undergo processing as per the tRNA punctuation model. In general, the machinery for mitochondrial gene expression is structurally and functionally conserved between fission yeast and humans. Furthermore, molecular research on S. pombe is supported by a considerable number of experimental techniques and database resources. Owing to these advantages, fission yeast has significantly contributed to biomedical and fundamental research. Here, we review the current state of knowledge regarding S. pombe mitochondrial gene expression, and emphasise the pertinence of fission yeast as both a model and tool, especially for studies on mitochondrial translation.
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Affiliation(s)
- Nhu Dinh
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette cedex, France
| | - Nathalie Bonnefoy
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette cedex, France
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5
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Key J, Gispert S, Koepf G, Steinhoff-Wagner J, Reichlmeir M, Auburger G. Translation Fidelity and Respiration Deficits in CLPP-Deficient Tissues: Mechanistic Insights from Mitochondrial Complexome Profiling. Int J Mol Sci 2023; 24:17503. [PMID: 38139332 PMCID: PMC10743472 DOI: 10.3390/ijms242417503] [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: 11/13/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The mitochondrial matrix peptidase CLPP is crucial during cell stress. Its loss causes Perrault syndrome type 3 (PRLTS3) with infertility, neurodegeneration, and a growth deficit. Its target proteins are disaggregated by CLPX, which also regulates heme biosynthesis via unfolding ALAS enzymes, providing access for pyridoxal-5'-phosphate (PLP). Despite efforts in diverse organisms with multiple techniques, CLPXP substrates remain controversial. Here, avoiding recombinant overexpression, we employed complexomics in mitochondria from three mouse tissues to identify endogenous targets. A CLPP absence caused the accumulation and dispersion of CLPX-VWA8 as AAA+ unfoldases, and of PLPBP. Similar changes and CLPX-VWA8 co-migration were evident for mitoribosomal central protuberance clusters, translation factors like GFM1-HARS2, the RNA granule components LRPPRC-SLIRP, and enzymes OAT-ALDH18A1. Mitochondrially translated proteins in testes showed reductions to <30% for MTCO1-3, the mis-assembly of the complex IV supercomplex, and accumulated metal-binding assembly factors COX15-SFXN4. Indeed, heavy metal levels were increased for iron, molybdenum, cobalt, and manganese. RT-qPCR showed compensatory downregulation only for Clpx mRNA; most accumulated proteins appeared transcriptionally upregulated. Immunoblots validated VWA8, MRPL38, MRPL18, GFM1, and OAT accumulation. Co-immunoprecipitation confirmed CLPX binding to MRPL38, GFM1, and OAT, so excess CLPX and PLP may affect their activity. Our data mechanistically elucidate the mitochondrial translation fidelity deficits which underlie progressive hearing impairment in PRLTS3.
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Affiliation(s)
- Jana Key
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Suzana Gispert
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Gabriele Koepf
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Julia Steinhoff-Wagner
- TUM School of Life Sciences, Animal Nutrition and Metabolism, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising-Weihenstephan, Germany;
| | - Marina Reichlmeir
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Georg Auburger
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
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6
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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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7
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Wang C, Hou X, Guan Q, Zhou H, Zhou L, Liu L, Liu J, Li F, Li W, Liu H. RNA modification in cardiovascular disease: implications for therapeutic interventions. Signal Transduct Target Ther 2023; 8:412. [PMID: 37884527 PMCID: PMC10603151 DOI: 10.1038/s41392-023-01638-7] [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: 11/23/2022] [Revised: 08/15/2023] [Accepted: 09/03/2023] [Indexed: 10/28/2023] Open
Abstract
Cardiovascular disease (CVD) is the leading cause of death in the world, with a high incidence and a youth-oriented tendency. RNA modification is ubiquitous and indispensable in cell, maintaining cell homeostasis and function by dynamically regulating gene expression. Accumulating evidence has revealed the role of aberrant gene expression in CVD caused by dysregulated RNA modification. In this review, we focus on nine common RNA modifications: N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), N7-methylguanosine (m7G), N4-acetylcytosine (ac4C), pseudouridine (Ψ), uridylation, adenosine-to-inosine (A-to-I) RNA editing, and modifications of U34 on tRNA wobble. We summarize the key regulators of RNA modification and their effects on gene expression, such as RNA splicing, maturation, transport, stability, and translation. Then, based on the classification of CVD, the mechanisms by which the disease occurs and progresses through RNA modifications are discussed. Potential therapeutic strategies, such as gene therapy, are reviewed based on these mechanisms. Herein, some of the CVD (such as stroke and peripheral vascular disease) are not included due to the limited availability of literature. Finally, the prospective applications and challenges of RNA modification in CVD are discussed for the purpose of facilitating clinical translation. Moreover, we look forward to more studies exploring the mechanisms and roles of RNA modification in CVD in the future, as there are substantial uncultivated areas to be explored.
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Affiliation(s)
- Cong Wang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xuyang Hou
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Qing Guan
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Huiling Zhou
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Li Zhou
- Department of Pathology, National Clinical Research Center for Geriatric Disorders, The Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Lijun Liu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jijia Liu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Feng Li
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Wei Li
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Haidan Liu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
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8
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Ferreira RP, Duarte JA. Protein Turnover in Skeletal Muscle: Looking at Molecular Regulation towards an Active Lifestyle. Int J Sports Med 2023; 44:763-777. [PMID: 36854391 DOI: 10.1055/a-2044-8277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Skeletal muscle is a highly plastic tissue, able to change its mass and functional properties in response to several stimuli. Skeletal muscle mass is influenced by the balance between protein synthesis and breakdown, which is regulated by several signaling pathways. The relative contribution of Akt/mTOR signaling, ubiquitin-proteasome pathway, autophagy among other signaling pathways to protein turnover and, therefore, to skeletal muscle mass, differs depending on the wasting or loading condition and muscle type. By modulating mitochondria biogenesis, PGC-1α has a major role in the cell's bioenergetic status and, thus, on protein turnover. In fact, rates of protein turnover regulate differently the levels of distinct protein classes in response to atrophic or hypertrophic stimuli. Mitochondrial protein turnover rates may be enhanced in wasting conditions, whereas the increased turnover of myofibrillar proteins triggers muscle mass gain. The present review aims to update the knowledge on the molecular pathways implicated in the regulation of protein turnover in skeletal muscle, focusing on how distinct muscle proteins may be modulated by lifestyle interventions with emphasis on exercise training. The comprehensive analysis of the anabolic effects of exercise programs will pave the way to the tailored management of muscle wasting conditions.
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Affiliation(s)
- Rita Pinho Ferreira
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Jose Alberto Duarte
- TOXRUN - Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
- CIAFEL, Faculty of Sports, University of Porto and Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
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9
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Loguercio Polosa P, Capriglia F, Bruni F. Molecular Investigation of Mitochondrial RNA19 Role in the Pathogenesis of MELAS Disease. Life (Basel) 2023; 13:1863. [PMID: 37763267 PMCID: PMC10532844 DOI: 10.3390/life13091863] [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: 07/19/2023] [Revised: 08/16/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
In mammalian mitochondria, the processing of primary RNA transcripts involves a coordinated series of cleavage and modification events, leading to the formation of processing intermediates and mature mt-RNAs. RNA19 is an unusually stable unprocessed precursor, physiologically polyadenylated, which includes the 16S mt-rRNA, the mt-tRNALeuUUR and the mt-ND1 mRNA. These peculiarities, together with the alteration of its steady-state levels in cellular models with defects in mitochondrial function, make RNA19 a potentially important molecule for the physiological regulation of mitochondrial molecular processes as well as for the pathogenesis of mitochondrial diseases. In this work, we quantitatively and qualitatively examined RNA19 in MELAS trans-mitochondrial cybrids carrying the mtDNA 3243A>G transition and displaying a profound mitochondrial translation defect. Through a combination of isokinetic sucrose gradient and RT-qPCR experiments, we found that RNA19 accumulated and co-sedimented with the mitoribosomal large subunit (mt-LSU) in mutant cells. Intriguingly, exogenous expression of the isolated LARS2 C-terminal domain (Cterm), which was shown to rescue defective translation in MELAS cybrids, decreased the levels of mt-LSU-associated RNA19 by relegating it to the pool of free unbound RNAs. Overall, the data reported here support a regulatory role for RNA19 in mitochondrial physiopathological processes, designating this RNA precursor as a possible molecular target in view of therapeutic strategy development.
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Affiliation(s)
| | | | - Francesco Bruni
- Department of Biosciences, Biotechnologies and Environment, University of Bari ‘Aldo Moro’, 70125 Bari, Italy; (P.L.P.); (F.C.)
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10
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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: 0] [Impact Index Per Article: 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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11
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Boughanem H, Böttcher Y, Tomé-Carneiro J, López de Las Hazas MC, Dávalos A, Cayir A, Macias-González M. The emergent role of mitochondrial RNA modifications in metabolic alterations. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1753. [PMID: 35872632 DOI: 10.1002/wrna.1753] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/14/2022] [Accepted: 06/27/2022] [Indexed: 11/11/2022]
Abstract
Mitochondrial epitranscriptomics refers to the modifications occurring in all the different RNA types of mitochondria. Although the number of mitochondrial RNA modifications is less than those in cytoplasm, substantial evidence indicates that they play a critical role in accurate protein synthesis. Recent evidence supported those modifications in mitochondrial RNAs also have crucial implications in mitochondrial-related diseases. In the light of current knowledge about the involvement, the association between mitochondrial RNA modifications and diseases arises from studies focusing on mutations in both mitochondrial and nuclear DNA genes encoding enzymes involved in such modifications. Here, we review the current evidence available for mitochondrial RNA modifications and their role in metabolic disorders, and we also explore the possibility of using them as promising targets for prevention and early detection. Finally, we discuss future directions of mitochondrial epitranscriptomics in these metabolic alterations, and how these RNA modifications may offer a new diagnostic and theragnostic avenue for preventive purposes. This article is categorized under: RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Hatim Boughanem
- Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clínica de Endocrinología y Nutrición del Hospital Virgen de la Victoria and University of Málaga, Spain.,Instituto de Salud Carlos III (ISCIII), Consorcio CIBER, M.P. Fisiopatología de la Obesidad y Nutrición (CIBERObn), Madrid, Spain
| | - Yvonne Böttcher
- Institute of Clinical Medicine, Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway.,Akershus Universitetssykehus, Medical Department, Lørenskog, Norway
| | - João Tomé-Carneiro
- Laboratory of Functional Foods, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Madrid, Spain
| | - María-Carmen López de Las Hazas
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Madrid, Spain
| | - Alberto Dávalos
- Laboratory of Epigenetics of Lipid Metabolism, Madrid Institute for Advanced Studies (IMDEA)-Food, CEI UAM + CSIC, Madrid, Spain
| | - Akin Cayir
- Vocational Health College, Canakkale Onsekiz Mart University, Canakkale, Turkey.,Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus Universitetssykehus, Lørenskog, Norway
| | - Manuel Macias-González
- Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clínica de Endocrinología y Nutrición del Hospital Virgen de la Victoria and University of Málaga, Spain.,Instituto de Salud Carlos III (ISCIII), Consorcio CIBER, M.P. Fisiopatología de la Obesidad y Nutrición (CIBERObn), Madrid, Spain
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12
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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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13
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Whole genome sequencing exploitation analysis of dibutyl phthalate by strain Stenotrophomonas acidaminiphila BDBP 071. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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14
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Ziemann M, Wu W, Deng XL, Du XJ. Transcriptomic Analysis of Dysregulated Genes of the nDNA-mtDNA Axis in a Mouse Model of Dilated Cardiomyopathy. Front Genet 2022; 13:921610. [PMID: 35754828 PMCID: PMC9214240 DOI: 10.3389/fgene.2022.921610] [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] [Received: 04/22/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022] Open
Abstract
Background: Mitochondrial dysfunction is implicated in the development of cardiomyopathy and heart failure. Transcription of mitochondrial DNA (mtDNA) encoded genes and subsequent protein synthesis are tightly regulated by nuclear DNA (nDNA) encoded proteins forming the nDNA-mtDNA axis. The scale of abnormalities in this axis in dilated cardiomyopathy (DCM) is unclear. We previously demonstrated, in a mouse DCM model with cardiac Mst1 overexpression, extensive downregulation of mitochondrial genes and mitochondrial dysfunction. Using the pre-acquired transcriptome sequencing database, we studied expression of gene sets of the nDNA-mtDNA axis. Methods: Using RNA-sequencing data from DCM hearts of mice at early and severe disease stages, transcriptome was performed for dysregulated nDNA-encoded gene sets that govern mtDNA transcription and in situ protein synthesis. To validate gene data, expression of a panel of proteins was determined by immunoblotting. Results: Relative to littermate controls, DCM hearts showed significant downregulation of all mtDNA encoded mRNAs, as well as mtDNA transcriptional activators. Downregulation was also evident for gene sets of mt-rRNA processing, aminoacyl-tRNA synthases, and mitoribosome subunits for in situ protein synthesis. Multiple downregulated genes belong to mitochondrial protein-importing machinery indicating compromised importing of proteins for mtDNA transcription and translation. Diverse changes were genes of mtRNA-binding proteins that govern maturation and stability of mtDNA-derived RNAs. Expression of mtDNA replicome genes was largely unchanged. These changes were similarly observed in mouse hearts at early and severe stages of DCM. Conclusion: Transcriptome revealed in our DCM model dysregulation of multiple gene sets of the nDNA-mtDNA axis, that is, expected to interfere with mtDNA transcription and in situ protein synthesis. Dysfunction of the nDNA-mtDNA axis might contribute to mitochondrial dysfunction and ultimately development of DCM.
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Affiliation(s)
- Mark Ziemann
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Wei Wu
- Key Laboratory of Environment and Genes Related to Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ministry of Education, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiu-Ling Deng
- Key Laboratory of Environment and Genes Related to Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ministry of Education, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiao-Jun Du
- Key Laboratory of Environment and Genes Related to Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ministry of Education, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
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15
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Mitochondrial Ribosome Dysfunction in Human Alveolar Type II Cells in Emphysema. Biomedicines 2022; 10:biomedicines10071497. [PMID: 35884802 PMCID: PMC9313339 DOI: 10.3390/biomedicines10071497] [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: 11/10/2021] [Revised: 04/17/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022] Open
Abstract
Pulmonary emphysema is characterized by airspace enlargement and the destruction of alveoli. Alveolar type II (ATII) cells are very abundant in mitochondria. OXPHOS complexes are composed of proteins encoded by the mitochondrial and nuclear genomes. Mitochondrial 12S and 16S rRNAs are required to assemble the small and large subunits of the mitoribosome, respectively. We aimed to determine the mechanism of mitoribosome dysfunction in ATII cells in emphysema. ATII cells were isolated from control nonsmokers and smokers, and emphysema patients. Mitochondrial transcription and translation were analyzed. We also determined the miRNA expression. Decreases in ND1 and UQCRC2 expression levels were found in ATII cells in emphysema. Moreover, nuclear NDUFS1 and SDHB levels increased, and mitochondrial transcribed ND1 protein expression decreased. These results suggest an impairment of the nuclear and mitochondrial stoichiometry in this disease. We also detected low levels of the mitoribosome structural protein MRPL48 in ATII cells in emphysema. Decreased 16S rRNA expression and increased 12S rRNA levels were observed. Moreover, we analyzed miR4485-3p levels in this disease. Our results suggest a negative feedback loop between miR-4485-3p and 16S rRNA. The obtained results provide molecular mechanisms of mitoribosome dysfunction in ATII cells in emphysema.
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16
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Wu T, Mao L, Chen C, Yin F, Peng J. A novel homozygous missense mutation in the FASTKD2 gene leads to Lennox-Gastaut syndrome. J Hum Genet 2022; 67:589-594. [PMID: 35729327 DOI: 10.1038/s10038-022-01056-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/27/2022] [Accepted: 06/13/2022] [Indexed: 11/09/2022]
Abstract
FASTKD2 encodes an RNA-binding protein, which is a key post-transcriptional regulator of mitochondrial gene expression. Mutations in FASTKD2 have recently been found in mitochondrial encephalomyopathy, which is characterized by a deficiency in mitochondrial function. To date, seven patients have been reported. Six patients were identified with nonsense or frameshift mutations in the FASTKD2 gene, and only one patient harbored a missense mutation and a nonsense mutation. Here, we identified a novel FASTKD2 homozygous mutation, c.911 T > C, in a patient diagnosed with Lennox-Gastaut syndrome. We observed that the expression of FASTKD2 and the levels of mitochondrial 16 S rRNA were lower in the patient than in the unaffected controls. In conclusion, the missense mutation c.911 T > C caused loss of function in FASTKD2, which was associated with a new phenotype, Lennox-Gastaut syndrome.
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Affiliation(s)
- Tenghui Wu
- Department of Pediatrics, Xiangya Hospital Central South University, Changsha, 410008, China.,Hunan Children's Mental Disorders Research Center, XiangYa Hospital, Central South University, Changsha, 410008, China
| | - Leilei Mao
- Department of Pediatrics, Xiangya Hospital Central South University, Changsha, 410008, China.,Hunan Children's Mental Disorders Research Center, XiangYa Hospital, Central South University, Changsha, 410008, China
| | - Chen Chen
- Department of Pediatrics, Xiangya Hospital Central South University, Changsha, 410008, China.,Hunan Children's Mental Disorders Research Center, XiangYa Hospital, Central South University, Changsha, 410008, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital Central South University, Changsha, 410008, China.,Hunan Children's Mental Disorders Research Center, XiangYa Hospital, Central South University, Changsha, 410008, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital Central South University, Changsha, 410008, China. .,Hunan Children's Mental Disorders Research Center, XiangYa Hospital, Central South University, Changsha, 410008, China.
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17
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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: 1] [Impact Index Per Article: 0.5] [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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18
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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: 37] [Impact Index Per Article: 18.5] [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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19
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Croon M, Szczepanowska K, Popovic M, Lienkamp C, Senft K, Brandscheid CP, Bock T, Gnatzy-Feik L, Ashurov A, Acton RJ, Kaul H, Pujol C, Rosenkranz S, Krüger M, Trifunovic A. FGF21 modulates mitochondrial stress response in cardiomyocytes only under mild mitochondrial dysfunction. SCIENCE ADVANCES 2022; 8:eabn7105. [PMID: 35385313 PMCID: PMC8986112 DOI: 10.1126/sciadv.abn7105] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/11/2022] [Indexed: 05/10/2023]
Abstract
The mitochondrial integrated stress response (mitoISR) has emerged as a major adaptive pathway to respiratory chain deficiency, but both the tissue specificity of its regulation, and how mitoISR adapts to different levels of mitochondrial dysfunction are largely unknown. Here, we report that diverse levels of mitochondrial cardiomyopathy activate mitoISR, including high production of FGF21, a cytokine with both paracrine and endocrine function, shown to be induced by respiratory chain dysfunction. Although being fully dispensable for the cell-autonomous and systemic responses to severe mitochondrial cardiomyopathy, in the conditions of mild-to-moderate cardiac OXPHOS dysfunction, FGF21 regulates a portion of mitoISR. In the absence of FGF21, a large part of the metabolic adaptation to mitochondrial dysfunction (one-carbon metabolism, transsulfuration, and serine and proline biosynthesis) is strongly blunted, independent of the primary mitoISR activator ATF4. Collectively, our work highlights the complexity of mitochondrial stress responses by revealing the importance of the tissue specificity and dose dependency of mitoISR.
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Affiliation(s)
- Marijana Croon
- Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, D-50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Karolina Szczepanowska
- Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, D-50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine (CMMC), University of Cologne, 50931 Cologne, Germany
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
| | - Milica Popovic
- Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, D-50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
- Cologne Cardiovascular Research Center (CCRC), University of Cologne, 50931 Cologne, Germany
| | - Christina Lienkamp
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Katharina Senft
- Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, D-50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Christoph Paul Brandscheid
- Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, D-50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Theresa Bock
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
- Institute of Genetics, University of Cologne, 50931 Cologne, Germany
| | - Leoni Gnatzy-Feik
- Cologne Cardiovascular Research Center (CCRC), University of Cologne, 50931 Cologne, Germany
- Klinik III für Innere Medizin, Herzzentrum, University of Cologne, Kerpener Str, 62, 50937 Cologne, Germany
| | - Artem Ashurov
- Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, D-50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Richard James Acton
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Harshita Kaul
- Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, D-50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Claire Pujol
- Institut Pasteur, UMR3691 CNRS, Université de Paris, 75015 Paris, France
| | - Stephan Rosenkranz
- Center for Molecular Medicine (CMMC), University of Cologne, 50931 Cologne, Germany
- Cologne Cardiovascular Research Center (CCRC), University of Cologne, 50931 Cologne, Germany
- Klinik III für Innere Medizin, Herzzentrum, University of Cologne, Kerpener Str, 62, 50937 Cologne, Germany
| | - Marcus Krüger
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine (CMMC), University of Cologne, 50931 Cologne, Germany
- Institute of Genetics, University of Cologne, 50931 Cologne, Germany
| | - Aleksandra Trifunovic
- Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, D-50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine (CMMC), University of Cologne, 50931 Cologne, Germany
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20
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Miranda M, Bonekamp NA, Kühl I. Starting the engine of the powerhouse: mitochondrial transcription and beyond. Biol Chem 2022; 403:779-805. [PMID: 35355496 DOI: 10.1515/hsz-2021-0416] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/09/2022] [Indexed: 12/25/2022]
Abstract
Mitochondria are central hubs for cellular metabolism, coordinating a variety of metabolic reactions crucial for human health. Mitochondria provide most of the cellular energy via their oxidative phosphorylation (OXPHOS) system, which requires the coordinated expression of genes encoded by both the nuclear (nDNA) and mitochondrial genomes (mtDNA). Transcription of mtDNA is not only essential for the biogenesis of the OXPHOS system, but also generates RNA primers necessary to initiate mtDNA replication. Like the prokaryotic system, mitochondria have no membrane-based compartmentalization to separate the different steps of mtDNA maintenance and expression and depend entirely on nDNA-encoded factors imported into the organelle. Our understanding of mitochondrial transcription in mammalian cells has largely progressed, but the mechanisms regulating mtDNA gene expression are still poorly understood despite their profound importance for human disease. Here, we review mechanisms of mitochondrial gene expression with a focus on the recent findings in the field of mammalian mtDNA transcription and disease phenotypes caused by defects in proteins involved in this process.
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Affiliation(s)
- Maria Miranda
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, D-50931, Germany
| | - Nina A Bonekamp
- Department of Neuroanatomy, Mannheim Center for Translational Neurosciences (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, D-68167, Germany
| | - Inge Kühl
- Department of Cell Biology, Institute of Integrative Biology of the Cell (I2BC), UMR9198, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, F-91190, France
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21
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Lee RG, Balasubramaniam S, Stentenbach M, Kralj T, McCubbin T, Padman B, Smith J, Riley LG, Priyadarshi A, Peng L, Nuske MR, Webster R, Peacock K, Roberts P, Stark Z, Lemire G, Ito YA, Boycott KM, Geraghty MT, van Klinken JB, Ferdinandusse S, Zhou Y, Walsh R, Marcellin E, Thorburn DR, Rosciolli T, Fletcher J, Rackham O, Vaz FM, Reid GE, Filipovska A. Deleterious variants in CRLS1 lead to cardiolipin deficiency and cause an autosomal recessive multi-system mitochondrial disease. Hum Mol Genet 2022; 31:3597-3612. [PMID: 35147173 PMCID: PMC9616573 DOI: 10.1093/hmg/ddac040] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/01/2022] [Accepted: 02/06/2022] [Indexed: 01/27/2023] Open
Abstract
Mitochondrial diseases are a group of inherited diseases with highly varied and complex clinical presentations. Here, we report four individuals, including two siblings, affected by a progressive mitochondrial encephalopathy with biallelic variants in the cardiolipin biosynthesis gene CRLS1. Three affected individuals had a similar infantile presentation comprising progressive encephalopathy, bull's eye maculopathy, auditory neuropathy, diabetes insipidus, autonomic instability, cardiac defects and early death. The fourth affected individual presented with chronic encephalopathy with neurodevelopmental regression, congenital nystagmus with decreased vision, sensorineural hearing loss, failure to thrive and acquired microcephaly. Using patient-derived fibroblasts, we characterized cardiolipin synthase 1 (CRLS1) dysfunction that impaired mitochondrial morphology and biogenesis, providing functional evidence that the CRLS1 variants cause mitochondrial disease. Lipid profiling in fibroblasts from two patients further confirmed the functional defect demonstrating reduced cardiolipin levels, altered acyl-chain composition and significantly increased levels of phosphatidylglycerol, the substrate of CRLS1. Proteomic profiling of patient cells and mouse Crls1 knockout cell lines identified both endoplasmic reticular and mitochondrial stress responses, and key features that distinguish between varying degrees of cardiolipin insufficiency. These findings support that deleterious variants in CRLS1 cause an autosomal recessive mitochondrial disease, presenting as a severe encephalopathy with multi-systemic involvement. Furthermore, we identify key signatures in cardiolipin and proteome profiles across various degrees of cardiolipin loss, facilitating the use of omics technologies to guide future diagnosis of mitochondrial diseases.
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Affiliation(s)
| | | | - Maike Stentenbach
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA 6009, Australia,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia,ARC Centre of Excellence in Synthetic Biology, Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Tom Kralj
- School of Chemistry, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Tim McCubbin
- Australian Institute for Bioengineering and Nanotechnology, and Queensland Node of Metabolomics Australia,The University of Queensland, St Lucia, QLD 4072, Australia
| | - Benjamin Padman
- Centre for Microscopy, Characterisation and Analysis, The University of WA, Perth, WA 6009, Australia
| | - Janine Smith
- Discipline of Genomic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia,Department of Clinical Genetics, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Lisa G Riley
- Rare Diseases Functional Genomics, Kids Research, The Children’s Hospital at Westmead and Children’s Medical Research Institute, Sydney, NSW 2145, Australia,Discipline of Child and Adolescent Health, University of Sydney, Sydney, NSW 2145, Australia
| | - Archana Priyadarshi
- Discipline of Child and Adolescent Health, University of Sydney, Sydney, NSW 2145, Australia,Neonatal Intensive Care Unit, Westmead Hospital, Sydney, NSW 2145, Australia
| | - Liuyu Peng
- School of Chemistry, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Madison R Nuske
- School of Chemistry, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Richard Webster
- Department of Paediatrics, University of Melbourne, VIC 3052, Australia
| | - Ken Peacock
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia,General Paediatric Medicine, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Philip Roberts
- Heart Centre for Children, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Zornitza Stark
- University of Melbourne, Parkville, VIC 3052, Australia,Australian Genomics, Melbourne, VIC 3052, Australia,Victorian Clinical Genetics Services, Melbourne, VIC 3052, Australia
| | - Gabrielle Lemire
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Yoko A Ito
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | | | - Kym M Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Michael T Geraghty
- Metabolics and Newborn Screening, Pediatrics, Children’s Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Jan Bert van Klinken
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands,Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands,Department of Human Genetics, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
| | - Sacha Ferdinandusse
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands
| | - Ying Zhou
- NSW Health Pathology, Randwick, NSW 2145, Australia
| | | | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, and Queensland Node of Metabolomics Australia,The University of Queensland, St Lucia, QLD 4072, Australia
| | - David R Thorburn
- University of Melbourne, Parkville, VIC 3052, Australia,Victorian Clinical Genetics Services, Melbourne, VIC 3052, Australia,Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | - Tony Rosciolli
- NSW Health Pathology, Randwick, NSW 2145, Australia,Neuroscience Research Australia (NeuRA), University of New South Wales, Sydney, NSW 2145, Australia
| | | | - Oliver Rackham
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, Nedlands, WA 6009, Australia,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia,ARC Centre of Excellence in Synthetic Biology, Centre for Medical Research, The University of Western Australia, 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
| | - Frédéric M Vaz
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, 1105 AZ Amsterdam, The Netherlands,Core Facility Metabolomics, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands,Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Gavin E Reid
- School of Chemistry, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
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22
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Ohkubo A, Van Haute L, Rudler DL, Stentenbach M, Steiner FA, Rackham O, Minczuk M, Filipovska A, Martinou JC. The FASTK family proteins fine-tune mitochondrial RNA processing. PLoS Genet 2021; 17:e1009873. [PMID: 34748562 PMCID: PMC8601606 DOI: 10.1371/journal.pgen.1009873] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/18/2021] [Accepted: 10/11/2021] [Indexed: 12/28/2022] Open
Abstract
Transcription of the human mitochondrial genome and correct processing of the two long polycistronic transcripts are crucial for oxidative phosphorylation. According to the tRNA punctuation model, nucleolytic processing of these large precursor transcripts occurs mainly through the excision of the tRNAs that flank most rRNAs and mRNAs. However, some mRNAs are not punctuated by tRNAs, and it remains largely unknown how these non-canonical junctions are resolved. The FASTK family proteins are emerging as key players in non-canonical RNA processing. Here, we have generated human cell lines carrying single or combined knockouts of several FASTK family members to investigate their roles in non-canonical RNA processing. The most striking phenotypes were obtained with loss of FASTKD4 and FASTKD5 and with their combined double knockout. Comprehensive mitochondrial transcriptome analyses of these cell lines revealed a defect in processing at several canonical and non-canonical RNA junctions, accompanied by an increase in specific antisense transcripts. Loss of FASTKD5 led to the most severe phenotype with marked defects in mitochondrial translation of key components of the electron transport chain complexes and in oxidative phosphorylation. We reveal that the FASTK protein family members are crucial regulators of non-canonical junction and non-coding mitochondrial RNA processing. As a legacy of their bacterial origin, mitochondria have retained their own genome with a unique gene expression system. All mitochondrially encoded proteins are essential components of the respiratory chain. Therefore, the mitochondrial gene expression is crucial for their iconic role as the ‘powerhouse of the cell’–ATP synthesis through oxidative phosphorylation. Consistently, defects in enzymes involved in this gene expression system are a common source of incurable inherited metabolic disorders, called mitochondrial diseases. The human mitochondrial transcription generates long polycistronic transcripts that carry information for multiple genes, so that the expression level of each gene is mainly regulated through post-transcriptional events. The polycistronic transcript first undergoes RNA processing, where individual mRNA, rRNA, and tRNA are cleaved off. However, its entire molecular mechanism remains unclear, and in particular, ‘non-canonical’ RNA processing has been poorly understood. To address this question, we studied the FASTK family proteins, emerging key mitochondrial post-transcriptional regulators. We generated different human cell lines carrying single or combined disruption of FASTKD3, FASTKD4, and FASTKD5 genes, and analyzed them using biochemical and genetic approaches. We show that the FASTK family members fine-tune the processing of both ‘canonical’ and ‘non-canonical’ mitochondrial RNA junctions.
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Affiliation(s)
- Akira Ohkubo
- Department of Cell Biology, University of Geneva, Geneva, Switzerland
| | - Lindsey Van Haute
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Danielle L. Rudler
- Harry Perkins Institute of Medical Research, Queen Elizabeth II Medical Centre, Perth, Australia
- ARC Centre of Excellence in Synthetic Biology, Queen Elizabeth II Medical Centre, Perth, Australia
- Centre for Medical Research, The University of Western Australia, Queen Elizabeth II Medical Centre, Perth, Australia
| | - Maike Stentenbach
- Harry Perkins Institute of Medical Research, Queen Elizabeth II Medical Centre, Perth, Australia
- ARC Centre of Excellence in Synthetic Biology, Queen Elizabeth II Medical Centre, Perth, Australia
- Centre for Medical Research, The University of Western Australia, Queen Elizabeth II Medical Centre, Perth, Australia
| | - Florian A. Steiner
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, Queen Elizabeth II Medical Centre, Perth, Australia
- ARC Centre of Excellence in Synthetic Biology, Queen Elizabeth II Medical Centre, Perth, Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Australia
- Curtin Health Innovation Research Institute, Curtin University, Perth, Australia
- Telethon Kids Institute, Perth Children’s Hospital, Perth, Australia
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, Queen Elizabeth II Medical Centre, Perth, Australia
- ARC Centre of Excellence in Synthetic Biology, Queen Elizabeth II Medical Centre, Perth, Australia
- Centre for Medical Research, The University of Western Australia, Queen Elizabeth II Medical Centre, Perth, Australia
- Telethon Kids Institute, Perth Children’s Hospital, Perth, Australia
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
- * E-mail: (AF); (J-CM)
| | - Jean-Claude Martinou
- Department of Cell Biology, University of Geneva, Geneva, Switzerland
- * E-mail: (AF); (J-CM)
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23
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Tang JX, Pyle A, Taylor RW, Oláhová M. Interrogating Mitochondrial Biology and Disease Using CRISPR/Cas9 Gene Editing. Genes (Basel) 2021; 12:genes12101604. [PMID: 34680998 PMCID: PMC8536160 DOI: 10.3390/genes12101604] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/07/2021] [Accepted: 10/09/2021] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial disease originates from genetic changes that impact human bodily functions by disrupting the mitochondrial oxidative phosphorylation system. MitoCarta is a curated and published inventory that sheds light on the mitochondrial proteome, but the function of some mitochondrially-localised proteins remains poorly characterised. Consequently, various gene editing systems have been employed to uncover the involvement of these proteins in mitochondrial biology and disease. CRISPR/Cas9 is an efficient, versatile, and highly accurate genome editing tool that was first introduced over a decade ago and has since become an indispensable tool for targeted genetic manipulation in biological research. The broad spectrum of CRISPR/Cas9 applications serves as an attractive and tractable system to study genes and pathways that are essential for the regulation and maintenance of mitochondrial health. It has opened possibilities of generating reliable cell and animal models of human disease, and with further exploitation of the technology, large-scale genomic screenings have uncovered a wealth of fundamental mechanistic insights. In this review, we describe the applications of CRISPR/Cas9 system as a genome editing tool to uncover new insights into pathomechanisms of mitochondrial diseases and/or biological processes involved in mitochondrial function.
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Affiliation(s)
- Jia-Xin Tang
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (J.-X.T.); (A.P.); (R.W.T.)
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (J.-X.T.); (A.P.); (R.W.T.)
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (J.-X.T.); (A.P.); (R.W.T.)
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4HH, UK
| | - Monika Oláhová
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (J.-X.T.); (A.P.); (R.W.T.)
- Correspondence:
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24
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Xavier VJ, Martinou JC. RNA Granules in the Mitochondria and Their Organization under Mitochondrial Stresses. Int J Mol Sci 2021; 22:9502. [PMID: 34502411 PMCID: PMC8431320 DOI: 10.3390/ijms22179502] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 12/25/2022] Open
Abstract
The human mitochondrial genome (mtDNA) regulates its transcription products in specialised and distinct ways as compared to nuclear transcription. Thanks to its mtDNA mitochondria possess their own set of tRNAs, rRNAs and mRNAs that encode a subset of the protein subunits of the electron transport chain complexes. The RNA regulation within mitochondria is organised within specialised, membraneless, compartments of RNA-protein complexes, called the Mitochondrial RNA Granules (MRGs). MRGs were first identified to contain nascent mRNA, complexed with many proteins involved in RNA processing and maturation and ribosome assembly. Most recently, double-stranded RNA (dsRNA) species, a hybrid of the two complementary mRNA strands, were found to form granules in the matrix of mitochondria. These RNA granules are therefore components of the mitochondrial post-transcriptional pathway and as such play an essential role in mitochondrial gene expression. Mitochondrial dysfunctions in the form of, for example, RNA processing or RNA quality control defects, or inhibition of mitochondrial fission, can cause the loss or the aberrant accumulation of these RNA granules. These findings underline the important link between mitochondrial maintenance and the efficient expression of its genome.
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Affiliation(s)
| | - Jean-Claude Martinou
- Department of Cell Biology, Faculty of Sciences, University of Geneva, 1205 Geneva, Switzerland;
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25
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Hilander T, Jackson CB, Robciuc M, Bashir T, Zhao H. The roles of assembly factors in mammalian mitoribosome biogenesis. Mitochondrion 2021; 60:70-84. [PMID: 34339868 DOI: 10.1016/j.mito.2021.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 02/08/2023]
Abstract
As ancient bacterial endosymbionts of eukaryotic cells, mitochondria have retained their own circular DNA as well as protein translation system including mitochondrial ribosomes (mitoribosomes). In recent years, methodological advancements in cryoelectron microscopy and mass spectrometry have revealed the extent of the evolutionary divergence of mitoribosomes from their bacterial ancestors and their adaptation to the synthesis of 13 mitochondrial DNA encoded oxidative phosphorylation complex subunits. In addition to the structural data, the first assembly pathway maps of mitoribosomes have started to emerge and concomitantly also the assembly factors involved in this process to achieve fully translational competent particles. These transiently associated factors assist in the intricate assembly process of mitoribosomes by enhancing protein incorporation, ribosomal RNA folding and modification, and by blocking premature or non-native protein binding, for example. This review focuses on summarizing the current understanding of the known mammalian mitoribosome assembly factors and discussing their possible roles in the assembly of small or large mitoribosomal subunits.
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Affiliation(s)
- Taru Hilander
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland.
| | - Christopher B Jackson
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Finland.
| | - Marius Robciuc
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Tanzeela Bashir
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Hongxia Zhao
- Faculty of Biological and Environmental Sciences, University of Helsinki, Finland; Key Laboratory of Stem Cell and Biopharmaceutical Technology, School of Life Sciences, Guangxi Normal University, Guangxi, China.
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26
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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: 10] [Impact Index Per Article: 3.3] [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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27
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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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28
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Sciarretta S, Forte M, Frati G, Sadoshima J. The complex network of mTOR signaling in the heart. Cardiovasc Res 2021; 118:424-439. [PMID: 33512477 DOI: 10.1093/cvr/cvab033] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/13/2020] [Accepted: 01/26/2021] [Indexed: 12/13/2022] Open
Abstract
The mechanistic target of rapamycin (mTOR) integrates several intracellular and extracellular signals involved in the regulation of anabolic and catabolic processes. mTOR assembles into two macromolecular complexes, named mTORC1 and mTORC2, which have different regulators, substrates and functions. Studies of gain- and loss-of-function animal models of mTOR signaling revealed that mTORC1/2 elicit both adaptive and maladaptive functions in the cardiovascular system. Both mTORC1 and mTORC2 are indispensable for driving cardiac development and cardiac adaption to stress, such as pressure overload. However, persistent and deregulated mTORC1 activation in the heart is detrimental during stress and contributes to the development and progression of cardiac remodeling and genetic and metabolic cardiomyopathies. In this review, we discuss the latest findings regarding the role of mTOR in the cardiovascular system, both under basal conditions and during stress, such as pressure overload, ischemia and metabolic stress. Current data suggest that mTOR modulation may represent a potential therapeutic strategy for the treatment of cardiac diseases.
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Affiliation(s)
- Sebastiano Sciarretta
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy.,IRCCS Neuromed, Pozzilli (IS), Italy
| | | | - Giacomo Frati
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy.,IRCCS Neuromed, Pozzilli (IS), Italy
| | - Junichi Sadoshima
- Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, Rutgers New Jersey Medical School, Newark, NJ, USA
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29
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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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30
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Isokallio MA, Stewart JB. High-Throughput Detection of mtDNA Mutations Leading to tRNA Processing Errors. Methods Mol Biol 2021; 2192:117-132. [PMID: 33230770 DOI: 10.1007/978-1-0716-0834-0_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Some mutations in the tRNA genes of mitochondrial DNA (mtDNA) have been demonstrated to affect the processing of the mitochondrial transcriptome in human patients with mitochondrial disease. A recent analysis of mtDNA mutations in 527 human tumors revealed that approximately a quarter of the somatic mt-tRNA gene mutations lead to aberrant processing of the mitochondrial transcriptome in these tumors. Here, we describe a method, based on mtDNA mutations induced by the mtDNA mutator mouse, to map the sites that lead to transcript processing abnormalities. Mutations in the mtDNA are identified and quantified by amplicon-based mtDNA sequencing, and compared to the allelic ratios observed in matched RNASeq data. Strong deviation in the variant allele frequencies between the amplicon and RNASeq data suggests that such mutations lead to disruptions in mitochondrial transcript processing.
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31
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Investigating Mitochondrial Transcriptomes and RNA Processing Using Circular RNA Sequencing. Methods Mol Biol 2021; 2192:43-57. [PMID: 33230764 DOI: 10.1007/978-1-0716-0834-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Transcriptomic technologies have revolutionized the study of gene expression and RNA biology. Different RNA sequencing methods enable the analyses of diverse species of transcripts, including their abundance, processing, stability, and other specific features. Mitochondrial transcriptomics has benefited from these technologies that have revealed the surprising complexity of its RNAs. Here we describe a method based upon cyclization of mitochondrial RNAs and next generation sequencing to analyze the steady-state levels and sizes of mitochondrial RNAs, their degradation products, as well as their processing intermediates by capturing both 5' and 3' ends of transcripts.
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32
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Perks KL, Ferreira N, Ermer JA, Rudler DL, Richman TR, Rossetti G, Matthews VB, Ward NC, Rackham O, Filipovska A. Reduced mitochondrial translation prevents diet-induced metabolic dysfunction but not inflammation. Aging (Albany NY) 2020; 12:19677-19700. [PMID: 33024056 PMCID: PMC7732297 DOI: 10.18632/aging.104010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/21/2020] [Indexed: 01/24/2023]
Abstract
The contribution of dysregulated mitochondrial gene expression and consequent imbalance in biogenesis is not well understood in metabolic disorders such as insulin resistance and obesity. The ribosomal RNA maturation protein PTCD1 is essential for mitochondrial protein synthesis and its reduction causes adult-onset obesity and liver steatosis. We used haploinsufficient Ptcd1 mice fed normal or high fat diets to understand how changes in mitochondrial biogenesis can lead to metabolic dysfunction. We show that Akt-stimulated reduction in lipid content and upregulation of mitochondrial biogenesis effectively protected mice with reduced mitochondrial protein synthesis from excessive weight gain on a high fat diet, resulting in improved glucose and insulin tolerance and reduced lipid accumulation in the liver. However, inflammation of the white adipose tissue and early signs of fibrosis in skeletal muscle, as a consequence of reduced protein synthesis, were exacerbated with the high fat diet. We identify that reduced mitochondrial protein synthesis and OXPHOS biogenesis can be recovered in a tissue-specific manner via Akt-mediated increase in insulin sensitivity and transcriptional activation of the mitochondrial stress response.
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Affiliation(s)
- Kara L. Perks
- Harry Perkins Institute of Medical Research, Centre for Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, Western Australia, Australia,School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Nicola Ferreira
- Harry Perkins Institute of Medical Research, Centre for Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, Western Australia, Australia
| | - Judith A. Ermer
- Harry Perkins Institute of Medical Research, Centre for Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, Western Australia, Australia
| | - Danielle L. Rudler
- Harry Perkins Institute of Medical Research, Centre for Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, Western Australia, Australia
| | - Tara R. Richman
- Harry Perkins Institute of Medical Research, Centre for Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, Western Australia, Australia
| | - Giulia Rossetti
- Harry Perkins Institute of Medical Research, Centre for Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, Western Australia, Australia
| | - Vance B. Matthews
- School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Natalie C. Ward
- Medical School, Royal Perth Hospital Unit, University of Western Australia, Perth, Western Australia, Australia,School of Public Health and Curtin Health Innovation Research Institute, Curtin University, Perth, Western Australia, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, Centre for Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, Western Australia, Australia,School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Western Australia, Australia,Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, Centre for Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, Western Australia, Australia,School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia
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33
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Singh AP, Salvatori R, Aftab W, Kohler A, Carlström A, Forne I, Imhof A, Ott M. Molecular Connectivity of Mitochondrial Gene Expression and OXPHOS Biogenesis. Mol Cell 2020; 79:1051-1065.e10. [PMID: 32877643 DOI: 10.1016/j.molcel.2020.07.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 01/05/2023]
Abstract
Mitochondria contain their own gene expression systems, including membrane-bound ribosomes dedicated to synthesizing a few hydrophobic subunits of the oxidative phosphorylation (OXPHOS) complexes. We used a proximity-dependent biotinylation technique, BioID, coupled with mass spectrometry to delineate in baker's yeast a comprehensive network of factors involved in biogenesis of mitochondrial encoded proteins. This mitochondrial gene expression network (MiGENet) encompasses proteins involved in transcription, RNA processing, translation, or protein biogenesis. Our analyses indicate the spatial organization of these processes, thereby revealing basic mechanistic principles and the proteins populating strategically important sites. For example, newly synthesized proteins are directly handed over to ribosomal tunnel exit-bound factors that mediate membrane insertion, co-factor acquisition, or their mounting into OXPHOS complexes in a special early assembly hub. Collectively, the data reveal the connectivity of mitochondrial gene expression, reflecting a unique tailoring of the mitochondrial gene expression system.
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Affiliation(s)
- Abeer Prakash Singh
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden; Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Roger Salvatori
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden; Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Wasim Aftab
- BioMedical Center, Faculty of Medicine, Ludwig Maximilians University of Munich, 82152 Planegg-Martinsried, Germany; Graduate School for Quantitative Biosciences (QBM), Ludwig Maximilians University of Munich, 81377 Munich, Germany
| | - Andreas Kohler
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Andreas Carlström
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Ignasi Forne
- BioMedical Center, Faculty of Medicine, Ludwig Maximilians University of Munich, 82152 Planegg-Martinsried, Germany
| | - Axel Imhof
- BioMedical Center, Faculty of Medicine, Ludwig Maximilians University of Munich, 82152 Planegg-Martinsried, Germany
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden; Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden.
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34
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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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35
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Lee RG, Gao J, Siira SJ, Shearwood AM, Ermer JA, Hofferek V, Mathews JC, Zheng M, Reid GE, Rackham O, Filipovska A. Cardiolipin is required for membrane docking of mitochondrial ribosomes and protein synthesis. J Cell Sci 2020; 133:jcs240374. [PMID: 32576663 DOI: 10.1242/jcs.240374] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 06/12/2020] [Indexed: 01/01/2023] Open
Abstract
The mitochondrial inner membrane contains a unique phospholipid known as cardiolipin (CL), which stabilises the protein complexes embedded in the membrane and supports its overall structure. Recent evidence indicates that the mitochondrial ribosome may associate with the inner membrane to facilitate co-translational insertion of the hydrophobic oxidative phosphorylation (OXPHOS) proteins into the inner membrane. We generated three mutant knockout cell lines for the CL biosynthesis gene Crls1 to investigate the effects of CL loss on mitochondrial protein synthesis. Reduced CL levels caused altered mitochondrial morphology and transcriptome-wide changes that were accompanied by uncoordinated mitochondrial translation rates and impaired respiratory chain supercomplex formation. Aberrant protein synthesis was caused by impaired formation and distribution of mitochondrial ribosomes. Reduction or loss of CL resulted in divergent mitochondrial and endoplasmic reticulum stress responses. We show that CL is required to stabilise the interaction of the mitochondrial ribosome with the membrane via its association with OXA1 (also known as OXA1L) during active translation. This interaction facilitates insertion of newly synthesised mitochondrial proteins into the inner membrane and stabilises the respiratory supercomplexes.
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Affiliation(s)
- Richard G Lee
- 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
| | - Junjie Gao
- School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Stefan J Siira
- 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
| | - Anne-Marie Shearwood
- 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
| | - Judith A Ermer
- 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
| | - Vinzenz Hofferek
- School of Chemistry, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - James C Mathews
- 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
| | - Minghao Zheng
- School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Gavin E Reid
- School of Chemistry, The University of Melbourne, Parkville, Victoria, 3010, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, 3010, 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
- 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
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
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36
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Black M, Arumugam P, Shukla S, Pradhan A, Ustiyan V, Milewski D, Kalinichenko VV, Kalin TV. FOXM1 nuclear transcription factor translocates into mitochondria and inhibits oxidative phosphorylation. Mol Biol Cell 2020; 31:1411-1424. [PMID: 32348194 PMCID: PMC7353143 DOI: 10.1091/mbc.e19-07-0413] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 12/31/2022] Open
Abstract
Forkhead box M1 (FOXM1), a nuclear transcription factor that activates cell cycle regulatory genes, is highly expressed in a majority of human cancers. The function of FOXM1 independent of nuclear transcription is unknown. In the present study, we found the FOXM1 protein inside the mitochondria. Using site-directed mutagenesis, we generated FOXM1 mutant proteins that localized to distinct cellular compartments, uncoupling the nuclear and mitochondrial functions of FOXM1. Directing FOXM1 into the mitochondria decreased mitochondrial mass, membrane potential, respiration, and electron transport chain (ETC) activity. In mitochondria, the FOXM1 directly bound to and increased the pentatricopeptide repeat domain 1 (PTCD1) protein, a mitochondrial leucine-specific tRNA binding protein that inhibits leucine-rich ETC complexes. Mitochondrial FOXM1 did not change cellular proliferation. Thus, FOXM1 translocates into mitochondria and inhibits mitochondrial respiration by increasing PTCD1. We identify a new paradigm that FOXM1 regulates mitochondrial homeostasis in a process independent of nuclear transcription.
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Affiliation(s)
- Markaisa Black
- Perinatal Institute and Division of Neonatology, Perinatal and Pulmonary Biology
| | - Paritha Arumugam
- Translational Pulmonary Science Center and Division of Pulmonary Biology, Cincinnati, OH 45229-3039
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267
| | - Samriddhi Shukla
- Perinatal Institute and Division of Neonatology, Perinatal and Pulmonary Biology
| | - Arun Pradhan
- Perinatal Institute and Division of Neonatology, Perinatal and Pulmonary Biology
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267
| | - Vladimir Ustiyan
- Perinatal Institute and Division of Neonatology, Perinatal and Pulmonary Biology
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267
| | - David Milewski
- Perinatal Institute and Division of Neonatology, Perinatal and Pulmonary Biology
| | - Vladimir V. Kalinichenko
- Perinatal Institute and Division of Neonatology, Perinatal and Pulmonary Biology
- Center for Lung Regenerative Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229-3039
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267
| | - Tanya V. Kalin
- Perinatal Institute and Division of Neonatology, Perinatal and Pulmonary Biology
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267
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37
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Ccm1p is a 15S rRNA primary transcript processing factor as elucidated by a novel in vivo system in Saccharomyces cerevisiae. Curr Genet 2020; 66:775-789. [PMID: 32152734 DOI: 10.1007/s00294-020-01064-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/15/2020] [Accepted: 02/24/2020] [Indexed: 10/24/2022]
Abstract
In Saccharomyces cerevisiae, the mitoribosomal RNA of the minor subunit, 15S rRNA, is transcribed as a bicistronic transcript along with tRNAW. 5' and 3' sequences flanking the mature transcript must be removed by cleavage at the respective junctions before incorporating it into the mitoribosome. An in vivo dose-response triphasic system was created to elucidate the role of Ccm1p in the processing of 15S rRNA: Ccm1p supply ("On"), deprivation ("Off"), and resupply ("Back on"). After 72 h under "Off" status, the cells started to exhibit a complete mutant phenotype as assessed by their lack of growth in glycerol medium, while keeping their mitochondrial DNA integrity (ρ+). Full functionality of mitochondria was reacquired upon "Back on." 15S rRNA levels and phenotype followed the Ccm1p intramitochondrial concentrations throughout the "On-Off-Back on" course. Under "Off" status, cells gradually accumulated unprocessed 5' and 3' junctions, which reached significant levels at 72-96 h, probably due to a saturation of the mitochondrial degradosome (mtEXO). The Ccm1p/mtEXO mutant (Δccm1/Δdss1) showed a copious accumulation of 15S rRNA primary transcript forms, which were cleaved upon Ccm1p resupply. The gene that codes for the RNA component of RNase P was conserved in wild-type and mutant strains. Our results indicate that Ccm1p is crucial in processing the 15S rRNA primary transcript and does not stabilize the already mature 15S rRNA. Consequently, failure of this function in Δccm1 cells results, as it happens to any other unprocessed primary transcripts, in total degradation of 15S rRNA by mtEXO, whose mechanism of action is discussed.
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38
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Kim E, Jung H. Local mRNA translation in long-term maintenance of axon health and function. Curr Opin Neurobiol 2020; 63:15-22. [PMID: 32087477 DOI: 10.1016/j.conb.2020.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 12/22/2022]
Abstract
Distal axons, remote from their cell bodies and nuclei, must survive the lifetime of an organism. Recent studies have provided compelling evidence that proteins are locally synthesized in healthy, mature central nervous system axons and presynaptic terminals in vivo. Presynaptic, mitochondrial and ribosomal proteins are locally synthesized in most adult axons of diverse cell types, linking local translation to axon function and survival. Accordingly, inhibiting the intra-axonal translation of key mRNAs or the function of their translational regulators causes dying-back axon degeneration, and human mutations in RNA metabolic pathways are increasingly being associated with neurodegenerative diseases that accompany axon degeneration. Here, we summarize recent relevant findings in a highly simplified 'RNA operon'-based model and discuss open questions and future directions.
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Affiliation(s)
- Eunjin Kim
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hosung Jung
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea; Department of Anatomy, Brain Research Institute, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea.
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39
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Thompson K, Collier JJ, Glasgow RIC, Robertson FM, Pyle A, Blakely EL, Alston CL, Oláhová M, McFarland R, Taylor RW. Recent advances in understanding the molecular genetic basis of mitochondrial disease. J Inherit Metab Dis 2020; 43:36-50. [PMID: 31021000 PMCID: PMC7041634 DOI: 10.1002/jimd.12104] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/03/2019] [Accepted: 04/24/2019] [Indexed: 12/22/2022]
Abstract
Mitochondrial disease is hugely diverse with respect to associated clinical presentations and underlying genetic causes, with pathogenic variants in over 300 disease genes currently described. Approximately half of these have been discovered in the last decade due to the increasingly widespread application of next generation sequencing technologies, in particular unbiased, whole exome-and latterly, whole genome sequencing. These technologies allow more genetic data to be collected from patients with mitochondrial disorders, continually improving the diagnostic success rate in a clinical setting. Despite these significant advances, some patients still remain without a definitive genetic diagnosis. Large datasets containing many variants of unknown significance have become a major challenge with next generation sequencing strategies and these require significant functional validation to confirm pathogenicity. This interface between diagnostics and research is critical in continuing to expand the list of known pathogenic variants and concomitantly enhance our knowledge of mitochondrial biology. The increasing use of whole exome sequencing, whole genome sequencing and other "omics" techniques such as transcriptomics and proteomics will generate even more data and allow further interrogation and validation of genetic causes, including those outside of coding regions. This will improve diagnostic yields still further and emphasizes the integral role that functional assessment of variant causality plays in this process-the overarching focus of this review.
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Affiliation(s)
- Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Jack J. Collier
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Ruth I. C. Glasgow
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Fiona M. Robertson
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUK
| | - Emma L. Blakely
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Mitochondrial Diagnostic LaboratoryNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Charlotte L. Alston
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Mitochondrial Diagnostic LaboratoryNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Monika Oláhová
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Mitochondrial Diagnostic LaboratoryNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
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40
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Rudler DL, Hughes LA, Perks KL, Richman TR, Kuznetsova I, Ermer JA, Abudulai LN, Shearwood AMJ, Viola HM, Hool LC, Siira SJ, Rackham O, Filipovska A. Fidelity of translation initiation is required for coordinated respiratory complex assembly. SCIENCE ADVANCES 2019; 5:eaay2118. [PMID: 31903419 PMCID: PMC6924987 DOI: 10.1126/sciadv.aay2118] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/30/2019] [Indexed: 05/22/2023]
Abstract
Mammalian mitochondrial ribosomes are unique molecular machines that translate 11 leaderless mRNAs; however, it is not clear how mitoribosomes initiate translation, since mitochondrial mRNAs lack untranslated regions. Mitochondrial translation initiation shares similarities with prokaryotes, such as the formation of a ternary complex of fMet-tRNAMet, mRNA and the 28S subunit, but differs in the requirements for initiation factors. Mitochondria have two initiation factors: MTIF2, which closes the decoding center and stabilizes the binding of the fMet-tRNAMet to the leaderless mRNAs, and MTIF3, whose role is not clear. We show that MTIF3 is essential for survival and that heart- and skeletal muscle-specific loss of MTIF3 causes cardiomyopathy. We identify increased but uncoordinated mitochondrial protein synthesis in mice lacking MTIF3, resulting in loss of specific respiratory complexes. Ribosome profiling shows that MTIF3 is required for recognition and regulation of translation initiation of mitochondrial mRNAs and for coordinated assembly of OXPHOS complexes in vivo.
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Affiliation(s)
- Danielle L. Rudler
- Harry Perkins Institute of Medical Research, 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
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, Western Australia 6009, Australia
| | - Kara L. Perks
- Harry Perkins Institute of Medical Research, 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
| | - Tara R. Richman
- Harry Perkins Institute of Medical Research, 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
| | - Irina Kuznetsova
- Harry Perkins Institute of Medical Research, 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
| | - Judith A. Ermer
- Harry Perkins Institute of Medical Research, 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
| | - Laila N. Abudulai
- Centre for Microscopy, Characterisation and Analysis and School of Biomedical Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Anne-Marie J. Shearwood
- Harry Perkins Institute of Medical Research, 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 (Physiology), The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Livia C. Hool
- School of Human Sciences (Physiology), The University of Western Australia, Crawley, Western Australia 6009, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - Stefan J. Siira
- Harry Perkins Institute of Medical Research, 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
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, 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
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, 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
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
- Corresponding author.
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41
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Ferreira N, Perks KL, Rossetti G, Rudler DL, Hughes LA, Ermer JA, Scott LH, Kuznetsova I, Richman TR, Narayana VK, Abudulai LN, Shearwood AMJ, Cserne Szappanos H, Tull D, Yeoh GC, Hool LC, Filipovska A, Rackham O. Stress signaling and cellular proliferation reverse the effects of mitochondrial mistranslation. EMBO J 2019; 38:e102155. [PMID: 31721250 DOI: 10.15252/embj.2019102155] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 12/12/2022] Open
Abstract
Translation fidelity is crucial for prokaryotes and eukaryotic nuclear-encoded proteins; however, little is known about the role of mistranslation in mitochondria and its potential effects on metabolism. We generated yeast and mouse models with error-prone and hyper-accurate mitochondrial translation, and found that translation rate is more important than translational accuracy for cell function in mammals. Specifically, we found that mitochondrial mistranslation causes reduced overall mitochondrial translation and respiratory complex assembly rates. In mammals, this effect is compensated for by increased mitochondrial protein stability and upregulation of the citric acid cycle. Moreover, this induced mitochondrial stress signaling, which enables the recovery of mitochondrial translation via mitochondrial biogenesis, telomerase expression, and cell proliferation, and thereby normalizes metabolism. Conversely, we show that increased fidelity of mitochondrial translation reduces the rate of protein synthesis without eliciting a mitochondrial stress response. Consequently, the rate of translation cannot be recovered and this leads to dilated cardiomyopathy in mice. In summary, our findings reveal mammalian-specific signaling pathways that respond to changes in the fidelity of mitochondrial protein synthesis and affect metabolism.
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Affiliation(s)
- Nicola Ferreira
- Harry Perkins Institute of Medical Research, Nedlands, WA, Australia.,The University of Western Australia Centre for Medical Research, Crawley, WA, Australia
| | - Kara L Perks
- Harry Perkins Institute of Medical Research, Nedlands, WA, Australia.,The University of Western Australia Centre for Medical Research, Crawley, WA, Australia
| | - Giulia Rossetti
- Harry Perkins Institute of Medical Research, Nedlands, WA, Australia.,The University of Western Australia Centre for Medical Research, Crawley, WA, Australia
| | - Danielle L Rudler
- Harry Perkins Institute of Medical Research, Nedlands, WA, Australia.,The University of Western Australia Centre for Medical Research, Crawley, WA, Australia
| | - Laetitia A Hughes
- Harry Perkins Institute of Medical Research, Nedlands, WA, Australia.,The University of Western Australia Centre for Medical Research, Crawley, WA, Australia
| | - Judith A Ermer
- Harry Perkins Institute of Medical Research, Nedlands, WA, Australia.,The University of Western Australia Centre for Medical Research, Crawley, WA, Australia
| | - Louis H Scott
- Harry Perkins Institute of Medical Research, Nedlands, WA, Australia.,The University of Western Australia Centre for Medical Research, Crawley, WA, Australia
| | - Irina Kuznetsova
- Harry Perkins Institute of Medical Research, Nedlands, WA, Australia.,The University of Western Australia Centre for Medical Research, Crawley, WA, Australia
| | - Tara R Richman
- Harry Perkins Institute of Medical Research, Nedlands, WA, Australia.,The University of Western Australia Centre for Medical Research, Crawley, WA, Australia
| | - Vinod K Narayana
- Metabolomics Australia, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Vic., Australia
| | - Laila N Abudulai
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, Australia.,School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia.,The School of Biomedical Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Anne-Marie J Shearwood
- Harry Perkins Institute of Medical Research, Nedlands, WA, Australia.,The University of Western Australia Centre for Medical Research, Crawley, WA, Australia
| | | | - Dedreia Tull
- Metabolomics Australia, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Vic., Australia
| | - George C Yeoh
- Harry Perkins Institute of Medical Research, Nedlands, WA, Australia
| | - Livia C Hool
- School of Human Sciences (Physiology), The University of Western Australia, Crawley, WA, Australia.,Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, Nedlands, WA, Australia.,The University of Western Australia Centre for Medical Research, Crawley, WA, Australia.,School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, Nedlands, WA, Australia.,School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia
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42
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Busch JD, Cipullo M, Atanassov I, Bratic A, Silva Ramos E, Schöndorf T, Li X, Pearce SF, Milenkovic D, Rorbach J, Larsson NG. MitoRibo-Tag Mice Provide a Tool for In Vivo Studies of Mitoribosome Composition. Cell Rep 2019; 29:1728-1738.e9. [PMID: 31693908 PMCID: PMC6859486 DOI: 10.1016/j.celrep.2019.09.080] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/14/2019] [Accepted: 09/26/2019] [Indexed: 11/16/2022] Open
Abstract
Mitochondria harbor specialized ribosomes (mitoribosomes) necessary for the synthesis of key membrane proteins of the oxidative phosphorylation (OXPHOS) machinery located in the mitochondrial inner membrane. To date, no animal model exists to study mitoribosome composition and mitochondrial translation coordination in mammals in vivo. Here, we create MitoRibo-Tag mice as a tool enabling affinity purification and proteomics analyses of mitoribosomes and their interactome in different tissues. We also define the composition of an assembly intermediate formed in the absence of MTERF4, necessary for a late step in mitoribosomal biogenesis. We identify the orphan protein PUSL1, which interacts with a large subunit assembly intermediate, and demonstrate that it is an inner-membrane-associated mitochondrial matrix protein required for efficient mitochondrial translation. This work establishes MitoRibo-Tag mice as a powerful tool to study mitoribosomes in vivo, enabling future studies on the mitoribosome interactome under different physiological states, as well as in disease and aging. MitoRibo-Tag mice with a tag on mL62 were generated to study mitoribosomes in vivo The mitoribosome interactome of different mouse tissues was defined with proteomics PUSL1 was identified as a mitoribosome-interacting protein using MitoRibo-Tag mice MitoRibo-Tag mice allow mitoribosome analysis under different conditions and setups
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Affiliation(s)
- Jakob D Busch
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany; Faculty of Mathematics and Natural Sciences, University of Cologne, Albertus-Magnus-Platz, 50923 Cologne, Germany
| | - Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Research Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, 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, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Ana Bratic
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Eduardo Silva Ramos
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Thomas Schöndorf
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany; Faculty of Mathematics and Natural Sciences, University of Cologne, Albertus-Magnus-Platz, 50923 Cologne, Germany
| | - Xinping Li
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Sarah F Pearce
- Department of Medical Biochemistry and Biophysics, Research Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden; Max-Planck-Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Dusanka Milenkovic
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Research Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden; Max-Planck-Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany; Department of Medical Biochemistry and Biophysics, Research Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden; Max-Planck-Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.
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43
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Fleck D, Phu L, Verschueren E, Hinkle T, Reichelt M, Bhangale T, Haley B, Wang Y, Graham R, Kirkpatrick DS, Sheng M, Bingol B. PTCD1 Is Required for Mitochondrial Oxidative-Phosphorylation: Possible Genetic Association with Alzheimer's Disease. J Neurosci 2019; 39:4636-4656. [PMID: 30948477 PMCID: PMC6561697 DOI: 10.1523/jneurosci.0116-19.2019] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 12/30/2022] Open
Abstract
In addition to amyloid-β plaques and tau tangles, mitochondrial dysfunction is implicated in the pathology of Alzheimer's disease (AD). Neurons heavily rely on mitochondrial function, and deficits in brain energy metabolism are detected early in AD; however, direct human genetic evidence for mitochondrial involvement in AD pathogenesis is limited. We analyzed whole-exome sequencing data of 4549 AD cases and 3332 age-matched controls and discovered that rare protein altering variants in the gene pentatricopeptide repeat-containing protein 1 (PTCD1) show a trend for enrichment in cases compared with controls. We show here that PTCD1 is required for normal mitochondrial rRNA levels, proper assembly of the mitochondrial ribosome and hence for mitochondrial translation and assembly of the electron transport chain. Loss of PTCD1 function impairs oxidative phosphorylation and forces cells to rely on glycolysis for energy production. Cells expressing the AD-linked variant of PTCD1 fail to sustain energy production under increased metabolic stress. In neurons, reduced PTCD1 expression leads to lower ATP levels and impacts spontaneous synaptic activity. Thus, our study uncovers a possible link between a protein required for mitochondrial function and energy metabolism and AD risk.SIGNIFICANCE STATEMENT Mitochondria are the main source of cellular energy and mitochondrial dysfunction is implicated in the pathology of Alzheimer's disease (AD) and other neurodegenerative disorders. Here, we identify a variant in the gene PTCD1 that is enriched in AD patients and demonstrate that PTCD1 is required for ATP generation through oxidative phosphorylation. PTCD1 regulates the level of 16S rRNA, the backbone of the mitoribosome, and is essential for mitochondrial translation and assembly of the electron transport chain. Cells expressing the AD-associated variant fail to maintain adequate ATP production during metabolic stress, and reduced PTCD1 activity disrupts neuronal energy homeostasis and dampens spontaneous transmission. Our work provides a mechanistic link between a protein required for mitochondrial function and genetic AD risk.
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Affiliation(s)
| | - Lilian Phu
- Microchemistry, Proteomics, and Lipidomics
| | | | | | | | | | - Benjamin Haley
- Molecular Biology, Genentech Inc., South San Francisco, California 94080
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44
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Nikonova E, Kao SY, Ravichandran K, Wittner A, Spletter ML. Conserved functions of RNA-binding proteins in muscle. Int J Biochem Cell Biol 2019; 110:29-49. [PMID: 30818081 DOI: 10.1016/j.biocel.2019.02.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 02/21/2019] [Accepted: 02/23/2019] [Indexed: 12/13/2022]
Abstract
Animals require different types of muscle for survival, for example for circulation, motility, reproduction and digestion. Much emphasis in the muscle field has been placed on understanding how transcriptional regulation generates diverse types of muscle during development. Recent work indicates that alternative splicing and RNA regulation are as critical to muscle development, and altered function of RNA-binding proteins causes muscle disease. Although hundreds of genes predicted to bind RNA are expressed in muscles, many fewer have been functionally characterized. We present a cross-species view summarizing what is known about RNA-binding protein function in muscle, from worms and flies to zebrafish, mice and humans. In particular, we focus on alternative splicing regulated by the CELF, MBNL and RBFOX families of proteins. We discuss the systemic nature of diseases associated with loss of RNA-binding proteins in muscle, focusing on mis-regulation of CELF and MBNL in myotonic dystrophy. These examples illustrate the conservation of RNA-binding protein function and the marked utility of genetic model systems in understanding mechanisms of RNA regulation.
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Affiliation(s)
- Elena Nikonova
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Shao-Yen Kao
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Keshika Ravichandran
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Anja Wittner
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Maria L Spletter
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany; Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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45
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Borna NN, Kishita Y, Kohda M, Lim SC, Shimura M, Wu Y, Mogushi K, Yatsuka Y, Harashima H, Hisatomi Y, Fushimi T, Ichimoto K, Murayama K, Ohtake A, Okazaki Y. Mitochondrial ribosomal protein PTCD3 mutations cause oxidative phosphorylation defects with Leigh syndrome. Neurogenetics 2019; 20:9-25. [PMID: 30607703 DOI: 10.1007/s10048-018-0561-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/06/2018] [Indexed: 02/06/2023]
Abstract
Pentatricopeptide repeat domain proteins are a large family of RNA-binding proteins involved in mitochondrial RNA editing, stability, and translation. Mitochondrial translation machinery defects are an expanding group of genetic diseases in humans. We describe a patient who presented with low birth weight, mental retardation, and optic atrophy. Brain MRI showed abnormal bilateral signals at the basal ganglia and brainstem, and the patient was diagnosed as Leigh syndrome. Exome sequencing revealed two potentially loss-of-function variants [c.415-2A>G, and c.1747_1748insCT (p.Phe583Serfs*3)] in PTCD3 (also known as MRPS39). PTCD3, a member of the pentatricopeptide repeat domain protein family, is a component of the small mitoribosomal subunit. The patient had marked decreases in mitochondrial complex I and IV levels and activities, oxygen consumption and ATP biosynthesis, and generalized mitochondrial translation defects in fibroblasts. Quantitative proteomic analysis revealed decreased levels of the small mitoribosomal subunits. Complementation experiments rescued oxidative phosphorylation complex I and IV levels and activities, ATP biosynthesis, and MT-RNR1 rRNA transcript level, providing functional validation of the pathogenicity of identified variants. This is the first report of an association of PTCD3 mutations with Leigh syndrome along with combined oxidative phosphorylation deficiencies caused by defects in the mitochondrial translation machinery.
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Affiliation(s)
- Nurun Nahar Borna
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yoshihito Kishita
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Masakazu Kohda
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Sze Chern Lim
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Masaru Shimura
- Department of Metabolism, Chiba Children's Hospital, Midori, Chiba, 266-0007, Japan
| | - Yibo Wu
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Kaoru Mogushi
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yukiko Yatsuka
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Hiroko Harashima
- Department of Pediatrics, Saitama Medical University, Moroyama, Saitama, 350-0495, Japan
| | - Yuichiro Hisatomi
- Department of Pediatrics, Kumamoto City Hospital, Higashi-ku, Kumamoto, 862-8505, Japan
| | - Takuya Fushimi
- Department of Metabolism, Chiba Children's Hospital, Midori, Chiba, 266-0007, Japan
| | - Keiko Ichimoto
- Department of Metabolism, Chiba Children's Hospital, Midori, Chiba, 266-0007, Japan
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Midori, Chiba, 266-0007, Japan
| | - Akira Ohtake
- Department of Pediatrics, Saitama Medical University, Moroyama, Saitama, 350-0495, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan. .,Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
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46
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Is mitochondrial gene expression coordinated or stochastic? Biochem Soc Trans 2018; 46:1239-1246. [PMID: 30301847 DOI: 10.1042/bst20180174] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 08/29/2018] [Accepted: 08/30/2018] [Indexed: 12/25/2022]
Abstract
Mitochondrial biogenesis is intimately dependent on the coordinated expression of the nuclear and mitochondrial genomes that is necessary for the assembly and function of the respiratory complexes to produce most of the energy required by cells. Although highly compacted in animals, the mitochondrial genome and its expression are essential for survival, development, and optimal energy production. The machinery that regulates gene expression within mitochondria is localised within the same compartment and, like in their ancestors, the bacteria, this machinery does not use membrane-based compartmentalisation to order the gene expression pathway. Therefore, the lifecycle of mitochondrial RNAs from transcription through processing, maturation, translation to turnover is mediated by a gamut of RNA-binding proteins (RBPs), all contained within the mitochondrial matrix milieu. Recent discoveries indicate that multiple processes regulating RNA metabolism occur at once but since mitochondria have a new complement of RBPs, many evolved de novo from nuclear genes, we are left wondering how co-ordinated are these processes? Here, we review recently identified examples of the co-ordinated and stochastic processes that govern the mitochondrial transcriptome. These new discoveries reveal the complexity of mitochondrial gene expression and the need for its in-depth exploration to understand how these organelles can respond to the energy demands of the cell.
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47
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Spåhr H, Chia T, Lingford JP, Siira SJ, Cohen SB, Filipovska A, Rackham O. Modular ssDNA binding and inhibition of telomerase activity by designer PPR proteins. Nat Commun 2018; 9:2212. [PMID: 29880855 PMCID: PMC5992170 DOI: 10.1038/s41467-018-04388-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 04/25/2018] [Indexed: 02/06/2023] Open
Abstract
DNA is typically found as a double helix, however it must be separated into single strands during all phases of DNA metabolism; including transcription, replication, recombination and repair. Although recent breakthroughs have enabled the design of modular RNA- and double-stranded DNA-binding proteins, there are currently no tools available to manipulate single-stranded DNA (ssDNA). Here we show that artificial pentatricopeptide repeat (PPR) proteins can be programmed for sequence-specific ssDNA binding. Interactions occur using the same code and specificity as for RNA binding. We solve the structures of DNA-bound and apo proteins revealing the basis for ssDNA binding and how hydrogen bond rearrangements enable the PPR structure to envelope its ssDNA target. Finally, we show that engineered PPRs can be designed to bind telomeric ssDNA and can block telomerase activity. The modular mode of ssDNA binding by PPR proteins provides tools to target ssDNA and to understand its importance in cells. Pentatricopeptide repeat proteins bind single-stranded RNA and have been used to study ssRNA biology. Here the authors co-opt these proteins to target ssDNA and demonstrate specific binding of telomere sequences, the structural basis for ssDNA wrapping, and use them as potent telomerase inhibitors.
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Affiliation(s)
- Henrik Spåhr
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, D-50931, Cologne, Germany
| | - Tiongsun Chia
- Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, WA, 6009, Australia
| | - James P Lingford
- Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, WA, 6009, Australia
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, WA, 6009, Australia
| | - Scott B Cohen
- Children's Medical Research Institute, University of Sydney, 214 Hawkesbury Road, Westmead, NSW, 2145, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, WA, 6009, Australia.,School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, WA, 6009, Australia. .,School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia.
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