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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Ng KY, Lutfullahoglu Bal G, Richter U, Safronov O, Paulin L, Dunn CD, Paavilainen VO, Richer J, Newman WG, Taylor RW, Battersby BJ. Nonstop mRNAs generate a ground state of mitochondrial gene expression noise. SCIENCE ADVANCES 2022; 8:eabq5234. [PMID: 36399564 PMCID: PMC9674279 DOI: 10.1126/sciadv.abq5234] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 10/22/2022] [Indexed: 05/29/2023]
Abstract
A stop codon within the mRNA facilitates coordinated termination of protein synthesis, releasing the nascent polypeptide from the ribosome. This essential step in gene expression is impeded with transcripts lacking a stop codon, generating nonstop ribosome complexes. Here, we use deep sequencing to investigate sources of nonstop mRNAs generated from the human mitochondrial genome. We identify diverse types of nonstop mRNAs on mitochondrial ribosomes that are resistant to translation termination by canonical release factors. Failure to resolve these aberrations by the mitochondrial release factor in rescue (MTRFR) imparts a negative regulatory effect on protein synthesis that is associated with human disease. Our findings reveal a source of underlying noise in mitochondrial gene expression and the importance of responsive ribosome quality control mechanisms for cell fitness and human health.
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Affiliation(s)
- Kah Ying Ng
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Guleycan Lutfullahoglu Bal
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Uwe Richter
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Omid Safronov
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- DNA Sequencing and Genomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Cory D. Dunn
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ville O. Paavilainen
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Julie Richer
- Department of Medical Genetics, Children’s Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - William G. Newman
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Brendan J. Battersby
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
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3
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Korostelev AA. Diversity and Similarity of Termination and Ribosome Rescue in Bacterial, Mitochondrial, and Cytoplasmic Translation. BIOCHEMISTRY (MOSCOW) 2021; 86:1107-1121. [PMID: 34565314 DOI: 10.1134/s0006297921090066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
When a ribosome encounters the stop codon of an mRNA, it terminates translation, releases the newly made protein, and is recycled to initiate translation on a new mRNA. Termination is a highly dynamic process in which release factors (RF1 and RF2 in bacteria; eRF1•eRF3•GTP in eukaryotes) coordinate peptide release with large-scale molecular rearrangements of the ribosome. Ribosomes stalled on aberrant mRNAs are rescued and recycled by diverse bacterial, mitochondrial, or cytoplasmic quality control mechanisms. These are catalyzed by rescue factors with peptidyl-tRNA hydrolase activity (bacterial ArfA•RF2 and ArfB, mitochondrial ICT1 and mtRF-R, and cytoplasmic Vms1), that are distinct from each other and from release factors. Nevertheless, recent structural studies demonstrate a remarkable similarity between translation termination and ribosome rescue mechanisms. This review describes how these pathways rely on inherent ribosome dynamics, emphasizing the active role of the ribosome in all translation steps.
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Affiliation(s)
- Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA.
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4
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Chicherin IV, Dukhalin SV, Khannanov RA, Baleva MV, Levitskii SA, Patrushev MV, Sergiev PV, Kamenski P. Functional Diversity of Mitochondrial Peptidyl-tRNA Hydrolase ICT1 in Human Cells. Front Mol Biosci 2021; 8:716885. [PMID: 34336930 PMCID: PMC8322449 DOI: 10.3389/fmolb.2021.716885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 06/30/2021] [Indexed: 11/13/2022] Open
Abstract
Mitochondria are energy producing organelles of the eukaryotic cell, involved in the synthesis of key metabolites, calcium homeostasis and apoptosis. Protein biosynthesis in these organelles is a relic of its endosymbiotic origin. While mitochondrial translational factors have homologues among prokaryotes, they possess a number of unique traits. Remarkably as many as four mammalian mitochondrial proteins possess a clear similarity with translation termination factors. The review focuses on the ICT1, which combines several functions. It is a non-canonical termination factor for protein biosynthesis, a rescue factor for stalled mitochondrial ribosomes, a structural protein and a regulator of proliferation, cell cycle, and apoptosis. Such a diversity of roles demonstrates the high functionality of mitochondrial translation associated proteins and their relationship with numerous processes occurring in a living cell.
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Affiliation(s)
- I V Chicherin
- Department of Molecular Biology, M.V.Lomonosov Moscow State University, Moscow, Russia.,National Research Center "Kurchatov Institute", NBICS Center, Moscow, Russia
| | - S V Dukhalin
- Department of Molecular Biology, M.V.Lomonosov Moscow State University, Moscow, Russia
| | - R A Khannanov
- Department of Molecular Biology, M.V.Lomonosov Moscow State University, Moscow, Russia
| | - M V Baleva
- Department of Molecular Biology, M.V.Lomonosov Moscow State University, Moscow, Russia
| | - S A Levitskii
- Department of Molecular Biology, M.V.Lomonosov Moscow State University, Moscow, Russia
| | - M V Patrushev
- National Research Center "Kurchatov Institute", NBICS Center, Moscow, Russia
| | - P V Sergiev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, Russia
| | - P Kamenski
- Department of Molecular Biology, M.V.Lomonosov Moscow State University, Moscow, Russia
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5
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Wang F, Zhang D, Zhang D, Li P, Gao Y. Mitochondrial Protein Translation: Emerging Roles and Clinical Significance in Disease. Front Cell Dev Biol 2021; 9:675465. [PMID: 34277617 PMCID: PMC8280776 DOI: 10.3389/fcell.2021.675465] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/09/2021] [Indexed: 12/28/2022] Open
Abstract
Mitochondria are one of the most important organelles in cells. Mitochondria are semi-autonomous organelles with their own genetic system, and can independently replicate, transcribe, and translate mitochondrial DNA. Translation initiation, elongation, termination, and recycling of the ribosome are four stages in the process of mitochondrial protein translation. In this process, mitochondrial protein translation factors and translation activators, mitochondrial RNA, and other regulatory factors regulate mitochondrial protein translation. Mitochondrial protein translation abnormalities are associated with a variety of diseases, including cancer, cardiovascular diseases, and nervous system diseases. Mutation or deletion of various mitochondrial protein translation factors and translation activators leads to abnormal mitochondrial protein translation. Mitochondrial tRNAs and mitochondrial ribosomal proteins are essential players during translation and mutations in genes encoding them represent a large fraction of mitochondrial diseases. Moreover, there is crosstalk between mitochondrial protein translation and cytoplasmic translation, and the imbalance between mitochondrial protein translation and cytoplasmic translation can affect some physiological and pathological processes. This review summarizes the regulation of mitochondrial protein translation factors, mitochondrial ribosomal proteins, mitochondrial tRNAs, and mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) in the mitochondrial protein translation process and its relationship with diseases. The regulation of mitochondrial protein translation and cytoplasmic translation in multiple diseases is also summarized.
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Affiliation(s)
- Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Deyu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.,Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, China
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6
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Kummer E, Schubert KN, Schoenhut T, Scaiola A, Ban N. Structural basis of translation termination, rescue, and recycling in mammalian mitochondria. Mol Cell 2021; 81:2566-2582.e6. [PMID: 33878294 DOI: 10.1016/j.molcel.2021.03.042] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/12/2021] [Accepted: 03/24/2021] [Indexed: 12/26/2022]
Abstract
The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as a screening tool to identify mitochondrial translation termination mechanisms and to describe them in molecular detail. We show how mitochondrial release factor 1a releases the nascent chain from the ribosome when it encounters the canonical stop codons UAA and UAG. Furthermore, we define how the peptidyl-tRNA hydrolase ICT1 acts as a rescue factor on mitoribosomes that have stalled on truncated messages to recover them for protein synthesis. Finally, we present structural models detailing the process of mitochondrial ribosome recycling to explain how a dedicated elongation factor, mitochondrial EFG2 (mtEFG2), has specialized for cooperation with the mitochondrial ribosome recycling factor to dissociate the mitoribosomal subunits at the end of the translation process.
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Affiliation(s)
- Eva Kummer
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland.
| | - Katharina Noel Schubert
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Tanja Schoenhut
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Alain Scaiola
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Nenad Ban
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland.
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7
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Hoshino S, Kanemura R, Kurita D, Soutome Y, Himeno H, Takaine M, Watanabe M, Nameki N. A stalled-ribosome rescue factor Pth3 is required for mitochondrial translation against antibiotics in Saccharomyces cerevisiae. Commun Biol 2021; 4:300. [PMID: 33686140 PMCID: PMC7940416 DOI: 10.1038/s42003-021-01835-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 02/09/2021] [Indexed: 11/09/2022] Open
Abstract
Mitochondrial translation appears to involve two stalled-ribosome rescue factors (srRFs). One srRF is an ICT1 protein from humans that rescues a "non-stop" type of mitochondrial ribosomes (mitoribosomes) stalled on mRNA lacking a stop codon, while the other, C12orf65, reportedly has functions that overlap with those of ICT1; however, its primary role remains unclear. We herein demonstrated that the Saccharomyces cerevisiae homolog of C12orf65, Pth3 (Rso55), preferentially rescued antibiotic-dependent stalled mitoribosomes, which appear to represent a "no-go" type of ribosomes stalled on intact mRNA. On media containing a non-fermentable carbon source, which requires mitochondrial gene expression, respiratory growth was impaired significantly more by the deletion of PTH3 than that of the ICT1 homolog PTH4 in the presence of antibiotics that inhibit mitochondrial translation, such as tetracyclines and macrolides. Additionally, the in organello labeling of mitochondrial translation products and quantification of mRNA levels by quantitative RT-PCR suggested that in the presence of tetracycline, the deletion of PTH3, but not PTH4, reduced the protein expression of all eight mtDNA-encoded genes at the post-transcriptional or translational level. These results indicate that Pth3 can function as a mitochondrial srRF specific for ribosomes stalled by antibiotics and plays a role in antibiotic resistance in fungi.
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Affiliation(s)
- Soichiro Hoshino
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma, Japan
| | - Ryohei Kanemura
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma, Japan
| | - Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Yukihiro Soutome
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma, Japan
| | - Hyouta Himeno
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Masak Takaine
- Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi, Japan.,Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
| | - Masakatsu Watanabe
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Nobukazu Nameki
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma, Japan.
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8
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Carbone CE, Demo G, Madireddy R, Svidritskiy E, Korostelev AA. ArfB can displace mRNA to rescue stalled ribosomes. Nat Commun 2020; 11:5552. [PMID: 33144582 PMCID: PMC7641280 DOI: 10.1038/s41467-020-19370-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/08/2020] [Indexed: 12/16/2022] Open
Abstract
Ribosomes stalled during translation must be rescued to replenish the pool of translation-competent ribosomal subunits. Bacterial alternative rescue factor B (ArfB) releases nascent peptides from ribosomes stalled on mRNAs truncated at the A site, allowing ribosome recycling. Prior structural work revealed that ArfB recognizes such ribosomes by inserting its C-terminal α-helix into the vacant mRNA tunnel. In this work, we report that ArfB can efficiently recognize a wider range of mRNA substrates, including longer mRNAs that extend beyond the A-site codon. Single-particle cryo-EM unveils that ArfB employs two modes of function depending on the mRNA length. ArfB acts as a monomer to accommodate a shorter mRNA in the ribosomal A site. By contrast, longer mRNAs are displaced from the mRNA tunnel by more than 20 Å and are stabilized in the intersubunit space by dimeric ArfB. Uncovering distinct modes of ArfB function resolves conflicting biochemical and structural studies, and may lead to re-examination of other ribosome rescue pathways, whose functions depend on mRNA lengths.
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Affiliation(s)
- Christine E Carbone
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States
| | - Gabriel Demo
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Rohini Madireddy
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States
- Medicago Inc., 7 Triangle drive, Durham, NC, 27713, USA
| | - Egor Svidritskiy
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States.
- Sanofi, 49 New York Ave, Suite 3660, Framingham, MA, 01701, USA.
| | - Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, Massachusetts, 01605, United States.
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9
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Perrone E, Cavole TR, Oliveira MG, Virmond LDA, Silva MDFB, Soares MDFF, Iglesias SBDO, Falconi A, Silva JS, Nakano V, Milanezi MF, Mendes CSC, Curiati MA, Micheletti C. Leigh syndrome in a patient with a novel C12orf65 pathogenic variant: case report and literature review. Genet Mol Biol 2020; 43:e20180271. [PMID: 32478789 PMCID: PMC7263430 DOI: 10.1590/1678-4685-gmb-2018-0271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 08/21/2019] [Indexed: 01/30/2023] Open
Abstract
Leigh syndrome is an early onset progressive disorder caused by defects in
mitochondrial oxidative phosphorylation. Pathogenic variants in nuclear and
mitochondrial genes are associated with the syndrome. Homozygous pathogenic
variants in the C12orf65 gene impair the mitochondrial
oxidative phosphorylation system. We describe a new case of Leigh syndrome
caused by a novel pathogenic variant of the C12orf65 gene
resulting in the lack of the Gly-Gly-Gln (GGQ) domain in the predicted protein,
and review clinical and molecular data from previously reported patients. Our
study supports that the phenotype caused by C12orf65 gene
variants is heterogeneous and varies from spastic paraparesis to Leigh syndrome.
Loss-of-function variants are more likely to cause the disease, and variants
affecting the GGQ domain tend to be associated with more severe phenotypes,
reinforcing a possible genotype-phenotype correlation.
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Affiliation(s)
- Eduardo Perrone
- Universidade Federal de São Paulo, Departamento de Genética Médica, São Paulo, SP, Brazil.,GeneOne, Dasa, São Paulo, SP, Brazil
| | - Thiago R Cavole
- Universidade Federal de São Paulo, Departamento de Genética Médica, São Paulo, SP, Brazil
| | - Manuella G Oliveira
- Universidade Federal de São Paulo, Departamento de Genética Médica, São Paulo, SP, Brazil
| | - Luiza do A Virmond
- Universidade Federal de São Paulo, Departamento de Genética Médica, São Paulo, SP, Brazil
| | | | | | | | | | | | | | | | | | | | - Cecília Micheletti
- Universidade Federal de São Paulo, Departamento de Pediatria, São Paulo, SP, Brazil
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10
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Ayyub SA, Gao F, Lightowlers RN, Chrzanowska-Lightowlers ZM. Rescuing stalled mammalian mitoribosomes - what can we learn from bacteria? J Cell Sci 2020; 133:133/1/jcs231811. [PMID: 31896602 DOI: 10.1242/jcs.231811] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In the canonical process of translation, newly completed proteins escape from the ribosome following cleavage of the ester bond that anchors the polypeptide to the P-site tRNA, after which the ribosome can be recycled to initiate a new round of translation. Not all protein synthesis runs to completion as various factors can impede the progression of ribosomes. Rescuing of stalled ribosomes in mammalian mitochondria, however, does not share the same mechanisms that many bacteria use. The classic method for rescuing bacterial ribosomes is trans-translation. The key components of this system are absent from mammalian mitochondria; however, four members of a translation termination factor family are present, with some evidence of homology to members of a bacterial back-up rescue system. To date, there is no definitive demonstration of any other member of this family functioning in mitoribosome rescue. Here, we provide an overview of the processes and key players of canonical translation termination in both bacteria and mammalian mitochondria, followed by a perspective of the bacterial systems used to rescue stalled ribosomes. We highlight any similarities or differences with the mitochondrial translation release factors, and suggest potential roles for these proteins in ribosome rescue in mammalian mitochondria.
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Affiliation(s)
- Shreya Ahana Ayyub
- The Wellcome Centre for Mitochondrial Research, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Fei Gao
- The Wellcome Centre for Mitochondrial Research, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert N Lightowlers
- The Wellcome Centre for Mitochondrial Research, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Zofia M Chrzanowska-Lightowlers
- The Wellcome Centre for Mitochondrial Research, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
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11
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Toompuu M, Tuomela T, Laine P, Paulin L, Dufour E, Jacobs HT. Polyadenylation and degradation of structurally abnormal mitochondrial tRNAs in human cells. Nucleic Acids Res 2019. [PMID: 29518244 PMCID: PMC6007314 DOI: 10.1093/nar/gky159] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
RNA 3' polyadenylation is known to serve diverse purposes in biology, in particular, regulating mRNA stability and translation. Here we determined that, upon exposure to high levels of the intercalating agent ethidium bromide (EtBr), greater than those required to suppress mitochondrial transcription, mitochondrial tRNAs in human cells became polyadenylated. Relaxation of the inducing stress led to rapid turnover of the polyadenylated tRNAs. The extent, kinetics and duration of tRNA polyadenylation were EtBr dose-dependent, with mitochondrial tRNAs differentially sensitive to the stress. RNA interference and inhibitor studies indicated that ongoing mitochondrial ATP synthesis, plus the mitochondrial poly(A) polymerase and SUV3 helicase were required for tRNA polyadenylation, while polynucleotide phosphorylase counteracted the process and was needed, along with SUV3, for degradation of the polyadenylated tRNAs. Doxycycline treatment inhibited both tRNA polyadenylation and turnover, suggesting a possible involvement of the mitoribosome, although other translational inhibitors had only minor effects. The dysfunctional tRNALeu(UUR) bearing the pathological A3243G mutation was constitutively polyadenylated at a low level, but this was markedly enhanced after doxycycline treatment. We propose that polyadenylation of structurally and functionally abnormal mitochondrial tRNAs entrains their PNPase/SUV3-mediated destruction, and that this pathway could play an important role in mitochondrial diseases associated with tRNA mutations.
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Affiliation(s)
- Marina Toompuu
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland
| | - Tea Tuomela
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland
| | - Pia Laine
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Eric Dufour
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland
| | - Howard T Jacobs
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland.,Institute of Biotechnology, FI-00014 University of Helsinki, Finland
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12
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Fang XJ, Zhang W, Lyu H, Wang ZX, Wang WW, Yuan Y. Compound Heterozygote Mutation of C12orf65 Causes Distal Motor Neuropathy and Optic Atrophy. Chin Med J (Engl) 2017; 130:242-244. [PMID: 28091420 PMCID: PMC5282685 DOI: 10.4103/0366-6999.198019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Xiao-Jing Fang
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Wei Zhang
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - He Lyu
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Zhao-Xia Wang
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Wei-Wei Wang
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Yun Yuan
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
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13
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Feaga HA, Quickel MD, Hankey-Giblin PA, Keiler KC. Human Cells Require Non-stop Ribosome Rescue Activity in Mitochondria. PLoS Genet 2016; 12:e1005964. [PMID: 27029019 PMCID: PMC4814080 DOI: 10.1371/journal.pgen.1005964] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/07/2016] [Indexed: 12/04/2022] Open
Abstract
Bacteria use trans-translation and the alternative rescue factors ArfA (P36675) and ArfB (Q9A8Y3) to hydrolyze peptidyl-tRNA on ribosomes that stall near the 3' end of an mRNA during protein synthesis. The eukaryotic protein ICT1 (Q14197) is homologous to ArfB. In vitro ribosome rescue assays of human ICT1 and Caulobacter crescentus ArfB showed that these proteins have the same activity and substrate specificity. Both ArfB and ICT1 hydrolyze peptidyl-tRNA on nonstop ribosomes or ribosomes stalled with ≤6 nucleotides extending past the A site, but are unable to hydrolyze peptidyl-tRNA when the mRNA extends ≥14 nucleotides past the A site. ICT1 provided sufficient ribosome rescue activity to support viability in C. crescentus cells that lacked both trans-translation and ArfB. Likewise, expression of ArfB protected human cells from death when ICT1 was silenced with siRNA. These data indicate that ArfB and ICT1 are functionally interchangeable, and demonstrate that ICT1 is a ribosome rescue factor. Because ICT1 is essential in human cells, these results suggest that ribosome rescue activity in mitochondria is required in humans. Ribosomes can stall during protein synthesis on truncated or damaged mRNAs that lack a stop codon. In bacteria, these “non-stop” ribosomes are rescued by trans-translation or by an alternative rescue factor, ArfA or ArfB. Most eukaryotes do not have trans-translation, but mammals have a homolog of ArfB named ICT1. ICT1 is targeted to mitochondria, and is essential in human cells. Here, we show that human ICT1 and ArfB from the bacterium Caulobacter crescentus have the same biochemical activity and specificity. We also demonstrate that ICT1 and ArfB are functionally interchangeable in both bacteria and human cells. Collectively, this work demonstrates a new essential function in human cells—rescue of mitochondrial non-stop translation complexes.
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Affiliation(s)
- Heather A. Feaga
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Michael D. Quickel
- Department of Veterinary and Biomedical Science, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Pamela A. Hankey-Giblin
- Department of Veterinary and Biomedical Science, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Kenneth C. Keiler
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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Richter U, Lahtinen T, Marttinen P, Suomi F, Battersby BJ. Quality control of mitochondrial protein synthesis is required for membrane integrity and cell fitness. J Cell Biol 2016; 211:373-89. [PMID: 26504172 PMCID: PMC4621829 DOI: 10.1083/jcb.201504062] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Impaired turnover of newly synthesized mitochondrial proteins of the oxidative phosphorylation complexes leads to protein over-accumulation in the inner mitochondrial membrane, thereby generating a stress that dissipates the mitochondrial membrane potential and therefore compromises organelle and cellular fitness. Mitochondrial ribosomes synthesize a subset of hydrophobic proteins required for assembly of the oxidative phosphorylation complexes. This process requires temporal and spatial coordination and regulation, so quality control of mitochondrial protein synthesis is paramount to maintain proteostasis. We show how impaired turnover of de novo mitochondrial proteins leads to aberrant protein accumulation in the mitochondrial inner membrane. This creates a stress in the inner membrane that progressively dissipates the mitochondrial membrane potential, which in turn stalls mitochondrial protein synthesis and fragments the mitochondrial network. The mitochondrial m-AAA protease subunit AFG3L2 is critical to this surveillance mechanism that we propose acts as a sensor to couple the synthesis of mitochondrial proteins with organelle fitness, thus ensuring coordinated assembly of the oxidative phosphorylation complexes from two sets of ribosomes.
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Affiliation(s)
- Uwe Richter
- Research Programs for Molecular Neurology, Biomedicum Helsinki, University of Helsinki, 00290 Helsinki, Finland
| | - Taina Lahtinen
- Research Programs for Molecular Neurology, Biomedicum Helsinki, University of Helsinki, 00290 Helsinki, Finland
| | - Paula Marttinen
- Research Programs for Molecular Neurology, Biomedicum Helsinki, University of Helsinki, 00290 Helsinki, Finland
| | - Fumi Suomi
- Research Programs for Molecular Neurology, Biomedicum Helsinki, University of Helsinki, 00290 Helsinki, Finland
| | - Brendan J Battersby
- Research Programs for Molecular Neurology, Biomedicum Helsinki, University of Helsinki, 00290 Helsinki, Finland
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Imagawa E, Fattal-Valevski A, Eyal O, Miyatake S, Saada A, Nakashima M, Tsurusaki Y, Saitsu H, Miyake N, Matsumoto N. Homozygous p.V116* mutation in C12orf65 results in Leigh syndrome. J Neurol Neurosurg Psychiatry 2016; 87:212-6. [PMID: 25995486 DOI: 10.1136/jnnp-2014-310084] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/05/2015] [Indexed: 11/03/2022]
Abstract
BACKGROUND Leigh syndrome (LS) is an early-onset progressive neurodegenerative disorder associated with mitochondrial dysfunction. LS is characterised by elevated lactate and pyruvate and bilateral symmetric hyperintense lesions in the basal ganglia, thalamus, brainstem, cerebral white matter or spinal cord on T2-weighted MRI. LS is a genetically heterogeneous disease, and to date mutations in approximately 40 genes related to mitochondrial function have been linked to the disorder. METHODS We investigated a pair of female monozygotic twins diagnosed with LS from consanguineous healthy parents of Indian origin. Their common clinical features included optic atrophy, ophthalmoplegia, spastic paraparesis and mild intellectual disability. High-blood lactate and high-intensity signal in the brainstem on T2-weighted MRI were consistent with a clinical diagnosis of LS. To identify the genetic cause of their condition, we performed whole exome sequencing. RESULTS We identified a homozygous nonsense mutation in C12orf65 (NM_001143905; c.346delG, p.V116*) in the affected twins. Interestingly, the identical mutation was previously reported in an Indian family with Charcot-Marie Tooth disease type 6, which displayed some overlapping clinical features with the twins. CONCLUSIONS We demonstrate that the identical nonsense mutation in C12orf65 can result in different clinical features, suggesting the involvement of unknown modifiers.
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Affiliation(s)
- Eri Imagawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Aviva Fattal-Valevski
- Paediatric Neurology Unit, Tel Aviv Sourasky Medical Centre, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ori Eyal
- Paediatric Endocrinology Unit, Tel Aviv Sourasky Medical Centre, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ann Saada
- Monique and Jacques Roboh Department of Genetic Research and the Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Mitsuko Nakashima
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yoshinori Tsurusaki
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hirotomo Saitsu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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16
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Optic atrophy and a Leigh-like syndrome due to mutations in the c12orf65 gene: report of a novel mutation and review of the literature. J Neuroophthalmol 2014; 34:39-43. [PMID: 24284555 DOI: 10.1097/wno.0000000000000076] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Combined oxidative phosphorylation deficiency type 7 (COXPD7) is a rare disorder of mitochondrial metabolism that results in optic atrophy and Leigh syndrome-like disease. We describe 2 siblings with compound heterozygous mutations in the recently identified C12orf65 gene who presented with optic atrophy and mild developmental delays and subsequently developed bilateral, symmetric lesions in the brainstem reminiscent of Leigh syndrome. Repeat neuroimaging demonstrated reversibility of the findings in 1 sibling and persistent metabolic stroke in the other. This article highlights the phenotypic manifestations from a novel mutation in the C12orf65 gene and reviews the clinical presentation of the 5 other individuals reported to date who carry mutations in this gene.
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17
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Wesolowska MT, Richter-Dennerlein R, Lightowlers RN, Chrzanowska-Lightowlers ZMA. Overcoming stalled translation in human mitochondria. Front Microbiol 2014; 5:374. [PMID: 25101074 PMCID: PMC4103422 DOI: 10.3389/fmicb.2014.00374] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 07/03/2014] [Indexed: 12/30/2022] Open
Abstract
Protein synthesis is central to life and maintaining a highly accurate and efficient mechanism is essential. What happens when a translating ribosome stalls on a messenger RNA? Many highly intricate processes have been documented in the cytosol of numerous species, but how does organellar protein synthesis resolve this stalling issue? Mammalian mitochondria synthesize just thirteen highly hydrophobic polypeptides. These proteins are all integral components of the machinery that couples oxidative phosphorylation. Consequently, it is essential that stalled mitochondrial ribosomes can be efficiently recycled. To date, there is no evidence to support any particular molecular mechanism to resolve this problem. However, here we discuss the observation that there are four predicted members of the mitochondrial translation release factor family and that only one member, mtRF1a, is necessary to terminate the translation of all thirteen open reading frames in the mitochondrion. Could the other members be involved in the process of recycling stalled mitochondrial ribosomes?
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Affiliation(s)
| | | | | | - Zofia M. A. Chrzanowska-Lightowlers
- Wellcome Trust Centre for Mitochondrial Research, Institute for Cell and Molecular Biosciences, Newcastle University, Medical SchoolNewcastle upon Tyne, UK
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18
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Gleghorn ML, Maquat LE. 'Black sheep' that don't leave the double-stranded RNA-binding domain fold. Trends Biochem Sci 2014; 39:328-40. [PMID: 24954387 DOI: 10.1016/j.tibs.2014.05.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 05/19/2014] [Accepted: 05/19/2014] [Indexed: 12/28/2022]
Abstract
The canonical double-stranded RNA (dsRNA)-binding domain (dsRBD) is composed of an α1-β1-β2-β3-α2 secondary structure that folds in three dimensions to recognize dsRNA. Recently, structural and functional studies of divergent dsRBDs revealed adaptations that include intra- and/or intermolecular protein interactions, sometimes in the absence of detectable dsRNA-binding ability. We describe here how discrete dsRBD components can accommodate pronounced amino-acid sequence changes while maintaining the core fold. We exemplify the growing importance of divergent dsRBDs in mRNA decay by discussing Dicer, Staufen (STAU)1 and 2, trans-activation responsive RNA-binding protein (TARBP)2, protein activator of protein kinase RNA-activated (PKR) (PACT), DiGeorge syndrome critical region (DGCR)8, DEAH box helicase proteins (DHX) 9 and 30, and dsRBD-like fold-containing proteins that have ribosome-related functions. We also elaborate on the computational limitations to discovering yet-to-be-identified divergent dsRBDs.
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Affiliation(s)
- Michael L Gleghorn
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
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19
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Lightowlers RN, Rozanska A, Chrzanowska-Lightowlers ZM. Mitochondrial protein synthesis: figuring the fundamentals, complexities and complications, of mammalian mitochondrial translation. FEBS Lett 2014; 588:2496-503. [PMID: 24911204 PMCID: PMC4099522 DOI: 10.1016/j.febslet.2014.05.054] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 05/28/2014] [Accepted: 05/29/2014] [Indexed: 12/28/2022]
Abstract
Mitochondrial protein synthesis is essential for all mammals, being responsible for providing key components of the oxidative phosphorylation complexes. Although only thirteen different polypeptides are made, the molecular details of this deceptively simple process remain incomplete. Central to this process is a non-canonical ribosome, the mitoribosome, which has evolved to address its unique mandate. In this review, we integrate the current understanding of the molecular aspects of mitochondrial translation with recent advances in structural biology. We identify numerous key questions that we will need to answer if we are to increase our knowledge of the molecular mechanisms underlying mitochondrial protein synthesis.
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Affiliation(s)
- Robert N Lightowlers
- The Wellcome Trust Centre for Mitochondrial Research, Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
| | - Agata Rozanska
- The Wellcome Trust Centre for Mitochondrial Research, Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Zofia M Chrzanowska-Lightowlers
- The Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
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20
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Himeno H, Kurita D, Muto A. tmRNA-mediated trans-translation as the major ribosome rescue system in a bacterial cell. Front Genet 2014; 5:66. [PMID: 24778639 PMCID: PMC3985003 DOI: 10.3389/fgene.2014.00066] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 03/15/2014] [Indexed: 11/13/2022] Open
Abstract
Transfer messenger RNA (tmRNA; also known as 10Sa RNA or SsrA RNA) is a small RNA molecule that is conserved among bacteria. It has structural and functional similarities to tRNA: it has an upper half of the tRNA-like structure, its 5’ end is processed by RNase P, it has typical tRNA-specific base modifications, it is aminoacylated with alanine, it binds to EF-Tu after aminoacylation and it enters the ribosome with EF-Tu and GTP. However, tmRNA lacks an anticodon, and instead it has a coding sequence for a short peptide called tag-peptide. An elaborate interplay of actions of tmRNA as both tRNA and mRNA with the help of a tmRNA-binding protein, SmpB, facilitates trans-translation, which produces a single polypeptide from two mRNA molecules. Initially alanyl-tmRNA in complex with EF-Tu and SmpB enters the vacant A-site of the stalled ribosome like aminoacyl-tRNA but without a codon–anticodon interaction, and subsequently truncated mRNA is replaced with the tag-encoding region of tmRNA. During these processes, not only tmRNA but also SmpB structurally and functionally mimics both tRNA and mRNA. Thus trans-translation rescues the stalled ribosome, thereby allowing recycling of the ribosome. Since the tag-peptide serves as a target of AAA+ proteases, the trans-translation products are preferentially degraded so that they do not accumulate in the cell. Although alternative rescue systems have recently been revealed, trans-translation is the only system that universally exists in bacteria. Furthermore, it is unique in that it employs a small RNA and that it prevents accumulation of non-functional proteins from truncated mRNA in the cell. It might play the major role in rescuing the stalled translation in the bacterial cell.
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Affiliation(s)
- Hyouta Himeno
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University Hirosaki, Japan
| | - Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University Hirosaki, Japan
| | - Akira Muto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University Hirosaki, Japan
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21
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Delineation of C12orf65-related phenotypes: a genotype-phenotype relationship. Eur J Hum Genet 2014; 22:1019-25. [PMID: 24424123 DOI: 10.1038/ejhg.2013.284] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 10/13/2013] [Accepted: 11/09/2013] [Indexed: 11/08/2022] Open
Abstract
C12orf65 participates in the process of mitochondrial translation and has been shown to be associated with a spectrum of phenotypes, including early onset optic atrophy, progressive encephalomyopathy, peripheral neuropathy, and spastic paraparesis.We used whole-genome homozygosity mapping as well as exome sequencing and targeted gene sequencing to identify novel C12orf65 disease-causing mutations in seven affected individuals originating from two consanguineous families. In four family members affected with childhood-onset optic atrophy accompanied by slowly progressive peripheral neuropathy and spastic paraparesis, we identified a homozygous frame shift mutation c.413_417 delAACAA, which predicts a truncated protein lacking the C-terminal portion. In the second family, we studied three affected individuals who presented with early onset optic atrophy, peripheral neuropathy, and spastic gait in addition to moderate intellectual disability. Muscle biopsy in two of the patients revealed decreased activities of the mitochondrial respiratory chain complexes I and IV. In these patients, we identified a homozygous splice mutation, g.21043 T>A (c.282+2 T>A) which leads to skipping of exon 2. Our study broadens the phenotypic spectrum of C12orf65 defects and highlights the triad of optic atrophy, axonal neuropathy and spastic paraparesis as its key clinical features. In addition, a clear genotype-phenotype correlation is anticipated in which deleterious mutations which disrupt the GGQ-containing domain in the first coding exon are expected to result in a more severe phenotype, whereas down-stream C-terminal mutations may result in a more favorable phenotype, typically lacking cognitive impairment.
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22
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Pyle A, Ramesh V, Bartsakoulia M, Boczonadi V, Gomez-Duran A, Herczegfalvi A, Blakely EL, Smertenko T, Duff J, Eglon G, Moore D, Yu-Wai-Man P, Douroudis K, Santibanez-Koref M, Griffin H, Lochmüller H, Karcagi V, Taylor RW, Chinnery PF, Horvath R. Behr's Syndrome is Typically Associated with Disturbed Mitochondrial Translation and Mutations in the C12orf65 Gene. J Neuromuscul Dis 2014; 1:55-63. [PMID: 26380172 PMCID: PMC4568311 DOI: 10.3233/jnd-140003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Behr's syndrome is a classical phenotypic description of childhood-onset optic atrophy combined with various neurological symptoms, including ophthalmoparesis, nystagmus, spastic paraparesis, ataxia, peripheral neuropathy and learning difficulties. OBJECTIVE Here we describe 4 patients with the classical Behr's syndrome phenotype from 3 unrelated families who carry homozygous nonsense mutations in the C12orf65 gene encoding a protein involved in mitochondrial translation. METHODS Whole exome sequencing was performed in genomic DNA and oxygen consumption was measured in patient cell lines. RESULTS We detected 2 different homozygous C12orf65 nonsense mutations in 4 patients with a homogeneous clinical presentation matching the historical description of Behr's syndrome. The first symptom in all patients was childhood-onset optic atrophy, followed by spastic paraparesis, distal weakness, motor neuropathy and ophthalmoparesis. CONCLUSIONS We think that C12orf65 mutations are more frequent than previously suggested and screening of this gene should be considered not only in patients with mitochondrial respiratory chain deficiencies, but also in inherited peripheral neuropathies, spastic paraplegias and ataxias, especially with pre-existing optic atrophy.
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Affiliation(s)
- Angela Pyle
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Venkateswaran Ramesh
- Department of Pediatric Neurology, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Trust, UK
| | - Marina Bartsakoulia
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Veronika Boczonadi
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Aurora Gomez-Duran
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | - Emma L. Blakely
- Wellcome Trust Mitochondrial Research Centre, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, UK
| | - Tania Smertenko
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Jennifer Duff
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Gail Eglon
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - David Moore
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Patrick Yu-Wai-Man
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Konstantinos Douroudis
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | - Helen Griffin
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Hanns Lochmüller
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Veronika Karcagi
- Department of Molecular Genetics and Diagnostics, NIEH, Budapest, Hungary
| | - Robert W. Taylor
- Wellcome Trust Mitochondrial Research Centre, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, UK
| | - Patrick F. Chinnery
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Rita Horvath
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
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Lind C, Sund J, Åqvist J. Codon-reading specificities of mitochondrial release factors and translation termination at non-standard stop codons. Nat Commun 2013; 4:2940. [DOI: 10.1038/ncomms3940] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 11/13/2013] [Indexed: 11/09/2022] Open
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Kogure H, Handa Y, Nagata M, Kanai N, Güntert P, Kubota K, Nameki N. Identification of residues required for stalled-ribosome rescue in the codon-independent release factor YaeJ. Nucleic Acids Res 2013; 42:3152-63. [PMID: 24322300 PMCID: PMC3950681 DOI: 10.1093/nar/gkt1280] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The YaeJ protein is a codon-independent release factor with peptidyl-tRNA hydrolysis (PTH) activity, and functions as a stalled-ribosome rescue factor in Escherichia coli. To identify residues required for YaeJ function, we performed mutational analysis for in vitro PTH activity towards rescue of ribosomes stalled on a non-stop mRNA, and for ribosome-binding efficiency. We focused on residues conserved among bacterial YaeJ proteins. Additionally, we determined the solution structure of the GGQ domain of YaeJ from E. coli using nuclear magnetic resonance spectroscopy. YaeJ and a human homolog, ICT1, had similar levels of PTH activity, despite various differences in sequence and structure. While no YaeJ-specific residues important for PTH activity occur in the structured GGQ domain, Arg118, Leu119, Lys122, Lys129 and Arg132 in the following C-terminal extension were required for PTH activity. All of these residues are completely conserved among bacteria. The equivalent residues were also found in the C-terminal extension of ICT1, allowing an appropriate sequence alignment between YaeJ and ICT1 proteins from various species. Single amino acid substitutions for each of these residues significantly decreased ribosome-binding efficiency. These biochemical findings provide clues to understanding how YaeJ enters the A-site of stalled ribosomes.
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Affiliation(s)
- Hiroyuki Kogure
- Division of Molecular Science, Faculty of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan, Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies, Goethe University, Frankfurt am Main, Germany and Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192-0397, Japan
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Mutations in the mitochondrial gene C12ORF65 lead to syndromic autosomal recessive intellectual disability and show genotype phenotype correlation. Eur J Med Genet 2013; 56:599-602. [PMID: 24080142 DOI: 10.1016/j.ejmg.2013.09.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 09/11/2013] [Indexed: 11/23/2022]
Abstract
Homozygosity mapping and exome sequencing in two affected siblings of a consanguineous family with mild intellectual disability, spastic paraplegia, and strabismus revealed a homozygous premature stop mutation at codon 139 of C12ORF65. Two previous studies reported truncating mutations at positions 84 and 132 of the protein. However, symptoms of the referred patients were only partially overlapping. Considering our findings, we now conclude that truncating mutations in C12ORF65 lead to a variable phenotype with intellectual disability, spastic paraplegia, and ophthalmoplegia as common symptoms. Further, we confirm a genotype-phenotype correlation between increasing length of the truncated protein and decreasing severity of symptoms.
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26
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Dujeancourt L, Richter R, Chrzanowska-Lightowlers ZM, Bonnefoy N, Herbert CJ. Interactions between peptidyl tRNA hydrolase homologs and the ribosomal release factor Mrf1 in S. pombe mitochondria. Mitochondrion 2013; 13:871-80. [PMID: 23892058 PMCID: PMC3919214 DOI: 10.1016/j.mito.2013.07.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 06/19/2013] [Accepted: 07/18/2013] [Indexed: 11/22/2022]
Abstract
Mitochondrial translation synthesizes key subunits of the respiratory complexes. In Schizosaccharomyces pombe, strains lacking Mrf1, the mitochondrial stop codon recognition factor, are viable, suggesting that other factors can play a role in translation termination. S. pombe contains four predicted peptidyl tRNA hydrolases, two of which (Pth3 and Pth4), have a GGQ motif that is conserved in class I release factors. We show that high dosage of Pth4 can compensate for the absence of Mrf1 and loss of Pth4 exacerbates the lack of Mrf1. Also Pth4 is a component of the mitochondrial ribosome, suggesting that it could help recycling stalled ribosomes. In S. pombe the peptidyl tRNA hydrolases Pth3 and Pth4 are mitochondrial proteins. Pth3 and Pth4 are associated with the mitochondrial ribosome and the large subunit. Deletion of pth4 and mrf1, encoding the mitochondrial release factor, is co-lethal. Over-expression of pth4 compensates for the deletion of mrf1. Pth4 can act as a release factor in S. pombe mitochondria.
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Affiliation(s)
- Laurent Dujeancourt
- Centre de Génétique Moléculaire, UPR3404, FRC3115, Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
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