1
|
The Mitochondrial tRNA Ser(UCN) Gene: A Novel m.7484A>G Mutation Associated with Mitochondrial Encephalomyopathy and Literature Review. Life (Basel) 2023; 13:life13020554. [PMID: 36836911 PMCID: PMC9963529 DOI: 10.3390/life13020554] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/26/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
Mitochondrial tRNASer(UCN) is considered a hot-spot for non-syndromic and aminoglycoside-induced hearing loss. However, many patients have been described with more extensive neurological diseases, mainly including epilepsy, myoclonus, ataxia, and myopathy. We describe a novel homoplasmic m.7484A>G mutation in the tRNASer(UCN) gene affecting the third base of the anticodon triplet in a girl with profound intellectual disability, spastic tetraplegia, sensorineural hearing loss, a clinical history of epilepsia partialis continua and vomiting, typical of MELAS syndrome, leading to a myoclonic epilepticus status, and myopathy with severe COX deficiency at muscle biopsy. The mutation was also found in the homoplasmic condition in the mother who presented with mild cognitive deficit, cerebellar ataxia, myoclonic epilepsy, sensorineural hearing loss and myopathy with COX deficient ragged-red fibers consistent with MERRF syndrome. This is the first anticodon mutation in the tRNASer(UCN) and the second homoplasmic mutation in the anticodon triplet reported to date.
Collapse
|
2
|
Meng F, Jia Z, Zheng J, Ji Y, Wang J, Xiao Y, Fu Y, Wang M, Ling F, Guan MX. A deafness-associated mitochondrial DNA mutation caused pleiotropic effects on DNA replication and tRNA metabolism. Nucleic Acids Res 2022; 50:9453-9469. [PMID: 36039763 PMCID: PMC9458427 DOI: 10.1093/nar/gkac720] [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: 06/19/2022] [Accepted: 08/09/2022] [Indexed: 12/24/2022] Open
Abstract
In this report, we investigated the molecular mechanism underlying a deafness-associated m.5783C > T mutation that affects the canonical C50-G63 base-pairing of TΨC stem of tRNACys and immediately adjacent to 5' end of light-strand origin of mitochondrial DNA (mtDNA) replication (OriL). Two dimensional agarose gel electrophoresis revealed marked decreases in the replication intermediates including ascending arm of Y-fork arcs spanning OriL in the mutant cybrids bearing m.5783C > T mutation. mtDNA replication alterations were further evidenced by decreased levels of PolγA, Twinkle and SSBP1, newly synthesized mtDNA and mtDNA contents in the mutant cybrids. The m.5783C > T mutation altered tRNACys structure and function, including decreased melting temperature, conformational changes, instability and deficient aminoacylation of mutated tRNACys. The m.5783C > T mutation impaired the 5' end processing efficiency of tRNACys precursors and reduced the levels of tRNACys and downstream tRNATyr. The aberrant tRNA metabolism impaired mitochondrial translation, which was especially pronounced effects in the polypeptides harboring higher numbers of cysteine and tyrosine codons. These alterations led to deficient oxidative phosphorylation including instability and reduced activities of the respiratory chain enzyme complexes I, III, IV and intact supercomplexes overall. Our findings highlight the impact of mitochondrial dysfunction on deafness arising from defects in mitochondrial DNA replication and tRNA metabolism.
Collapse
Affiliation(s)
| | | | - Jing Zheng
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Zhejiang Provincial Key Lab of Genetic and Developmental Disorder, Hangzhou, Zhejiang, China
| | - Yanchun Ji
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Zhejiang Provincial Key Lab of Genetic and Developmental Disorder, Hangzhou, Zhejiang, China
| | - Jing Wang
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yun Xiao
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yong Fu
- Division of Otolaryngology-Head and Neck Surgery, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Meng Wang
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Zhejiang Provincial Key Lab of Genetic and Developmental Disorder, Hangzhou, Zhejiang, China
| | - Feng Ling
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Hirosawa 2-1, Wako, Saitama, Japan
| | - Min-Xin Guan
- To whom correspondence should be addressed. Tel: +86 571 88206916; Fax: +86 571 88982377;
| |
Collapse
|
3
|
Cytochrome c oxidase deficiency. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148335. [PMID: 33171185 DOI: 10.1016/j.bbabio.2020.148335] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 12/23/2022]
Abstract
Cytochrome c oxidase (COX) deficiency is characterized by a high degree of genetic and phenotypic heterogeneity, partly reflecting the extreme structural complexity, multiple post-translational modification, variable, tissue-specific composition, and the high number of and intricate connections among the assembly factors of this enzyme. In fact, decreased COX specific activity can manifest with different degrees of severity, affect the whole organism or specific tissues, and develop a wide spectrum of disease natural history, including disease onsets ranging from birth to late adulthood. More than 30 genes have been linked to COX deficiency, but the list is still incomplete and in fact constantly updated. We here discuss the current knowledge about COX in health and disease, focusing on genetic aetiology and link to clinical manifestations. In addition, information concerning either fundamental biological features of the enzymes or biochemical signatures of its defects have been provided by experimental in vivo models, including yeast, fly, mouse and fish, which expanded our knowledge on the functional features and the phenotypical consequences of different forms of COX deficiency.
Collapse
|
4
|
Suzuki T, Yashiro Y, Kikuchi I, Ishigami Y, Saito H, Matsuzawa I, Okada S, Mito M, Iwasaki S, Ma D, Zhao X, Asano K, Lin H, Kirino Y, Sakaguchi Y, Suzuki T. Complete chemical structures of human mitochondrial tRNAs. Nat Commun 2020; 11:4269. [PMID: 32859890 PMCID: PMC7455718 DOI: 10.1038/s41467-020-18068-6] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/27/2020] [Indexed: 11/09/2022] Open
Abstract
Mitochondria generate most cellular energy via oxidative phosphorylation. Twenty-two species of mitochondrial (mt-)tRNAs encoded in mtDNA translate essential subunits of the respiratory chain complexes. mt-tRNAs contain post-transcriptional modifications introduced by nuclear-encoded tRNA-modifying enzymes. They are required for deciphering genetic code accurately, as well as stabilizing tRNA. Loss of tRNA modifications frequently results in severe pathological consequences. Here, we perform a comprehensive analysis of post-transcriptional modifications of all human mt-tRNAs, including 14 previously-uncharacterized species. In total, we find 18 kinds of RNA modifications at 137 positions (8.7% in 1575 nucleobases) in 22 species of human mt-tRNAs. An up-to-date list of 34 genes responsible for mt-tRNA modifications are provided. We identify two genes required for queuosine (Q) formation in mt-tRNAs. Our results provide insight into the molecular mechanisms underlying the decoding system and could help to elucidate the molecular pathogenesis of human mitochondrial diseases caused by aberrant tRNA modifications.
Collapse
Affiliation(s)
- Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yuka Yashiro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Ittoku Kikuchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yuma Ishigami
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Hironori Saito
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Ikuya Matsuzawa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Shunpei Okada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
- Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba, 278-0022, Japan
| | - Mari Mito
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shintaro Iwasaki
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Ding Ma
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Xuewei Zhao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kana Asano
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Huan Lin
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, Hainan, P.R. China
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| |
Collapse
|
5
|
Abstract
RNA species play host to a plethora of post-transcriptional modifications which together make up the epitranscriptome. 5-methyluridine (m5U) is one of the most common modifications made to cellular RNA, where it is found almost ubiquitously in bacterial and eukaryotic cytosolic tRNAs at position 54. Here, we demonstrate that m5U54 in human mitochondrial tRNAs is catalysed by the nuclear-encoded enzyme TRMT2B, and that its repertoire of substrates is expanded to ribosomal RNAs, catalysing m5U429 in 12S rRNA. We show that TRMT2B is not essential for viability in human cells and that knocking-out the gene shows no obvious phenotype with regards to RNA stability, mitochondrial translation, or cellular growth.
Collapse
Affiliation(s)
- Christopher A Powell
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| |
Collapse
|
6
|
Gong S, Wang X, Meng F, Cui L, Yi Q, Zhao Q, Cang X, Cai Z, Mo JQ, Liang Y, Guan MX. Overexpression of mitochondrial histidyl-tRNA synthetase restores mitochondrial dysfunction caused by a deafness-associated tRNAHis mutation. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49906-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
7
|
Gong S, Wang X, Meng F, Cui L, Yi Q, Zhao Q, Cang X, Cai Z, Mo JQ, Liang Y, Guan MX. Overexpression of mitochondrial histidyl-tRNA synthetase restores mitochondrial dysfunction caused by a deafness-associated tRNA His mutation. J Biol Chem 2019; 295:940-954. [PMID: 31819004 DOI: 10.1074/jbc.ra119.010998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/27/2019] [Indexed: 01/19/2023] Open
Abstract
The deafness-associated m.12201T>C mutation affects the A5-U68 base-pairing within the acceptor stem of mitochondrial tRNAHis The primary defect in this mutation is an alteration in tRNAHis aminoacylation. Here, we further investigate the molecular mechanism of the deafness-associated tRNAHis 12201T>C mutation and test whether the overexpression of the human mitochondrial histidyl-tRNA synthetase gene (HARS2) in cytoplasmic hybrid (cybrid) cells carrying the m.12201T>C mutation reverses mitochondrial dysfunctions. Using molecular dynamics simulations, we demonstrate that the m.12201T>C mutation perturbs the tRNAHis structure and function, supported by decreased melting temperature, conformational changes, and instability of mutated tRNA. We show that the m.12201T>C mutation-induced alteration of aminoacylation tRNAHis causes mitochondrial translational defects and respiratory deficiency. We found that the transfer of HARS2 into the cybrids carrying the m.12201T>C mutation raises the levels of aminoacylated tRNAHis from 56.3 to 75.0% but does not change the aminoacylation of other tRNAs. Strikingly, HARS2 overexpression increased the steady-state levels of tRNAHis and of noncognate tRNAs, including tRNAAla, tRNAGln, tRNAGlu, tRNALeu(UUR), tRNALys, and tRNAMet, in cells bearing the m.12201T>C mutation. This improved tRNA metabolism elevated the efficiency of mitochondrial translation, activities of oxidative phosphorylation complexes, and respiration capacity. Furthermore, HARS2 overexpression markedly increased mitochondrial ATP levels and membrane potential and reduced production of reactive oxygen species in cells carrying the m.12201T>C mutation. These results indicate that HARS2 overexpression corrects the mitochondrial dysfunction caused by the tRNAHis mutation. These findings provide critical insights into the pathophysiology of mitochondrial disease and represent a step toward improved therapeutic interventions for mitochondrial disorders.
Collapse
Affiliation(s)
- Shasha Gong
- Taizhou University Hospital, Taizhou University, Taizhou, Zhejiang 318000, China.,Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaoqiong Wang
- Department of Otolaryngology, Taizhou Municipal Hospital, Taizhou, Zhejiang 318000, China.,Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Feilong Meng
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Division of Medical Genetics and Genomics, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Limei Cui
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qiuzi Yi
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qiong Zhao
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaohui Cang
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhiyi Cai
- Department of Otolaryngology, Taizhou Municipal Hospital, Taizhou, Zhejiang 318000, China
| | - Jun Qin Mo
- Department of Pathology, Rady Children's Hospital, University of California School of Medicine, San Diego, California 92123
| | - Yong Liang
- Taizhou University Hospital, Taizhou University, Taizhou, Zhejiang 318000, China
| | - Min-Xin Guan
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang 310058, China .,Division of Medical Genetics and Genomics, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Key Laboratory of Reproductive Genetics, Ministry of Education of PRC, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Joint Institute of Genetics and Genomic Medicine between Zhejiang University and University of Toronto, Hangzhou, Zhejiang 310058, China
| |
Collapse
|
8
|
Carter JM, Emmett W, Mozos IR, Kotter A, Helm M, Ule J, Hussain S. FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA. Nucleic Acids Res 2019; 47:e113. [PMID: 31361898 PMCID: PMC6821191 DOI: 10.1093/nar/gkz658] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/03/2019] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
Methyl-5-uridine (m5U) is one the most abundant non-canonical bases present in cellular RNA, and in yeast is found at position U54 of tRNAs where modification is catalysed by the methyltransferase Trm2. Although the mammalian enzymes that catalyse m5U formation are yet to be identified via experimental evidence, based on sequence homology to Trm2, two candidates currently exist, TRMT2A and TRMT2B. Here we developed a genome-wide single-nucleotide resolution mapping method, Fluorouracil-Induced-Catalytic-Crosslinking-Sequencing (FICC-Seq), in order to identify the relevant enzymatic targets. We demonstrate that TRMT2A is responsible for the majority of m5U present in human RNA, and that it commonly targets U54 of cytosolic tRNAs. By comparison to current methods, we show that FICC-Seq is a particularly robust method for accurate and reliable detection of relevant enzymatic target sites. Our associated finding of extensive irreversible TRMT2A-tRNA crosslinking in vivo following 5-Fluorouracil exposure is also intriguing, as it suggests a tangible mechanism for a previously suspected RNA-dependent route of Fluorouracil-mediated cytotoxicity.
Collapse
Affiliation(s)
- Jean-Michel Carter
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Warren Emmett
- The Francis-Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,University College London Genetics Institute, Gower Street, London, WC1E 6BT, UK
| | - Igor Rdl Mozos
- The Francis-Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Annika Kotter
- Johannes Gutenberg-Universität, Institut für Pharmazie und Biochemie, Staudinger Weg 5, 55128 Mainz, Germany
| | - Mark Helm
- Johannes Gutenberg-Universität, Institut für Pharmazie und Biochemie, Staudinger Weg 5, 55128 Mainz, Germany
| | - Jernej Ule
- The Francis-Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Shobbir Hussain
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| |
Collapse
|
9
|
Yang P, Wu P, Liu X, Feng J, Zheng S, Wang Y, Fan Z. Mitochondrial tRNASer(UCN) 7471delC may be a novel mutation associated with maternally transmitted hypertension. Ir J Med Sci 2019; 189:489-496. [DOI: 10.1007/s11845-019-02143-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 11/14/2019] [Indexed: 02/07/2023]
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Abstract
BACKGROUND Given the etiologic heterogeneity of disease classification using clinical phenomenology, we employed contemporary criteria to classify variants associated with myoclonic epilepsy with ragged-red fibers (MERRF) syndrome and to assess the strength of evidence of gene-disease associations. Standardized approaches are used to clarify the definition of MERRF, which is essential for patient diagnosis, patient classification, and clinical trial design. METHODS Systematic literature and database search with application of standardized assessment of gene-disease relationships using modified Smith criteria and of variants reported to be associated with MERRF using modified Yarham criteria. RESULTS Review of available evidence supports a gene-disease association for two MT-tRNAs and for POLG. Using modified Smith criteria, definitive evidence of a MERRF gene-disease association is identified for MT-TK. Strong gene-disease evidence is present for MT-TL1 and POLG. Functional assays that directly associate variants with oxidative phosphorylation impairment were critical to mtDNA variant classification. In silico analysis was of limited utility to the assessment of individual MT-tRNA variants. With the use of contemporary classification criteria, several mtDNA variants previously reported as pathogenic or possibly pathogenic are reclassified as neutral variants. CONCLUSIONS MERRF is primarily an MT-TK disease, with pathogenic variants in this gene accounting for ~90% of MERRF patients. Although MERRF is phenotypically and genotypically heterogeneous, myoclonic epilepsy is the clinical feature that distinguishes MERRF from other categories of mitochondrial disorders. Given its low frequency in mitochondrial disorders, myoclonic epilepsy is not explained simply by an impairment of cellular energetics. Although MERRF phenocopies can occur in other genes, additional data are needed to establish a MERRF disease-gene association. This approach to MERRF emphasizes standardized classification rather than clinical phenomenology, thus improving patient diagnosis and clinical trial design.
Collapse
|
12
|
Tang X, Zheng J, Ying Z, Cai Z, Gao Y, He Z, Yu H, Yao J, Yang Y, Wang H, Chen Y, Guan MX. Mitochondrial tRNA(Ser(UCN)) variants in 2651 Han Chinese subjects with hearing loss. Mitochondrion 2015; 23:17-24. [PMID: 25968158 DOI: 10.1016/j.mito.2015.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 04/14/2015] [Accepted: 05/04/2015] [Indexed: 12/17/2022]
Abstract
Mutations in the mitochondrial DNA have been associated with hearing loss. However, the prevalence and spectrum of mitochondrial tRNA mutations in hearing-impaired subjects are poorly understood. In this report, we have investigated the prevalence and spectrum of mitochondrial tRNA(Ser(UCN)) mutations in a large cohort of 2651 Han Chinese subjects with hearing loss. The clinical evaluation showed that 744 subjects (432 males and 312 females) had a history of exposure to aminoglycosides and other probands exhibited nonsyndromic hearing loss. Mutational analysis of tRNA(Ser(UCN)) gene identified 9 (8 known and 1 novel) variants. The prevalence of the known deafness-associated 7511T>C, 7505T>C and 7445A>C mutations was 0.04%, 0.04% and 0.04%, respectively. Other variants were evaluated by the evolutionary conservation, allelic frequency of Chinese controls, potential structural and functional alterations and pedigree analysis. Three variants were polymorphisms, while the 7444G>A, 7471DelG and 7496A>G variants were putative deafness-associated mutations. These putative deafness-associated variants accounted for 0.68% cases of hearing-impaired subjects in this cohort. The low penetrance of hearing loss in pedigrees carrying one of these putative deafness-associated mutations indicated that the mutation(s) is necessary but itself insufficient to produce a clinical phenotype. Other genetic or environmental factor(s) may influence the phenotypic manifestation of these tRNA(Ser(UCN)) mutations. Moreover, mtDNAs in 20 probands carrying one of the putative deafness-associated mutations were widely dispersed among 8 Eastern Asian haplogroups. In particular, the occurrences of haplogroups D4a, M22, and H2 in patients carrying the deafness-associated variants were higher than those in Chinese controls. These data further support that the mitochondrial tRNA(Ser(UCN)) gene is the hot spot for mutations associated with hearing loss. Thus, our findings may provide valuable information for the further understanding of pathophysiology and management of hearing loss.
Collapse
Affiliation(s)
- Xiaowen Tang
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jing Zheng
- Institute of Genetics, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhengbiao Ying
- Department of Otolaryngology, Wenling People's Hospital, Wenzhou Medical University, Wenling, Zhejiang, China
| | - Zhaoyang Cai
- Department of Otolaryngology, Wenling People's Hospital, Wenzhou Medical University, Wenling, Zhejiang, China
| | - Yinglong Gao
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zheyun He
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Han Yu
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Juan Yao
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yaling Yang
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Hui Wang
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ye Chen
- Institute of Genetics, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Min-Xin Guan
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China; Institute of Genetics, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
| |
Collapse
|
13
|
Mustoe AM, Liu X, Lin PJ, Al-Hashimi HM, Fierke CA, Brooks CL. Noncanonical secondary structure stabilizes mitochondrial tRNA(Ser(UCN)) by reducing the entropic cost of tertiary folding. J Am Chem Soc 2015; 137:3592-9. [PMID: 25705930 PMCID: PMC4399864 DOI: 10.1021/ja5130308] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Mammalian mitochondrial tRNA(Ser(UCN)) (mt-tRNA(Ser)) and pyrrolysine tRNA (tRNA(Pyl)) fold to near-canonical three-dimensional structures despite having noncanonical secondary structures with shortened interhelical loops that disrupt the conserved tRNA tertiary interaction network. How these noncanonical tRNAs compensate for their loss of tertiary interactions remains unclear. Furthermore, in human mt-tRNA(Ser), lengthening the variable loop by the 7472insC mutation reduces mt-tRNA(Ser) concentration in vivo through poorly understood mechanisms and is strongly associated with diseases such as deafness and epilepsy. Using simulations of the TOPRNA coarse-grained model, we show that increased topological constraints encoded by the unique secondary structure of wild-type mt-tRNA(Ser) decrease the entropic cost of folding by ∼2.5 kcal/mol compared to canonical tRNA, offsetting its loss of tertiary interactions. Further simulations show that the pathogenic 7472insC mutation disrupts topological constraints and hence destabilizes the mutant mt-tRNA(Ser) by ∼0.6 kcal/mol relative to wild-type. UV melting experiments confirm that insertion mutations lower mt-tRNA(Ser) melting temperature by 6-9 °C and increase the folding free energy by 0.8-1.7 kcal/mol in a largely sequence- and salt-independent manner, in quantitative agreement with our simulation predictions. Our results show that topological constraints provide a quantitative framework for describing key aspects of RNA folding behavior and also provide the first evidence of a pathogenic mutation that is due to disruption of topological constraints.
Collapse
Affiliation(s)
- Anthony M. Mustoe
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Xin Liu
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Paul J. Lin
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Hashim M. Al-Hashimi
- Departments of Biochemistry and Chemistry, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Carol A. Fierke
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Charles L. Brooks
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| |
Collapse
|
14
|
Gong S, Peng Y, Jiang P, Wang M, Fan M, Wang X, Zhou H, Li H, Yan Q, Huang T, Guan MX. A deafness-associated tRNAHis mutation alters the mitochondrial function, ROS production and membrane potential. Nucleic Acids Res 2014; 42:8039-48. [PMID: 24920829 PMCID: PMC4081083 DOI: 10.1093/nar/gku466] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In this report, we investigated the molecular genetic mechanism underlying the deafness-associated mitochondrial tRNAHis 12201T>C mutation. The destabilization of a highly conserved base-pairing (5A-68U) by the m.12201T>C mutation alters structure and function of tRNAHis. Using cybrids constructed by transferring mitochondria from lymphoblastoid cell lines derived from a Chinese family into mtDNA-less (ρo) cells, we showed ∼70% decrease in the steady-state level of tRNAHis in mutant cybrids, compared with control cybrids. The mutation changed the conformation of tRNAHis, as suggested by slower electrophoretic mobility of mutated tRNA with respect to the wild-type molecule. However, ∼60% increase in aminoacylated level of tRNAHis was observed in mutant cells. The failure in tRNAHis metabolism was responsible for the variable reductions in seven mtDNA-encoded polypeptides in mutant cells, ranging from 37 to 81%, with the average of ∼46% reduction, as compared with those of control cells. The impaired mitochondrial translation caused defects in respiratory capacity in mutant cells. Furthermore, marked decreases in the levels of mitochondrial ATP and membrane potential were observed in mutant cells. These mitochondrial dysfunctions caused an increase in the production of reactive oxygen species in the mutant cells. The data provide the evidence for a mitochondrial tRNAHis mutation leading to deafness.
Collapse
Affiliation(s)
- Shasha Gong
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang, China 310058
| | - Yanyan Peng
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang, China 310058 Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA 45229
| | - Pingping Jiang
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang, China 310058
| | - Meng Wang
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang, China 310058
| | - Mingjie Fan
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang, China 310058
| | - Xinjian Wang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA 45229
| | - Hong Zhou
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang, China 310058
| | - Huawei Li
- Department of Otology and Skull Base Surgery, Eye and ENT Hospital, Fudan University, Shanghai, China 200031
| | - Qingfeng Yan
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang, China 310058
| | - Taosheng Huang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA 45229
| | - Min-Xin Guan
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang, China 310058 Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA 45229
| |
Collapse
|
15
|
Park JH, Yoon BR, Kim HJ, Lee PH, Choi BO, Chung KW. Compound mitochondrial DNA mutations in a neurological patient with ataxia, myoclonus and deafness. J Genet 2014; 93:173-7. [PMID: 24840835 DOI: 10.1007/s12041-014-0317-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ji Hoon Park
- Department of Biological Science, Kongju National University, 182 sinkwan-dong, Gongju, Chungnam 314-701, Republic of Korea.
| | | | | | | | | | | |
Collapse
|
16
|
Suzuki T, Suzuki T. A complete landscape of post-transcriptional modifications in mammalian mitochondrial tRNAs. Nucleic Acids Res 2014; 42:7346-57. [PMID: 24831542 PMCID: PMC4066797 DOI: 10.1093/nar/gku390] [Citation(s) in RCA: 216] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In mammalian mitochondria, 22 species of tRNAs encoded in mitochondrial DNA play crucial roles in the translation of 13 essential subunits of the respiratory chain complexes involved in oxidative phosphorylation. Following transcription, mitochondrial tRNAs are modified by nuclear-encoded tRNA-modifying enzymes. These modifications are required for the proper functioning of mitochondrial tRNAs (mt tRNAs), and the absence of these modifications can cause pathological consequences. To date, however, the information available about these modifications has been incomplete. To address this issue, we isolated all 22 species of mt tRNAs from bovine liver and comprehensively determined the post-transcriptional modifications in each tRNA by mass spectrometry. Here, we describe the primary structures with post-transcriptional modifications of seven species of mt tRNAs which were previously uncharacterized, and provide revised information regarding base modifications in five other mt tRNAs. In the complete set of bovine mt tRNAs, we found 15 species of modified nucleosides at 118 positions (7.48% of total bases). This result provides insight into the molecular mechanisms underlying the decoding system in mammalian mitochondria and enables prediction of candidate tRNA-modifying enzymes responsible for each modification of mt tRNAs.
Collapse
Affiliation(s)
- Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| |
Collapse
|
17
|
Zheng J, Sha-sha G, Xiao-wen T, Yi Z, Min-xin G. Human Mitochondrial tRNA Mutations in Maternally Inherited Deafness. J Otol 2013. [DOI: 10.1016/s1672-2930(13)50006-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
18
|
Guitart T, Picchioni D, Piñeyro D, Ribas de Pouplana L. Human mitochondrial disease-like symptoms caused by a reduced tRNA aminoacylation activity in flies. Nucleic Acids Res 2013; 41:6595-608. [PMID: 23677612 PMCID: PMC3711456 DOI: 10.1093/nar/gkt402] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The translation of genes encoded in the mitochondrial genome requires specific machinery that functions in the organelle. Among the many mutations linked to human disease that affect mitochondrial translation, several are localized to nuclear genes coding for mitochondrial aminoacyl-transfer RNA synthetases. The molecular significance of these mutations is poorly understood, but it is expected to be similar to that of the mutations affecting mitochondrial transfer RNAs. To better understand the molecular features of diseases caused by these mutations, and to improve their diagnosis and therapeutics, we have constructed a Drosophila melanogaster model disrupting the mitochondrial seryl-tRNA synthetase by RNA interference. At the molecular level, the knockdown generates a reduction in transfer RNA serylation, which correlates with the severity of the phenotype observed. The silencing compromises viability, longevity, motility and tissue development. At the cellular level, the knockdown alters mitochondrial morphology, biogenesis and function, and induces lactic acidosis and reactive oxygen species accumulation. We report that administration of antioxidant compounds has a palliative effect of some of these phenotypes. In conclusion, the fly model generated in this work reproduces typical characteristics of pathologies caused by mutations in the mitochondrial aminoacylation system, and can be useful to assess therapeutic approaches.
Collapse
Affiliation(s)
- Tanit Guitart
- Institute for Research in Biomedicine (IRB Barcelona), Gene Translation Laboratory, c/Baldiri Reixac 10, Barcelona, 08028, Catalonia, Spain
| | | | | | | |
Collapse
|
19
|
Götz A, Isohanni P, Liljeström B, Rummukainen J, Nikolajev K, Herrgård E, Marjavaara S, Suomalainen A. Fatal neonatal lactic acidosis caused by a novel de novo mitochondrial G7453A tRNA-Serine ((UCN)) mutation. Pediatr Res 2012; 72:90-4. [PMID: 22453297 DOI: 10.1038/pr.2012.43] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
INTRODUCTION Heteroplasmic mitochondrial DNA (mtDNA) mutations are an important cause of childhood disorders, but the role of homoplasmic mtDNA mutations in severe neonatal manifestations is not well understood. METHODS The following were performed: full mtDNA sequencing for mutation detection, blue-native protein analysis of autopsy-derived tissues to detect respiratory chain (RC) deficiency, light and electron microscopy for morphologic analysis, and northern blot and computational modeling to study the effect of mtDNA mutations on transfer RNA (tRNA) stability. RESULTS We describe data from a patient with fatal neonatal lactic acidosis caused by a novel homoplasmic mutation at a highly conserved nucleotide G7453A within the tRNA(Ser (UCN)) in mtDNA. The patient's heart, skeletal muscle, brain, and liver showed severe combined complex I and IV (CI and CIV) deficiencies, accompanied by severe depletion of mature tRNA(Ser (UCN)). The mutation was absent in the patient's mother and in a placental sample from a subsequent pregnancy of the mother, suggesting a de novo mutation. DISCUSSION We conclude that the G7453A mutation of mtDNA manifests with exceptional severity as compared with other tRNA(Ser (UCN)) mutations, typically associated with sensorineural deafness. De novo homoplasmic mtDNA tRNA-mutations should be considered as a cause of fatal neonatal lactic acidosis.
Collapse
Affiliation(s)
- Alexandra Götz
- Research Programs Unit, Molecular Neurology, Biomedicum-Helsinki, University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | | | | |
Collapse
|
20
|
Jing Z, Yan–chun J, Min–Xin G. Mitochondrial tRNA mutations associated with deafness. J Otol 2012. [DOI: 10.1016/s1672-2930(12)50009-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
21
|
Zheng J, Ji Y, Guan MX. Mitochondrial tRNA mutations associated with deafness. Mitochondrion 2012; 12:406-13. [PMID: 22538251 DOI: 10.1016/j.mito.2012.04.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 03/15/2012] [Accepted: 04/09/2012] [Indexed: 10/28/2022]
Abstract
Mitochondrial tRNA mutations are one of the important causes of both syndromic and non-syndromic deafness. Of those, syndromic deafness-associated tRNA mutations such as tRNA(Leu(UUR)) 3243A>G are often present in heteroplasmy, while non-syndromic deafness-associated tRNA mutations including tRNA(Ser(UCN)) 7445A>G often occur in homplasmy or in high levels of heteroplasmy. These tRNA mutations are the primary mutations leading to hearing loss. However, other tRNA mutations such as tRNA(Thr) 15927G>A and tRNA(Ser(UCN)) 7444G>A may act in synergy with the primary mitochondrial DNA mutations, modulating the phenotypic manifestation of the primary mitochondrial DNA mutations. Theses tRNA mutations cause structural and functional alteration. A failure in tRNA metabolism caused by these tRNA mutations impaired mitochondrial translation and respiration, thereby causing mitochondrial dysfunctions responsible for deafness. These data offer valuable information for the early diagnosis, management and treatment of maternally inherited deafness.
Collapse
Affiliation(s)
- Jing Zheng
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical College, Wenzhou, Zhejiang, China
| | | | | |
Collapse
|
22
|
Belostotsky R, Frishberg Y, Entelis N. Human mitochondrial tRNA quality control in health and disease: a channelling mechanism? RNA Biol 2012; 9:33-9. [PMID: 22258151 DOI: 10.4161/rna.9.1.18009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Mutations in human mitochondrial tRNA genes are associated with a number of multisystemic disorders. These single nucleotide substitutions in various domains of tRNA molecules may affect different steps of tRNA biogenesis. Often, the prominent decrease of aminoacylation and/or steady-state levels of affected mitochondrial tRNA have been demonstrated in patients' tissues and in cultured cells. Similar effect has been observed for pathogenic mutations in nuclear genes encoding mitochondrial aminoacyl-tRNA-synthetases, while over-expression of mitochondrial aminoacyl-tRNA synthetases or elongation factor EF-Tu rescued mutated tRNAs from degradation. In this review we summarize experimental data concerning the possible regulatory mechanisms governing mitochondrial tRNA steady-state levels, and propose a hypothesis based on the tRNA channelling principle. According to this hypothesis, interaction of mitochondrial tRNA with proteins ensures not only tRNA synthesis, maturation and function, but also protection from degradation. Mutations perturbing this interaction lead to decreased tRNA stability.
Collapse
Affiliation(s)
- Ruth Belostotsky
- Division of Pediatric Nephrology, Shaare Zedek Medical Center; Jerusalem, Israel
| | | | | |
Collapse
|
23
|
Rydzanicz M, Cywińska K, Wróbel M, Pollak A, Gawęcki W, Wojsyk-Banaszak I, Lechowicz U, Mueller-Malesińska M, Ołdak M, Płoski R, Skarżyński H, Szyfter K, Szyfter W. The contribution of the mitochondrial COI/tRNA(Ser(UCN)) gene mutations to non-syndromic and aminoglycoside-induced hearing loss in Polish patients. Mol Genet Metab 2011; 104:153-9. [PMID: 21621438 DOI: 10.1016/j.ymgme.2011.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 05/08/2011] [Accepted: 05/08/2011] [Indexed: 11/17/2022]
Abstract
Mutations in mitochondrial DNA have been implicated in both, non-syndromic and aminoglycoside-induced hearing loss. In the present study, we have performed the systematic mutation screening of the COI/tRNA(Ser(UCN)) genes in 250 unrelated Polish subjects with hearing impairment. Three different homoplasmic sequence variants were identified, including one common polymorphism m.7476 C>T in tRNA(Ser(UCN)) and two mutations, m.7444 G>A and m.7445 A>G localized in the COI/precursor of tRNA(Ser(UCN)). The incidence of m.7444 G>A substitution was estimated at 1.6% (4/250), however variable penetrance of hearing loss, age of onset and hearing thresholds among m.7444 G>A carriers was observed. Two subjects had the positive history of aminoglycoside exposure and one of them harbored both m.7444 G>A and 12S rRNA m.1555 A>G mutations. Those suggest that m.7444 G>A itself is not sufficient to produce a clinical phenotype and additional modifier factors are required for pathogenic manifestation of m.7444 G>A substitution. Moreover, we have described the first Polish family with non-syndromic hearing loss, harboring m.7445 A>G mutation. The penetrance of hearing loss in this pedigree was 58% when aminoglycoside-induced hearing impairment was included, and 8% when ototoxic effect was excluded. This finding strongly suggests the possible role of m.7445 A>G in susceptibility to aminoglycoside induced-hearing loss.
Collapse
Affiliation(s)
- Małgorzata Rydzanicz
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Hearing loss and epilepsy may be associated with the novel mito-chondrial Trna Ser(UCN) 7472delC mutation in a Chinese family. YI CHUAN = HEREDITAS 2009; 30:1557-62. [DOI: 10.3724/sp.j.1005.2008.01557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
25
|
Sasarman F, Antonicka H, Shoubridge EA. The A3243G tRNALeu(UUR) MELAS mutation causes amino acid misincorporation and a combined respiratory chain assembly defect partially suppressed by overexpression of EFTu and EFG2. Hum Mol Genet 2008; 17:3697-707. [DOI: 10.1093/hmg/ddn265] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
26
|
Scaglia F, Wong LJC. Human mitochondrial transfer RNAs: role of pathogenic mutation in disease. Muscle Nerve 2008; 37:150-71. [PMID: 17999409 DOI: 10.1002/mus.20917] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The human mitochondrial genome encodes 13 proteins. All are subunits of the respiratory chain complexes involved in energy metabolism. These proteins are translated by a set of 22 mitochondrial transfer RNAs (tRNAs) that are required for codon reading. Human mitochondrial tRNA genes are hotspots for pathogenic mutations and have attracted interest over the last two decades with the rapid discovery of point mutations associated with a vast array of neuromuscular disorders and diverse clinical phenotypes. In this review, we use a scoring system to determine the pathogenicity of the mutations and summarize the current knowledge of structure-function relationships of these mutant tRNAs. We also provide readers with an overview of a large variety of mechanisms by which mutations may affect the mitochondrial translation machinery and cause disease.
Collapse
Affiliation(s)
- Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | | |
Collapse
|
27
|
A homoplasmic mtDNA variant can influence the phenotype of the pathogenic m.7472Cins MTTS1 mutation: are two mutations better than one? Eur J Hum Genet 2008; 16:1265-74. [PMID: 18398437 DOI: 10.1038/ejhg.2008.65] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Mutations in mitochondrial tRNA (mt-tRNA) genes are well recognized as a common cause of human disease, exhibiting a significant degree of clinical heterogeneity. While these differences are explicable, in part, by differences in the innate pathogenicity of the mutation, its distribution and abundance, other factors, including nuclear genetic background, mitochondrial DNA (mtDNA) haplotype and additional mtDNA mutations may influence the expression of mt-tRNA mutations. We describe the clinical, biochemical and molecular findings in a family with progressive myopathy, deafness and diabetes and striking respiratory chain abnormalities due to a well-characterized heteroplasmic mt-tRNA mutation in the mt-tRNA(Ser(UCN)) (MTTS1) gene. In addition to the m.7472Cins mutation, all individuals were homoplasmic for another variant, m.7472A > C, affecting the adjacent nucleotide in the mt-tRNA(Ser(UCN)) structure. In addition to available patient tissues, we have analysed transmitochondrial cybrid clones harbouring homoplasmic levels of m.7472A > C and varying levels of the m.7472Cins mutation in an attempt to clarify the precise role of the m.7472A > C transversion in the underlying respiratory chain abnormality. Evidence from both in vivo and in vitro studies demonstrate that the m.7472A > C is able to modify the expression of the m.7472Cins mutation and would suggest that it is not a neutral variant but appears to cause a biochemical defect by itself, confirming that homoplasmic mtDNA variants can modulate the phenotypic expression of pathogenic, heteroplasmic mtDNA mutations.
Collapse
|
28
|
Ling J, Roy H, Qin D, Rubio MAT, Alfonzo JD, Fredrick K, Ibba M. Pathogenic mechanism of a human mitochondrial tRNAPhe mutation associated with myoclonic epilepsy with ragged red fibers syndrome. Proc Natl Acad Sci U S A 2007; 104:15299-304. [PMID: 17878308 PMCID: PMC2000536 DOI: 10.1073/pnas.0704441104] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Indexed: 11/18/2022] Open
Abstract
Human mitochondrial tRNA (hmt-tRNA) mutations are associated with a variety of diseases including mitochondrial myopathies, diabetes, encephalopathies, and deafness. Because the current understanding of the precise molecular mechanisms of these mutations is limited, there is no efficient method to treat their associated mitochondrial diseases. Here, we use a variety of known mutations in hmt-tRNA(Phe) to investigate the mechanisms that lead to malfunctions. We tested the impact of hmt-tRNA(Phe) mutations on aminoacylation, structure, and translation elongation-factor binding. The majority of the mutants were pleiotropic, exhibiting defects in aminoacylation, global structure, and elongation-factor binding. One notable exception was the G34A anticodon mutation of hmt-tRNA(Phe) (mitochondrial DNA mutation G611A), which is associated with MERRF (myoclonic epilepsy with ragged red fibers). In vitro, the G34A mutation decreases aminoacylation activity by 100-fold, but does not affect global folding or recognition by elongation factor. Furthermore, G34A hmt-tRNA(Phe) does not undergo adenosine-to-inosine (A-to-I) editing, ruling out miscoding as a possible mechanism for mitochondrial malfunction. To improve the aminoacylation state of the mutant tRNA, we modified the tRNA binding domain of the nucleus-encoded human mitochondrial phenylalanyl-tRNA synthetase, which aminoacylates hmt-tRNA(Phe) with cognate phenylalanine. This variant enzyme displayed significantly improved aminoacylation efficiency for the G34A mutant, suggesting a general strategy to treat certain classes of mitochondrial diseases by modification of the corresponding nuclear gene.
Collapse
Affiliation(s)
| | - Hervé Roy
- Department of Microbiology, and
- Ohio State RNA Group, Ohio State University, Columbus, OH 43210
| | | | - Mary Anne T. Rubio
- Department of Microbiology, and
- Ohio State RNA Group, Ohio State University, Columbus, OH 43210
| | - Juan D. Alfonzo
- *Ohio State Biochemistry Program
- Department of Microbiology, and
- Ohio State RNA Group, Ohio State University, Columbus, OH 43210
| | - Kurt Fredrick
- *Ohio State Biochemistry Program
- Department of Microbiology, and
- Ohio State RNA Group, Ohio State University, Columbus, OH 43210
| | - Michael Ibba
- *Ohio State Biochemistry Program
- Department of Microbiology, and
- Ohio State RNA Group, Ohio State University, Columbus, OH 43210
| |
Collapse
|
29
|
Abstract
The human ear is a delicate sensory apparatus of hearing for normal communication, and its proper functioning is highly dependent on mitochondrial oxidative phosphorylation. The first mitochondrial point mutation for nonsyndromic and aminoglycoside-induced hearing loss was identified in 1993. Since then a number of inherited mitochondrial mutations have been implicated in hearing loss. Most of the molecular defects responsible for mitochondrial disorder-associated hearing loss are mutations in the 12S rRNA gene and tRNA genes. In this review, after a short description of normal hearing mechanisms and mitochondrial genetics, we outline the recent advances that have been made in the identification of deafness-associated mitochondrial mutations, and discuss how mitochondrial dysfunction contributes to hearing loss.
Collapse
Affiliation(s)
- Guangqian Xing
- Department of Otolaryngology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China.
| | | | | |
Collapse
|
30
|
Abstract
Mitochondria are ubiquitous organelles that are intimately involved in many cellular processes, but whose principal task is to provide the energy necessary for normal cell functioning and maintenance. Disruption of this energy supply can have devastating consequences for the cell, organ, and individual. Over the last two decades, mutations in both mitochondrial DNA (mtDNA) and nuclear DNA have been identified as causative in a number of well-characterized clinical syndromes, although for mtDNA mutations in particular, this relationship between genotype and phenotype is often not straightforward. Despite this, a number of epidemiological studies have been undertaken to assess the prevalence of mtDNA mutations and these have highlighted the impact that mtDNA disease has on both the community and individual families. Although there has been considerable improvement in the diagnosis of mitochondrial disorders, disappointingly this has not been matched by developments toward effective treatment. Nevertheless, our understanding of mitochondrial biology is gathering pace and progress in this area will be crucial to devising future treatment strategies. In addition to mitochondrial disease, evidence for a central role of mitochondria in other processes, such as aging and neurodegeneration, is slowly accumulating, although their role in cancer remains controversial. In this chapter, we discuss these issues and offer our own views based on our cumulative experience of investigating and managing these diseases over the last 20 years.
Collapse
Affiliation(s)
- R McFarland
- Mitochondrial Research Group, School of Neurology, Neurobiology, and Psychiatry, The Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
| | | | | |
Collapse
|
31
|
Pohjoismäki JLO, Wanrooij S, Hyvärinen AK, Goffart S, Holt IJ, Spelbrink JN, Jacobs HT. Alterations to the expression level of mitochondrial transcription factor A, TFAM, modify the mode of mitochondrial DNA replication in cultured human cells. Nucleic Acids Res 2006; 34:5815-28. [PMID: 17062618 PMCID: PMC1635303 DOI: 10.1093/nar/gkl703] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Mitochondrial transcription factor A (TFAM) is an abundant mitochondrial protein of the HMG superfamily, with various putative roles in mitochondrial DNA (mtDNA) metabolism. In this study we have investigated the effects on mtDNA replication of manipulating TFAM expression in cultured human cells. Mammalian mtDNA replication intermediates (RIs) fall into two classes, whose mechanistic relationship is not properly understood. One class is characterized by extensive RNA incorporation on the lagging strand, whereas the other has the structure of products of conventional, strand-coupled replication. TFAM overexpression increased the overall abundance of RIs and shifted them substantially towards those of the conventional, strand-coupled type. The shift was most pronounced in the rDNA region and at various replication pause sites and was accompanied by a drop in the relative amount of replication-termination intermediates, a substantial reduction in mitochondrial transcripts, mtDNA decatenation and progressive copy number depletion. TFAM overexpression could be partially phenocopied by treatment of cells with dideoxycytidine, suggesting that its effects are partially attributable to a decreased rate of fork progression. TFAM knockdown also resulted in mtDNA depletion, but RIs remained mainly of the ribosubstituted type, although termination intermediates were enhanced. We propose that TFAM influences the mode of mtDNA replication via its combined effects on different aspects of mtDNA metabolism.
Collapse
Affiliation(s)
- Jaakko L. O. Pohjoismäki
- Institute of Medical Technology and Tampere University HospitalFI-33014 University of Tampere, Finland
| | - Sjoerd Wanrooij
- Institute of Medical Technology and Tampere University HospitalFI-33014 University of Tampere, Finland
| | - Anne K. Hyvärinen
- Institute of Medical Technology and Tampere University HospitalFI-33014 University of Tampere, Finland
| | - Steffi Goffart
- Institute of Medical Technology and Tampere University HospitalFI-33014 University of Tampere, Finland
| | - Ian J. Holt
- MRC-Dunn Human Nutrition Unit, Hill RoadCambridge CB2 2XY, England, UK
| | - Johannes N. Spelbrink
- Institute of Medical Technology and Tampere University HospitalFI-33014 University of Tampere, Finland
| | - Howard T. Jacobs
- Institute of Medical Technology and Tampere University HospitalFI-33014 University of Tampere, Finland
- IBLS Division of Molecular Genetics, University of GlasgowGlasgow G12 8QQ, Scotland, UK
- To whom correspondence should be addressed. Tel: +358 33 55 17 731; Fax: +358 32 15 77 10;
| |
Collapse
|
32
|
Yan H, Zareen N, Levinger L. Naturally occurring mutations in human mitochondrial pre-tRNASer(UCN) can affect the transfer ribonuclease Z cleavage site, processing kinetics, and substrate secondary structure. J Biol Chem 2005; 281:3926-35. [PMID: 16361254 DOI: 10.1074/jbc.m509822200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
tRNAs are transcribed as precursors with a 5' end leader and a 3' end trailer. The 5' end leader is processed by RNase P, and in most organisms in all three kingdoms, transfer ribonuclease (tRNase) Z can endonucleolytically remove the 3' end trailer. Long ((L)) and short ((S)) forms of the tRNase Z gene are present in the human genome. tRNase Z(L) processes a nuclear-encoded pre-tRNA approximately 1600-fold more efficiently than tRNase Z(S) and is predicted to have a strong mitochondrial transport signal. tRNase Z(L) could, thus, process both nuclear- and mitochondrially encoded pre-tRNAs. More than 150 pathogenesis-associated mutations have been found in the mitochondrial genome, most of them in the 22 mitochondrially encoded tRNAs. All the mutations investigated in human mitochondrial tRNA(Ser(UCN)) affect processing efficiency, and some affect the cleavage site and secondary structure. These changes could affect tRNase Z processing of mutant pre-tRNAs, perhaps contributing to mitochondrial disease.
Collapse
Affiliation(s)
- Hua Yan
- York College of The City University of New York, Jamaica, 11451, USA
| | | | | |
Collapse
|
33
|
Möllers M, Maniura-Weber K, Kiseljakovic E, Bust M, Hayrapetyan A, Jaksch M, Helm M, Wiesner RJ, von Kleist-Retzow JC. A new mechanism for mtDNA pathogenesis: impairment of post-transcriptional maturation leads to severe depletion of mitochondrial tRNASer(UCN) caused by T7512C and G7497A point mutations. Nucleic Acids Res 2005; 33:5647-58. [PMID: 16199753 PMCID: PMC1240115 DOI: 10.1093/nar/gki876] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have studied the consequences of two homoplasmic, pathogenic point mutations (T7512C and G7497A) in the tRNA(Ser(UCN)) gene of mitochondrial (mt) DNA using osteosarcoma cybrids. We identified a severe reduction of tRNA(Ser(UCN)) to levels below 10% of controls for both mutations, resulting in a 40% reduction in mitochondrial protein synthesis rate and in a respiratory chain deficiency resembling that in the patients muscle. Aminoacylation was apparently unaffected. On non-denaturating northern blots we detected an altered electrophoretic mobility for G7497A containing tRNA molecules suggesting a structural impact of this mutation, which was confirmed by structural probing. By comparing in vitro transcribed molecules with native RNA in such gels, we also identified tRNA(Ser(UCN)) being present in two isoforms in vivo, probably corresponding to the nascent, unmodified transcripts co-migrating with the in vitro transcripts and a second, faster moving isoform corresponding to the mature tRNA. In cybrids containing either mutations the unmodified isoforms were severely reduced. We hypothesize that both mutations lead to an impairment of post-transcriptional modification processes, ultimately leading to a preponderance of degradation by nucleases over maturation by modifying enzymes, resulting in severely reduced tRNA(Ser(UCN)) steady state levels. We infer that an increased degradation rate, caused by disturbance of tRNA maturation and, in the case of the G7497A mutant, alteration of tRNA structure, is a new pathogenic mechanism of mt tRNA point mutations.
Collapse
MESH Headings
- Aminoacylation
- Base Sequence
- Cell Line
- Child
- Child, Preschool
- DNA, Mitochondrial/genetics
- Electron Transport Complex I/metabolism
- Electron Transport Complex IV/metabolism
- Humans
- Male
- Mitochondrial Diseases/genetics
- Mitochondrial Diseases/metabolism
- Mitochondrial Proteins/biosynthesis
- Molecular Sequence Data
- Point Mutation
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional
- RNA Stability
- RNA, Mitochondrial
- RNA, Transfer, Ser/chemistry
- RNA, Transfer, Ser/genetics
- RNA, Transfer, Ser/metabolism
Collapse
Affiliation(s)
- Myriam Möllers
- Institute of Vegetative Physiology, University of KölnRobert-Koch-Strasse 39, 50931 Köln, Germany
| | - Katharina Maniura-Weber
- Institute of Vegetative Physiology, University of KölnRobert-Koch-Strasse 39, 50931 Köln, Germany
| | - Emina Kiseljakovic
- Institute of Vegetative Physiology, University of KölnRobert-Koch-Strasse 39, 50931 Köln, Germany
- Department of Biochemistry, Medical FacultySarajevo, Cekalusa 90, Bosnia and Herzegovina
| | - Maria Bust
- Institute of Vegetative Physiology, University of KölnRobert-Koch-Strasse 39, 50931 Köln, Germany
| | - Armine Hayrapetyan
- Institute of Pharmacy and Molecular Biotechnology, University of HeidelbergIm Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Michaela Jaksch
- Institute of Clinical Chemistry and Mitochondrial GeneticsKölner Platz 1, 80804 München, Germany
| | - Mark Helm
- Institute of Pharmacy and Molecular Biotechnology, University of HeidelbergIm Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Rudolf J. Wiesner
- Institute of Vegetative Physiology, University of KölnRobert-Koch-Strasse 39, 50931 Köln, Germany
- Center for Molecular Medicine Cologne (CMMC), University of KölnJoseph-Stelzmann-Strasse 52, 50931 Köln, Germany
- To whom correspondence should be addressed. Tel: +49 221 478 3610; Fax: +49 221 478 3538;
| | - Jürgen-Christoph von Kleist-Retzow
- Center for Molecular Medicine Cologne (CMMC), University of KölnJoseph-Stelzmann-Strasse 52, 50931 Köln, Germany
- Department of Pediatrics, University of KölnKerpener Strasse 62, 50924 Köln, Germany
| |
Collapse
|
34
|
Chimnaronk S, Gravers Jeppesen M, Suzuki T, Nyborg J, Watanabe K. Dual-mode recognition of noncanonical tRNAs(Ser) by seryl-tRNA synthetase in mammalian mitochondria. EMBO J 2005; 24:3369-79. [PMID: 16163389 PMCID: PMC1276171 DOI: 10.1038/sj.emboj.7600811] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Accepted: 08/22/2005] [Indexed: 11/09/2022] Open
Abstract
The secondary structures of metazoan mitochondrial (mt) tRNAs(Ser) deviate markedly from the paradigm of the canonical cloverleaf structure; particularly, tRNA(Ser)(GCU) corresponding to the AGY codon (Y=U and C) is highly truncated and intrinsically missing the entire dihydrouridine arm. None of the mt serine isoacceptors possesses the elongated variable arm, which is the universal landmark for recognition by seryl-tRNA synthetase (SerRS). Here, we report the crystal structure of mammalian mt SerRS from Bos taurus in complex with seryl adenylate at an atomic resolution of 1.65 A. Coupling structural information with a tRNA-docking model and the mutagenesis studies, we have unraveled the key elements that establish tRNA binding specificity, differ from all other known bacterial and eukaryotic systems, are the characteristic extensions in both extremities, as well as a few basic residues residing in the amino-terminal helical arm of mt SerRS. Our data further uncover an unprecedented mechanism of a dual-mode recognition employed to discriminate two distinct 'bizarre' mt tRNAs(Ser) by alternative combination of interaction sites.
Collapse
Affiliation(s)
- Sarin Chimnaronk
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
| | | | - Tsutomu Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
| | - Jens Nyborg
- Department of Molecular Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Kimitsuna Watanabe
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
- Present address: Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Biological Information Research Center, National Institute of Advanced Industrial Science & Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan. Tel.:+81 3 3599 8106; Fax: +81 3 5530 2064; E-mail:
| |
Collapse
|
35
|
Jacobs HT, Hutchin TP, Käppi T, Gillies G, Minkkinen K, Walker J, Thompson K, Rovio AT, Carella M, Melchionda S, Zelante L, Gasparini P, Pyykkö I, Shah ZH, Zeviani M, Mueller RF. Mitochondrial DNA mutations in patients with postlingual, nonsyndromic hearing impairment. Eur J Hum Genet 2005; 13:26-33. [PMID: 15292920 DOI: 10.1038/sj.ejhg.5201250] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Mitochondrial mutations have previously been reported anecdotally in families with maternally inherited, nonsyndromic hearing impairment. To ascertain the contribution of mitochondrial mutations to postlingual but early-onset, nonsyndromic hearing impairment, we screened patients collected from within two different populations (southern Italy and UK) for previously reported mtDNA mutations associated with hearing disorders. Primer extension (SNP analysis) was used to screen for specific mutations, revealing cases of heteroplasmy and its extent. The most frequently implicated tRNA genes, Leu(UUR) and Ser(UCN), were also sequenced in all Italian patients. All tRNA genes were sequenced in those UK patients showing the clearest likelihood of maternal inheritance. Causative mtDNA mutations were found in approximately 5% of patients in both populations, representing almost 10% of cases that were clearly familial. Age of onset, where known, was generally before adulthood, and hearing loss was typically progressive. Haplogroup analysis revealed a possible excess of haplogroup cluster HV in the patients, compared with population controls, but of borderline statistical significance. In contrast, we did not find any of the previously reported mtDNA mutations, nor a significant deviation from haplogroup cluster frequencies typical of the control population, in patients with late adult-onset hearing loss (age-related hearing impairment) from the UK or Finland.
Collapse
Affiliation(s)
- Howard T Jacobs
- Institute of Medical Technology & Tampere University Hospital, Tampere, Finland.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Li X, Zhang LS, Fischel-Ghodsian N, Guan MX. Biochemical characterization of the deafness-associated mitochondrial tRNASer(UCN) A7445G mutation in osteosarcoma cell cybrids. Biochem Biophys Res Commun 2005; 328:491-8. [PMID: 15694374 DOI: 10.1016/j.bbrc.2005.01.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2004] [Indexed: 10/25/2022]
Abstract
The deafness-associated A7445G mutation in the precursor of mitochondrial tRNA(Ser(UCN)) has been identified in several pedigrees from different ethnic backgrounds. To determine the role of nuclear background in the biochemical manifestation associated with the A7445G mutation, we performed a biochemical characterization of this mutation using cybrids constructed by transferring mitochondria from lymphoblastoid cell lines derived from a New Zealand family into human osteosarcoma mtDNA-less (rho(0)) cells. Compared with three control cybrids, three cybrids derived from an affected matrilineal relative carrying the homoplasmic A7445G mutation exhibited approximately 38-57% decrease in the steady-state level of tRNA(Ser(UCN)), which is less reduced levels than in lymphoblastoid cells in the previous study. Furthermore, approximately 22% reduction in the level of aminoacylation of tRNA(Ser(UCN)) was observed in the mutant cybrid cells. Interestingly, approximately 60-63% decrease of steady-state level of ND6 gene, which belongs to the same precursor as that of tRNA(Ser(UCN)), in cybrid cell lines carrying the A7445G mutation, is more than that observed in lymphoblastoid cells. These observations strongly point out a mechanistic link between the processing defect of the tRNA(Ser(UCN)) precursor and decreased stability of ND6 mRNA precursor. These results also imply the influence of nuclear background on the biochemical phenotype associated with the A7445G mutation.
Collapse
Affiliation(s)
- Xiaoming Li
- Division and Program in Human Genetics, Center for Hearing and Deafness Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | | | | | | |
Collapse
|
37
|
Fetoni V, Briem E, Carrara F, Mora M, Zeviani M. Monomelic amyotrophy associated with the 7472insC mutation in the mtDNA tRNASer(UCN) gene. Neuromuscul Disord 2004; 14:723-6. [PMID: 15482956 DOI: 10.1016/j.nmd.2004.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2004] [Revised: 07/05/2004] [Accepted: 07/08/2004] [Indexed: 11/19/2022]
Abstract
We describe a 49-year-old male patient who experienced progressive amyotrophy with no sensorial abnormality in the left arm since 45 years of age. The neuromuscular syndrome was identical to that known as Hirayama disease, a rare form of focal lower motor neuron disease affecting the C7-C8-T1 metamers of the spinal cord. Asymmetric neurosensorial hearing loss was present since age 35 in the patient, and was also documented in an elder sister and in the mother. A muscle biopsy showed cytochrome c oxidase (COX) negative fibers but no ragged-red fibers, and mild reduction of COX was confirmed biochemically. The patient was found to have high levels of a known pathogenic mutation of mtDNA, the 7472insC in the gene encoding the tRNA(Ser(UCN)). Investigation on several family members showed a correlation between mutation load and clinical severity. This is the second report documenting the association of lower motor neurone involvement with a specific mtDNA.
Collapse
Affiliation(s)
- Vincenza Fetoni
- Unit of Neurology, Public Health Hospital, Melegnano (Milan), Italy
| | | | | | | | | |
Collapse
|
38
|
Toompuu M, Levinger LL, Nadal A, Gomez J, Jacobs HT. The 7472insC mtDNA mutation impairs 5' and 3' processing of tRNA(Ser(UCN)). Biochem Biophys Res Commun 2004; 322:803-13. [PMID: 15336535 DOI: 10.1016/j.bbrc.2004.07.181] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2004] [Indexed: 10/26/2022]
Abstract
The deafness-associated 7472insC mtDNA mutation was previously shown to decrease the steady-state level of tRNA(Ser(UCN)) post-transcriptionally. To identify the affected tRNA maturation step(s) we analysed the effects of the mutation on processing in vivo and in vitro. tRNA(Ser(UCN)) from cybrid cells homoplasmic for 7472insC contained a high frequency (>11%) of molecules misprocessed at one or both termini. In vitro assays using partially purified HeLa cell RNase P and mitochondrial tRNA 3' processing endonuclease (tRNase Z) confirmed that the efficiency of both 5' and 3' processing was impaired. A mutant precursor not already processed at the 5' end was poorly processed in vitro by tRNase Z. Misprocessing at the 3' end further impaired the efficiency and accuracy of 5' processing of the mutant substrate. The mutation thus appears to affect several distinct, but interdependent, RNA processing steps, with the predicted outcome dependent on the exact processing pathway operating in vivo.
Collapse
Affiliation(s)
- Marina Toompuu
- Institute of Medical Technology and Tampere University Hospital, FI-33014 University of Tampere, Finland
| | | | | | | | | |
Collapse
|
39
|
Levinger L, Mörl M, Florentz C. Mitochondrial tRNA 3' end metabolism and human disease. Nucleic Acids Res 2004; 32:5430-41. [PMID: 15477393 PMCID: PMC524294 DOI: 10.1093/nar/gkh884] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Over 150 mutations in the mitochondrial genome have been shown to be associated with human disease. Remarkably, two-thirds of them are found in tRNA genes, which constitute only one-tenth of the mitochondrial genome. A total of 22 tRNAs punctuate the genome and are produced together with 11 mRNAs and 2 rRNAs from long polycistronic primary transcripts with almost no spacers. Pre-tRNAs thus require precise endonucleolytic excision. Furthermore, the CCA triplet which forms the 3' end of all tRNAs is not encoded, but must be synthesized by the CCA-adding enzyme after 3' end cleavage. Amino acid attachment to the CCA of mature tRNA is performed by aminoacyl-tRNA synthetases, which, like the preceding processing enzymes, are nuclear-encoded and imported into mitochondria. Here, we critically review the effectiveness and reliability of evidence obtained from reactions with in vitro transcripts that pathogenesis-associated mutant mitochondrial tRNAs can lead to deficiencies in tRNA 3' end metabolism (3' end cleavage, CCA addition and aminoacylation) toward an understanding of molecular mechanisms underlying human tRNA disorders. These defects probably contribute, individually and cumulatively, to the progression of human mitochondrial diseases.
Collapse
Affiliation(s)
- Louis Levinger
- York College/CUNY, 94-20 Guy R. Brewer Boulevard, Jamaica, NY 11451, USA.
| | | | | |
Collapse
|
40
|
Gibbons WJ, Yan Q, Li R, Li X, Guan MX. Genomic organization, expression, and subcellular localization of mouse mitochondrial seryl-tRNA synthetase. Biochem Biophys Res Commun 2004; 317:774-8. [PMID: 15081407 DOI: 10.1016/j.bbrc.2004.03.113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2004] [Indexed: 10/26/2022]
Abstract
We report here the identification and characterization of the mouse mitochondrial seryl-tRNA synthetase (mtSerRS). The genomic organization of mouse mtSerRS has been elucidated. The mouse mtSerRS gene containing 16 exons encodes a 519 residue protein with a strong homology to the mitochondria-like seryl-tRNA synthetase of bacteria, yeast, and other homologs. The mouse mtSerRS is ubiquitously expressed in various tissues, but more abundantly in tissues with high metabolic rates including heart and liver. Surprisingly, this gene, unlike other nuclear genes encoding mitochondrial proteins, exhibited a low expression in skeletal muscle and brain. Furthermore, immunofluorescence analysis of NIH3T3 cells expressing the mtSerRS-GFP fusion protein demonstrated that the mouse mtSerRS localizes in mitochondrion. These observations suggest that the mouse mtSerRS is an evolutionarily conserved protein involved in aminoacylation. Thus, it may play a role in the fidelity in mitochondrial translation and pathogenesis of deafness-associated mutations in the mitochondrial tRNA(Ser(UCN)).
Collapse
Affiliation(s)
- William J Gibbons
- Division and Program in Human Genetics and Center for Hearing and Deafness Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | | | | | | | | |
Collapse
|
41
|
Li X, Fischel-Ghodsian N, Schwartz F, Yan Q, Friedman RA, Guan MX. Biochemical characterization of the mitochondrial tRNASer(UCN) T7511C mutation associated with nonsyndromic deafness. Nucleic Acids Res 2004; 32:867-77. [PMID: 14960712 PMCID: PMC373379 DOI: 10.1093/nar/gkh226] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report here the biochemical characterization of the deafness-associated mitochondrial tRNA(Ser(UCN)) T7511C mutation, in conjunction with homoplasmic ND1 T3308C and tRNA(Ala) T5655C mutations using cybrids constructed by transferring mitochondria from lymphoblastoid cell lines derived from an African family into human mtDNA-less (rho degrees ) cells. Three cybrids derived from an affected matrilineal relative carrying the homoplasmic T7511C mutation, exhibited approximately 75% decrease in the tRNA(Ser(UCN)) level, compared with three control cybrids. This amount of reduction in the tRNA(Ser(UCN)) level is below a proposed threshold to support a normal rate of mitochondrial protein synthesis in lymphoblastoid cell lines. This defect is likely a primary contributor to approximately 52% reduction in the rate of mitochondrial protein synthesis and marked defects in respiration and growth properties in galactose-containing medium. Interestingly, the T5655C mutation produces approximately 50% reduction in the tRNA(Ala) level in mutant cells. Strikingly, the T3308C mutation causes a significant decrease both in the amount of ND1 mRNA and co-transcribed tRNA(Leu(UUR)) in mutant cells. Thus, mitochondrial dysfunctions caused by the T5655C and T3308C mutations may modulate the phenotypic manifestation of the T7511C mutation. These observations imply that a combination of the T7511C mutation with two mtDNA mutations accounts for the high penetrance of deafness in this family.
Collapse
MESH Headings
- Africa
- Base Sequence
- Cell Division/drug effects
- Cell Line
- Cell Respiration
- DNA, Mitochondrial/genetics
- Deafness/genetics
- Deafness/metabolism
- Galactose/pharmacology
- Glucose/pharmacology
- Hearing Loss, Sensorineural/genetics
- Hearing Loss, Sensorineural/metabolism
- Humans
- Mitochondrial Proteins/biosynthesis
- Molecular Sequence Data
- NADH Dehydrogenase/biosynthesis
- NADH Dehydrogenase/genetics
- Pedigree
- Point Mutation
- RNA, Messenger/metabolism
- RNA, Transfer, Ala/metabolism
- RNA, Transfer, Leu/metabolism
- RNA, Transfer, Ser/genetics
- RNA, Transfer, Ser/metabolism
Collapse
Affiliation(s)
- Xiaoming Li
- Division and Program in Human Genetics and Center for Hearing and Deafness Research, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | | | | | | | | | | |
Collapse
|
42
|
Abstract
Mitochondrial tRNA gene mutations, including heteroplasmic deletions that eliminate one or more tRNAs, as well as point mutations that may be either hetero- or homoplasmic, are associated with a wide spectrum of human diseases. These range from rare syndromic disorders to cases of commoner conditions such as sensorineural deafness or cardiomyopathy. The disease spectrum of mutations in a given gene, or even a single mutation, may vary, but some patterns are evident, for example the prominence of cardiomyopathy resulting from tRNAIle defects, or of MERFF-like disease from tRNALys defects. Molecular studies of many laboratories have reached a consensus on molecular mechanisms associated with these mutations. Although precise details vary, loss of translational function of the affected tRNA(s) seems to be the final outcome, whether by impaired pre-tRNA processing, half-life, base-modification or aminoacylation. However, a mechanistic understanding of the consequences of this for the assembly and function of the mitochondrial OXPHOS complexes and for the physiological functions of the affected tissues is still a distant prospect. This review presents some views of possible downstream consequences of specific tRNA deficiencies.
Collapse
Affiliation(s)
- Howard T Jacobs
- Institute of Medical Technology, Tampere University Hospital, University of Tampere, Finland.
| |
Collapse
|
43
|
Levinger L, Giegé R, Florentz C. Pathology-related substitutions in human mitochondrial tRNA(Ile) reduce precursor 3' end processing efficiency in vitro. Nucleic Acids Res 2003; 31:1904-12. [PMID: 12655007 PMCID: PMC152798 DOI: 10.1093/nar/gkg282] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2002] [Revised: 01/31/2003] [Accepted: 01/31/2003] [Indexed: 11/13/2022] Open
Abstract
The human mitochondrial genome encodes 22 tRNAs interspersed among the two rRNAs and 11 mRNAs, often without spacers, suggesting that tRNAs must be efficiently excised. Numerous maternally transmitted diseases and syndromes arise from mutations in mitochondrial tRNAs, likely due to defect(s) in tRNA metabolism. We have systematically explored the effect of pathogenic mutations on tRNA(Ile) precursor 3' end maturation in vitro by 3'-tRNase. Strikingly, four pathogenic tRNA(Ile) mutations reduce 3'-tRNase processing efficiency (V(max) / K(M)) to approximately 10-fold below that of wild-type, principally due to lower V(max). The structural impact of mutations was sought by secondary structure probing and wild-type tRNA(Ile) precursor was found to fold into a canonical cloverleaf. Among the mutant tRNA(Ile) precursors with the greatest 3' end processing deficiencies, only G4309A displays a secondary structure substantially different from wild-type, with changes in the T domain proximal to the substitution. Reduced efficiency of tRNA(Ile) precursor 3' end processing, in one case associated with structural perturbations, could thus contribute to human mitochondrial diseases caused by mutant tRNAs.
Collapse
Affiliation(s)
- Louis Levinger
- UPR 9002 de CNRS, IBMC 15 rue René Descartes, 67084 Strasbourg Cedex, France.
| | | | | |
Collapse
|
44
|
Feuermann M, Francisci S, Rinaldi T, De Luca C, Rohou H, Frontali L, Bolotin-Fukuhara M. The yeast counterparts of human 'MELAS' mutations cause mitochondrial dysfunction that can be rescued by overexpression of the mitochondrial translation factor EF-Tu. EMBO Rep 2003; 4:53-8. [PMID: 12524521 PMCID: PMC1315813 DOI: 10.1038/sj.embor.embor713] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2002] [Revised: 10/25/2002] [Accepted: 11/06/2002] [Indexed: 11/09/2022] Open
Abstract
We have taken advantage of the similarity between human and yeast (Saccharomyces cerevisiae) mitochondrial tRNA(Leu)(UUR), and of the possibility of transforming yeast mitochondria, to construct yeast mitochondrial mutations in the gene encoding tRNA(Leu)(UUR) equivalent to the human A3243G, C3256T and T3291C mutations that have been found in patients with the neurodegenerative disease MELAS (for mitochondrial 'myopathy, encephalopathy, lactic acidosis and stroke-like episodes'). The resulting yeast cells (bearing the equivalent mutations A14G, C26T and T69C) were defective for growth on respiratory substrates, exhibited an abnormal mitochondrial morphology, and accumulated mitochondrial DNA deletions at a very high rate, a trait characteristic of severe mitochondrial defects in protein synthesis. This effect was specific at least in the pathogenic mutation T69C, because when we introduced A or G instead of C, the respiratory defect was absent or very mild. All defective phenotypes returned to normal when the mutant cells were transformed by multicopy plasmids carrying the gene encoding the mitochondrial elongation factor EF-Tu. The ability to create and analyse such mutated strains and to select correcting genes should make yeast a good model for the study of tRNAs and their interacting partners and a practical tool for the study of pathological mutations and of tRNA sequence polymorphisms.
Collapse
MESH Headings
- Amino Acid Substitution
- Base Sequence
- Biolistics
- DNA, Mitochondrial/genetics
- Gene Expression Regulation, Fungal
- Genetic Vectors/genetics
- Humans
- MELAS Syndrome/genetics
- Mitochondria/physiology
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Mutation, Missense
- Peptide Elongation Factor Tu/genetics
- Peptide Elongation Factor Tu/physiology
- Phenotype
- Point Mutation
- Protein Biosynthesis
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Transfer, Leu/chemistry
- RNA, Transfer, Leu/genetics
- Recombinant Fusion Proteins/physiology
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/physiology
- Sequence Alignment
- Sequence Homology, Nucleic Acid
Collapse
Affiliation(s)
- M. Feuermann
- Laboratoire de Génétique Moléculaire, Institut de Génétique et Microbiologie, Bâtiment 400, Université Paris Sud, 91405 Orsay Cedex, France
- These authors contributed equally to the work
| | - S. Francisci
- Pasteur Institute—Cenci Bolognetti Foundation, Department of Cell and Developmental Biology, University of Rome I 'La Sapienza', Piazzale Aldo Moro 5, I-00185 Rome, Italy
- These authors contributed equally to the work
- Tel/Fax: +39 06 4461980;
| | - T. Rinaldi
- Pasteur Institute—Cenci Bolognetti Foundation, Department of Cell and Developmental Biology, University of Rome I 'La Sapienza', Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - C. De Luca
- Pasteur Institute—Cenci Bolognetti Foundation, Department of Cell and Developmental Biology, University of Rome I 'La Sapienza', Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - H. Rohou
- Laboratoire de Génétique Moléculaire, Institut de Génétique et Microbiologie, Bâtiment 400, Université Paris Sud, 91405 Orsay Cedex, France
| | - L. Frontali
- Pasteur Institute—Cenci Bolognetti Foundation, Department of Cell and Developmental Biology, University of Rome I 'La Sapienza', Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - M. Bolotin-Fukuhara
- Laboratoire de Génétique Moléculaire, Institut de Génétique et Microbiologie, Bâtiment 400, Université Paris Sud, 91405 Orsay Cedex, France
| |
Collapse
|