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Jacovetti C, Donnelly C, Menoud V, Suleiman M, Cosentino C, Sobel J, Wu K, Bouzakri K, Marchetti P, Guay C, Kayser B, Regazzi R. The mitochondrial tRNA-derived fragment, mt-tRF-Leu TAA, couples mitochondrial metabolism to insulin secretion. Mol Metab 2024; 84:101955. [PMID: 38704026 PMCID: PMC11112368 DOI: 10.1016/j.molmet.2024.101955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024] Open
Abstract
OBJECTIVE The contribution of the mitochondrial electron transfer system to insulin secretion involves more than just energy provision. We identified a small RNA fragment (mt-tRF-LeuTAA) derived from the cleavage of a mitochondrially-encoded tRNA that is conserved between mice and humans. The role of mitochondrially-encoded tRNA-derived fragments remains unknown. This study aimed to characterize the impact of mt-tRF-LeuTAA, on mitochondrial metabolism and pancreatic islet functions. METHODS We used antisense oligonucleotides to reduce mt-tRF-LeuTAA levels in primary rat and human islet cells, as well as in insulin-secreting cell lines. We performed a joint transcriptome and proteome analysis upon mt-tRF-LeuTAA inhibition. Additionally, we employed pull-down assays followed by mass spectrometry to identify direct interactors of the fragment. Finally, we characterized the impact of mt-tRF-LeuTAA silencing on the coupling between mitochondrial metabolism and insulin secretion using high-resolution respirometry and insulin secretion assays. RESULTS Our study unveils a modulation of mt-tRF-LeuTAA levels in pancreatic islets in different Type 2 diabetes models and in response to changes in nutritional status. The level of the fragment is finely tuned by the mechanistic target of rapamycin complex 1. Located within mitochondria, mt-tRF-LeuTAA interacts with core subunits and assembly factors of respiratory complexes of the electron transfer system. Silencing of mt-tRF-LeuTAA in islet cells limits the inner mitochondrial membrane potential and impairs mitochondrial oxidative phosphorylation, predominantly by affecting the Succinate (via Complex II)-linked electron transfer pathway. Lowering mt-tRF-LeuTAA impairs insulin secretion of rat and human pancreatic β-cells. CONCLUSIONS Our findings indicate that mt-tRF-LeuTAA interacts with electron transfer system complexes and is a pivotal regulator of mitochondrial oxidative phosphorylation and its coupling to insulin secretion.
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Affiliation(s)
- Cecile Jacovetti
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.
| | - Chris Donnelly
- Institute of Sport Sciences, University of Lausanne, Lausanne, Switzerland
| | - Véronique Menoud
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Mara Suleiman
- Department of Clinical and Experimental Medicine, Diabetes Unit, University of Pisa, Pisa, Italy
| | - Cristina Cosentino
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Jonathan Sobel
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Kejing Wu
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Karim Bouzakri
- UMR DIATHEC, EA 7294, Centre Européen d'Etude du Diabète, Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, Diabetes Unit, University of Pisa, Pisa, Italy
| | - Claudiane Guay
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Bengt Kayser
- Institute of Sport Sciences, University of Lausanne, Lausanne, Switzerland
| | - Romano Regazzi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland; Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
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2
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McCormick CA, Akeson S, Tavakoli S, Bloch D, Klink IN, Jain M, Rouhanifard SH. Multicellular, IVT-derived, unmodified human transcriptome for nanopore-direct RNA analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.06.535889. [PMID: 37066160 PMCID: PMC10104151 DOI: 10.1101/2023.04.06.535889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Nanopore direct RNA sequencing (DRS) enables measurements of RNA modifications. Modification-free transcripts are a practical and targeted control for DRS, providing a baseline measurement for canonical nucleotides within a matched and biologically derived sequence context. However, these controls can be challenging to generate and carry nanopore-specific nuances that can impact analysis. We produced DRS datasets using modification-free transcripts from in vitro transcription (IVT) of cDNA from six immortalized human cell lines. We characterized variation across cell lines and demonstrated how these may be interpreted. These data will serve as a versatile control and resource to the community for RNA modification analysis of human transcripts.
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Affiliation(s)
- Caroline A McCormick
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
| | - Stuart Akeson
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
| | - Sepideh Tavakoli
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
| | - Dylan Bloch
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
| | - Isabel N Klink
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
| | - Miten Jain
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
- Department of Physics, Northeastern University, Boston, MA, 02115, United States
| | - Sara H Rouhanifard
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
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3
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Smith TJ, Giles RN, Koutmou KS. Anticodon stem-loop tRNA modifications influence codon decoding and frame maintenance during translation. Semin Cell Dev Biol 2024; 154:105-113. [PMID: 37385829 DOI: 10.1016/j.semcdb.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/01/2023]
Abstract
RNAs are central to protein synthesis, with ribosomal RNA, transfer RNAs and messenger RNAs comprising the core components of the translation machinery. In addition to the four canonical bases (uracil, cytosine, adenine, and guanine) these RNAs contain an array of enzymatically incorporated chemical modifications. Transfer RNAs (tRNAs) are responsible for ferrying amino acids to the ribosome, and are among the most abundant and highly modified RNAs in the cell across all domains of life. On average, tRNA molecules contain 13 post-transcriptionally modified nucleosides that stabilize their structure and enhance function. There is an extensive chemical diversity of tRNA modifications, with over 90 distinct varieties of modifications reported within tRNA sequences. Some modifications are crucial for tRNAs to adopt their L-shaped tertiary structure, while others promote tRNA interactions with components of the protein synthesis machinery. In particular, modifications in the anticodon stem-loop (ASL), located near the site of tRNA:mRNA interaction, can play key roles in ensuring protein homeostasis and accurate translation. There is an abundance of evidence indicating the importance of ASL modifications for cellular health, and in vitro biochemical and biophysical studies suggest that individual ASL modifications can differentially influence discrete steps in the translation pathway. This review examines the molecular level consequences of tRNA ASL modifications in mRNA codon recognition and reading frame maintenance to ensure the rapid and accurate translation of proteins.
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Affiliation(s)
- Tyler J Smith
- University of Michigan, Department of Chemistry, 930 N University, Ann Arbor, MI 48109, USA
| | - Rachel N Giles
- University of Michigan, Department of Chemistry, 930 N University, Ann Arbor, MI 48109, USA
| | - Kristin S Koutmou
- University of Michigan, Department of Chemistry, 930 N University, Ann Arbor, MI 48109, USA.
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4
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Jorge-Smeding E, Leung YH, Ruiz-González A, Xu W, Astessiano AL, Trujillo AI, Rico DE, Kenéz Á. Plasma and milk metabolomics revealed changes in amino acid metabolism in Holstein dairy cows under heat stress. Animal 2024; 18:101049. [PMID: 38215677 DOI: 10.1016/j.animal.2023.101049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 01/14/2024] Open
Abstract
Our understanding of metabolic alterations triggered by heat stress is incomplete, which limits the designing of nutritional strategies to mitigate negative productive and health effects. Thus, this study aimed to explore the metabolic responses of heat-stressed dairy cows to dietary supplementation with vitamin D3/Ca and vitamin E/Se. Twelve multiparous Holstein cows were enrolled in a split-plot Latin square design with two distinct vitamin E/Se supplementation levels, either at a low (ESe-, n = 6, 11.1 IU/kg vitamin E and 0.55 mg/kg Se) or a high dose (ESe+, n = 6 223 IU/kg vitamin E and 1.8 mg/kg Se) as the main plot. Treatment subplots, arranged in a replicated 3 × 3 Latin square design, comprised heat challenge (Temperature Humidity Index, THI: 72.0-82.0) supplemented with different levels of vitamin D3/Ca: either low (HS/DCa-, 1 012 IU/kg and 0.73%, respectively) or high (HS/DCa+, 3 764 IU/kg and 0.97%, respectively), and a pair-fed control group in thermoneutrality (THI = 61.0-64.0) receiving the low dose of vitamin D3/Ca (TN). The liquid chromatography-mass spectrometry-based metabolome profile was determined in blood plasma and milk sampled at the beginning (day 0) and end (day 14) of each experimental period. The results were analyzed for the effect of (1) TN vs. HS/ESe-/DCa-, and (2) the vitamin E/Se and vitamin D3/Ca supplementation. No group or group × day effects were detected in the plasma metabolome (false discovery rate, FDR > 0.05), except for triglyceride 52:2 being higher (FDR = 0.03) on day 0 than 14. Taurine, creatinine and butyryl-carnitine showed group × day interactions in the milk metabolome (FDR ≤ 0.05) as creatinine (+22%) and butyryl-carnitine (+190%) were increased (P < 0.01) on day 14, and taurine was decreased (-65%, P < 0.01) on day 14 in the heat stress (HS) cows, compared with day 0. Most compounds were unaffected by vitamin E/Se or vitamin D3/Ca supplementation level or their interaction (FDR > 0.05) in plasma and milk, except for milk alanine which was lower (-69%, FDR = 0.03) in the E/Se+ groups, compared with E/Se-. Our results indicated that HS triggered more prominent changes in the milk than in the plasma metabolome, with consistent results in milk suggesting increased muscle catabolism, as reflected by increased creatinine, alanine and citrulline levels. Supplementing with high levels of vitamin E/Se or vitamin D3/Ca or their combination did not appear to affect the metabolic remodeling triggered by HS.
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Affiliation(s)
- E Jorge-Smeding
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China; Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República, Avda Garzón 780, Montevideo, CP 12900, Uruguay
| | - Y H Leung
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - A Ruiz-González
- Centre de Recherche en Sciences Animales de Deschambault (CRSAD), Deschambault G0A 1S0, QC, Canada; Département des Sciences Animales, Université Laval, Québec G1V 0A6, QC, Canada
| | - W Xu
- Department of Biosystems, Biosystems Technology Cluster, KU Leuven, Geel 3001, Belgium
| | - A L Astessiano
- Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República, Avda Garzón 780, Montevideo, CP 12900, Uruguay
| | - A I Trujillo
- Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República, Avda Garzón 780, Montevideo, CP 12900, Uruguay
| | - D E Rico
- Centre de Recherche en Sciences Animales de Deschambault (CRSAD), Deschambault G0A 1S0, QC, Canada
| | - Á Kenéz
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.
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Wang J, Yan D, Cui H, Zhang R, Ma X, Chen L, Hu C, Wu J. Identification of eight genomic protective alleles for mitochondrial diabetes by Kinship-graph convolutional network. J Diabetes Investig 2024; 15:52-62. [PMID: 38157301 PMCID: PMC10759726 DOI: 10.1111/jdi.14125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 01/03/2024] Open
Abstract
AIMS Nearly 85% of maternally inherited diabetes and deafness (MIDD) are caused by the m.3243A>G mutation in the mitochondrial DNA. However, the clinical phenotypes of MIDD may also be influenced by the nuclear genome, this study aimed to investigate nuclear genome variants that influence clinical phenotypes associated with m.3243A>G mutation in MIDD based on whole-genome sequencing of the patients belonging to pedigrees. MATERIALS AND METHODS We analyzed a whole-genome sequencing (WGS) dataset from blood samples of 38 MIDD patients with the m.3243A > G mutation belonging to 10 pedigrees, by developing a Kinship-graph convolutional network approach, called Ki-GCN, integrated with the conventional genome-wide association study (GWAS) methods. RESULTS We identified eight protective alleles in the nuclear genome that have protective effects against the onset of MIDD, related deafness, and also type 2 diabetes. Based on these eight protective alleles, we constructed an effective logistic regression model to predict the early or late onset of MIDD patients. CONCLUSIONS There are protective alleles in the nuclear genome that are associated with the onset-age of MIDD patients and might also provide protective effects on the deafness derived from MIDD patients.
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Affiliation(s)
- Jiahao Wang
- CAS Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Dandan Yan
- Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Centre for Diabetes, Shanghai Diabetes InstituteShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghaiChina
| | - Haoyue Cui
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Rong Zhang
- Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Centre for Diabetes, Shanghai Diabetes InstituteShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghaiChina
| | - Xiaojing Ma
- Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Centre for Diabetes, Shanghai Diabetes InstituteShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghaiChina
| | - Luonan Chen
- CAS Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouZhejiangChina
| | - Cheng Hu
- Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Centre for Diabetes, Shanghai Diabetes InstituteShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghaiChina
- Institute for Metabolic DiseaseFengxian Central Hospital Affiliated to Southern Medical UniversityShanghaiChina
| | - Jiarui Wu
- CAS Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouZhejiangChina
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6
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Maharjan S, Gamper H, Yamaki Y, Henley RY, Li NS, Suzuki T, Suzuki T, Piccirilli JA, Wanunu M, Seifert E, Wallace DC, Hou YM. Post-Transcriptional Methylation of Mitochondrial-tRNA Differentially Contributes to Mitochondrial Pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.09.569632. [PMID: 38106193 PMCID: PMC10723379 DOI: 10.1101/2023.12.09.569632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Human mitochondrial tRNAs (mt-tRNAs), critical for mitochondrial biogenesis, are frequently associated with pathogenic mutations. These mt-tRNAs have unusual sequence motifs and require post-transcriptional modifications to stabilize their fragile structures. However, whether a modification that stabilizes a wild-type (WT) mt-tRNA structure would also stabilize its pathogenic variants is unknown. Here we show that the N 1 -methylation of guanosine at position 9 (m 1 G9) of mt-Leu(UAA), while stabilizing the WT tRNA, has an opposite and destabilizing effect on variants associated with MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes). This differential effect is further demonstrated by the observation that demethylation of m 1 G9, while damaging to the WT tRNA, is beneficial to the major pathogenic variant, improving its structure and activity. These results have new therapeutic implications, suggesting that the N 1 -methylation of mt-tRNAs at position 9 is a determinant of pathogenicity and that controlling the methylation level is an important modulator of mt-tRNA-associated diseases.
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7
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Mitchener M, Begley TJ, Dedon PC. Molecular Coping Mechanisms: Reprogramming tRNAs To Regulate Codon-Biased Translation of Stress Response Proteins. Acc Chem Res 2023; 56:3504-3514. [PMID: 37992267 PMCID: PMC10702489 DOI: 10.1021/acs.accounts.3c00572] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 11/24/2023]
Abstract
As part of the classic central dogma of molecular biology, transfer RNAs (tRNAs) are integral to protein translation as the adaptor molecules that link the genetic code in messenger RNA (mRNA) to the amino acids in the growing peptide chain. tRNA function is complicated by the existence of 61 codons to specify 20 amino acids, with most amino acids coded by two or more synonymous codons. Further, there are often fewer tRNAs with unique anticodons than there are synonymous codons for an amino acid, with a single anticodon able to decode several codons by "wobbling" of the base pairs arising between the third base of the codon and the first position on the anticodon. The complications introduced by synonymous codons and wobble base pairing began to resolve in the 1960s with the discovery of dozens of chemical modifications of the ribonucleotides in tRNA, which, by analogy to the epigenome, are now collectively referred to as the epitranscriptome for not changing the genetic code inherent to all RNA sequences. tRNA modifications were found to stabilize codon-anticodon interactions, prevent misinitiation of translation, and promote translational fidelity, among other functions, with modification deficiencies causing pathological phenotypes. This led to hypotheses that modification-dependent tRNA decoding efficiencies might play regulatory roles in cells. However, it was only with the advent of systems biology and convergent "omic" technologies that the higher level function of synonymous codons and tRNA modifications began to emerge.Here, we describe our laboratories' discovery of tRNA reprogramming and codon-biased translation as a mechanism linking tRNA modifications and synonymous codon usage to regulation of gene expression at the level of translation. Taking a historical approach, we recount how we discovered that the 8-10 modifications in each tRNA molecule undergo unique reprogramming in response to cellular stresses to promote translation of mRNA transcripts with unique codon usage patterns. These modification tunable transcripts (MoTTs) are enriched with specific codons that are differentially decoded by modified tRNAs and that fall into functional families of genes encoding proteins necessary to survive the specific stress. By developing and applying systems-level technologies, we showed that cells lacking specific tRNA modifications are sensitized to certain cellular stresses by mistranslation of proteins, disruption of mitochondrial function, and failure to translate critical stress response proteins. In essence, tRNA reprogramming serves as a cellular coping strategy, enabling rapid translation of proteins required for stress-specific cell response programs. Notably, this phenomenon has now been characterized in all organisms from viruses to humans and in response to all types of environmental changes. We also elaborate on recent findings that cancer cells hijack this mechanism to promote their own growth, metastasis, and chemotherapeutic resistance. We close by discussing how understanding of codon-biased translation in various systems can be exploited to develop new therapeutics and biomanufacturing processes.
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Affiliation(s)
- Michelle
M. Mitchener
- Antimicrobial
Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602, Singapore
| | - Thomas J. Begley
- Department
of Biological Sciences, University at Albany, Albany, New York 12222, United States
- RNA
Institute, University at Albany, Albany, New York 12222, United States
| | - Peter C. Dedon
- Antimicrobial
Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602, Singapore
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
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8
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Wang C, Hou X, Guan Q, Zhou H, Zhou L, Liu L, Liu J, Li F, Li W, Liu H. RNA modification in cardiovascular disease: implications for therapeutic interventions. Signal Transduct Target Ther 2023; 8:412. [PMID: 37884527 PMCID: PMC10603151 DOI: 10.1038/s41392-023-01638-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 08/15/2023] [Accepted: 09/03/2023] [Indexed: 10/28/2023] Open
Abstract
Cardiovascular disease (CVD) is the leading cause of death in the world, with a high incidence and a youth-oriented tendency. RNA modification is ubiquitous and indispensable in cell, maintaining cell homeostasis and function by dynamically regulating gene expression. Accumulating evidence has revealed the role of aberrant gene expression in CVD caused by dysregulated RNA modification. In this review, we focus on nine common RNA modifications: N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), N7-methylguanosine (m7G), N4-acetylcytosine (ac4C), pseudouridine (Ψ), uridylation, adenosine-to-inosine (A-to-I) RNA editing, and modifications of U34 on tRNA wobble. We summarize the key regulators of RNA modification and their effects on gene expression, such as RNA splicing, maturation, transport, stability, and translation. Then, based on the classification of CVD, the mechanisms by which the disease occurs and progresses through RNA modifications are discussed. Potential therapeutic strategies, such as gene therapy, are reviewed based on these mechanisms. Herein, some of the CVD (such as stroke and peripheral vascular disease) are not included due to the limited availability of literature. Finally, the prospective applications and challenges of RNA modification in CVD are discussed for the purpose of facilitating clinical translation. Moreover, we look forward to more studies exploring the mechanisms and roles of RNA modification in CVD in the future, as there are substantial uncultivated areas to be explored.
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Affiliation(s)
- Cong Wang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xuyang Hou
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Qing Guan
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Huiling Zhou
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Li Zhou
- Department of Pathology, National Clinical Research Center for Geriatric Disorders, The Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Lijun Liu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jijia Liu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Feng Li
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Wei Li
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Haidan Liu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
- Clinical Center for Gene Diagnosis and Therapy, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
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9
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Wang L, Jiang L, Chu Y, Feng F, Tang W, Chen C, Qiu Y, Hu Z, Diao H, Tang Z. Dietary Taurine Improves Growth Performance and Intestine Health via the GSH/GSSG Antioxidant System and Nrf2/ARE Signaling Pathway in Weaned Piglets. Antioxidants (Basel) 2023; 12:1852. [PMID: 37891931 PMCID: PMC10604690 DOI: 10.3390/antiox12101852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Early weaning of piglets was prone to increase reactive oxygen species, disrupt the redox balance, decrease antioxidant capacity, cause oxidative stress and intestinal oxidative damage, and lead to diarrhea in piglets. This research aimed to study dietary taurine (Tau) supplementation at a level relieving intestinal oxidative damage in early-weaned piglets. A total of 48 piglets were assigned to four groups of 12 individuals and fed a basal diet with 0.0% Tau (CON), 0.2% Tau (L-Tau), 0.3% Tau (M-Tau), or 0.4% Tau (H-Tau), respectively. The animal experiment lasted 30 days. The final weight, weight gain, average daily gain, and feed conversion rate increased with the increase in dietary Tau (Linear, p < 0.05; Quadratic p < 0.05), while the diarrhea index of piglets decreased with the increase in dietary Tau (Linear, p < 0.05). Serum malondialdehyde, nitric oxide (NO), D-lactose, and oxidized glutathione (GSSG) concentrations decreased with the increase in dietary Tau (Linear, p < 0.05). The O2•- and •OH clearance rate in serum, liver, and jejunum mucosa increased with the increase in dietary Tau (Linear, p < 0.05). Serum superoxide dismutase (SOD) activity, glutathione peroxidase (GPX) activity, catalase (CAT) activity, and peroxidase (POD) activity and total antioxidant capacity increased with the increase in dietary Tau (Linear, p < 0.05). The serum glutathione (GSH) concentration and the ratio of GSH to GSSG increased with the increase in dietary Tau (Linear, p < 0.05). The POD and glutathione synthase activity in the liver and jejunum mucosa increased with the increase in dietary Tau (Linear, p < 0.05). The mRNA abundances of HO-1 and GPX1 in the H-Tau group were higher than that in the L-Tau, M-Tau, and CON groups (p < 0.05). The mRNA abundances of SOD1 and Nrf2 in the M-Tau and H-Tau groups were higher than in the L-Tau and CON groups (p < 0.05). The mRNA abundance of SOD2 in the L-Tau, M-Tau, and H-Tau groups was higher than in the CON group (p < 0.05). The VH and the ratio of VH to CD of jejunum and ileum increased with the increase in dietary Tau (Linear, p < 0.05). The mRNA abundances of occludens 1 and claudin 1 in the H-Tau group were higher than that in the CON, L-Tau, and M-Tau (p < 0.05). The mRNA abundance of occludin in the L-Tau, M-Tau, and H-Tau groups was higher than that in CON (p < 0.05). The abundance of Firmicutes increased with the increase in dietary Tau (Linear, p < 0.05), while Proteobacteria and Spirochaetota decreased with the increase in dietary Tau (Linear, p < 0.05). Collectively, dietary supplementation of 0.3% and 0.4% Tau in feed could significantly improve the growth performance and enhance the antioxidant capacity of piglets.
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Affiliation(s)
- Lingang Wang
- Laboratory for Bio-Feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (L.W.); (L.J.); (Y.C.); (F.F.); (C.C.); (Y.Q.); (Z.H.)
| | - Liwen Jiang
- Laboratory for Bio-Feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (L.W.); (L.J.); (Y.C.); (F.F.); (C.C.); (Y.Q.); (Z.H.)
| | - Yunyun Chu
- Laboratory for Bio-Feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (L.W.); (L.J.); (Y.C.); (F.F.); (C.C.); (Y.Q.); (Z.H.)
| | - Fu Feng
- Laboratory for Bio-Feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (L.W.); (L.J.); (Y.C.); (F.F.); (C.C.); (Y.Q.); (Z.H.)
| | - Wenjie Tang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China; (W.T.); (H.D.)
- Livestock and Poultry Biological Products Key Laboratory of Sichuan Province, Sichuan Animtche Group Co., Ltd., Chengdu 610066, China
| | - Chen Chen
- Laboratory for Bio-Feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (L.W.); (L.J.); (Y.C.); (F.F.); (C.C.); (Y.Q.); (Z.H.)
| | - Yibin Qiu
- Laboratory for Bio-Feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (L.W.); (L.J.); (Y.C.); (F.F.); (C.C.); (Y.Q.); (Z.H.)
| | - Zhijin Hu
- Laboratory for Bio-Feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (L.W.); (L.J.); (Y.C.); (F.F.); (C.C.); (Y.Q.); (Z.H.)
| | - Hui Diao
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China; (W.T.); (H.D.)
- Livestock and Poultry Biological Products Key Laboratory of Sichuan Province, Sichuan Animtche Group Co., Ltd., Chengdu 610066, China
| | - Zhiru Tang
- Laboratory for Bio-Feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (L.W.); (L.J.); (Y.C.); (F.F.); (C.C.); (Y.Q.); (Z.H.)
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10
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Davyt M, Bharti N, Ignatova Z. Effect of mRNA/tRNA mutations on translation speed: Implications for human diseases. J Biol Chem 2023; 299:105089. [PMID: 37495112 PMCID: PMC10470029 DOI: 10.1016/j.jbc.2023.105089] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023] Open
Abstract
Recent discoveries establish tRNAs as central regulators of mRNA translation dynamics, and therefore cotranslational folding and function of the encoded protein. The tRNA pool, whose composition and abundance change in a cell- and tissue-dependent manner, is the main factor which determines mRNA translation velocity. In this review, we discuss a group of pathogenic mutations, in the coding sequences of either protein-coding genes or in tRNA genes, that alter mRNA translation dynamics. We also summarize advances in tRNA biology that have uncovered how variations in tRNA levels on account of genetic mutations affect protein folding and function, and thereby contribute to phenotypic diversity in clinical manifestations.
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Affiliation(s)
- Marcos Davyt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Nikhil Bharti
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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11
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Liufu T, Yu H, Yu J, Yu M, Tian Y, Ou Y, Deng J, Xing G, Wang Z. Complex I deficiency in m.3243A>G fibroblasts is alleviated by reducing NADH accumulation. Front Physiol 2023; 14:1164287. [PMID: 37650111 PMCID: PMC10464909 DOI: 10.3389/fphys.2023.1164287] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/03/2023] [Indexed: 09/01/2023] Open
Abstract
Introduction: Mitochondrial disease is a spectrum of debilitating disorders caused by mutations in the mitochondrial DNA (mtDNA) or nuclear DNA that compromises the respiratory chain. Mitochondrial 3243A>G (m.3243 A>G) is the most common mutation showing great heterogeneity in phenotype. Previous studies have indicated that NADH: ubiquinone oxidoreductase (complex I) deficiency accompanied by a decreased nicotinamide adenine dinucleotide (NAD+)/reduced NAD+ (NADH) ratio may play a pivotal role in the pathogenesis of m.3243A>G mutation. Methods: To evaluate the potential effects of strategies targeting the imbalanced NAD+/NADH ratio in m.3243A>G mutation, we treated fibroblasts derived from patients with the m.3243 A>G mutation using nicotinamide riboside (NR) or mitochondria-targeted H2O-forming NADH oxidase (mitoLbNOX). Results: M.3243 A>G fibroblasts showed a significant reduction in complex I core subunit 6, complex I enzymatic activity, complex I-dependent oxygen consumption rate (OCR), and adenosine triphosphate (ATP) production compared to the controls. The NAD+/NADH ratio was also significantly reduced in m.3243 A>G fibroblasts, and, using fluorescence lifetime imaging microscopy, we also found that the NADH level was elevated in m.3243 A>G fibroblasts. After NR treatment, the NAD+/NADH ratio, complex I-dependent OCR, and ATP levels increased, whereas NADH levels remained unchanged. More excitingly, after treatment with mitoLbNOX, the NAD+/NADH ratio, complex I-independent OCR, and ATP levels increased more pronouncedly compared with the NR treatment group, accompanied by significantly reduced NADH levels. Discussion: The present study suggests that compared with repletion of NAD+ alone, the combination of this therapeutic modality with alleviation of NADH overload may amplify the treatment effect of restoring NAD+/NADH balance in m.3243A>G fibroblasts.
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Affiliation(s)
- Tongling Liufu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Haiyan Yu
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Jiaxi Yu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Meng Yu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Yue Tian
- Neuroscience Research Institute, Peking University, Beijing, China
| | - Yichun Ou
- Neuroscience Research Institute, Peking University, Beijing, China
| | - Jianwen Deng
- Department of Neurology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Neurovascular Disease Discovery, Beijing, China
| | - Guogang Xing
- Neuroscience Research Institute, Peking University, Beijing, China
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Neurovascular Disease Discovery, Beijing, China
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12
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Tsai PY, Shui B, Lee S, Liu Y, Qu Y, Cheng C, Edwards K, Wong C, Meng-Killeen R, Soloway PD, Barrow JJ. Ado-Mediated Depletion of Taurine Impairs Mitochondrial Respiratory Capacity and Alters the Chromatin Landscape of Inguinal Adipose Tissue. Nutrients 2023; 15:3532. [PMID: 37630723 PMCID: PMC10458711 DOI: 10.3390/nu15163532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Non-shivering thermogenesis (NST) has strong potential to combat obesity; however, a safe molecular approach to activate this process has not yet been identified. The sulfur amino acid taurine has the ability to safely activate NST and confer protection against obesity and metabolic disease in both mice and humans, but the mechanism of this action is unknown. In this study, we discover that a suite of taurine biosynthetic enzymes, especially that of cysteamine dioxygenase (ADO), significantly increases in response to β3 adrenergic signaling in inguinal adipose tissue (IWAT) in order to increase intracellular concentrations of taurine. We further show that ADO is critical for thermogenic mitochondrial respiratory function as its ablation in adipocytes significantly reduces taurine levels, which leads to declines in mitochondrial oxygen consumption rates. Finally, we demonstrate via assay for transposase-accessible chromatin with sequencing (ATAC-seq) that taurine supplementation in beige adipocytes has the ability to remodel the chromatin landscape to increase the chromatin accessibility and transcription of genes, such as glucose-6-phosphate isomerase 1 (Gpi1), which are critical for NST. Taken together, our studies highlight a potential mechanism for taurine in the activation of NST that can be leveraged toward the treatment of obesity and metabolic disease.
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Affiliation(s)
- Pei-Yin Tsai
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; (P.-Y.T.)
| | - Bo Shui
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Seoyeon Lee
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; (P.-Y.T.)
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Yang Liu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; (P.-Y.T.)
| | - Yue Qu
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; (P.-Y.T.)
| | - Chloe Cheng
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Kaydine Edwards
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; (P.-Y.T.)
| | - Callie Wong
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; (P.-Y.T.)
| | - Ryan Meng-Killeen
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; (P.-Y.T.)
| | - Paul D. Soloway
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; (P.-Y.T.)
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Joeva J. Barrow
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14850, USA; (P.-Y.T.)
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13
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Tomoda E, Nagao A, Shirai Y, Asano K, Suzuki T, Battersby B, Suzuki T. Restoration of mitochondrial function through activation of hypomodified tRNAs with pathogenic mutations associated with mitochondrial diseases. Nucleic Acids Res 2023; 51:7563-7579. [PMID: 36928678 PMCID: PMC10415153 DOI: 10.1093/nar/gkad139] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/14/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
Mutations in mitochondrial (mt-)tRNAs frequently cause mitochondrial dysfunction. Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS), and myoclonus epilepsy associated with ragged red fibers (MERRF) are major clinical subgroups of mitochondrial diseases caused by pathogenic point mutations in tRNA genes encoded in mtDNA. We previously reported a severe reduction in the frequency of 5-taurinomethyluridine (τm5U) and its 2-thiouridine derivative (τm5s2U) in the anticodons of mutant mt-tRNAs isolated from the cells of patients with MELAS and MERRF, respectively. The hypomodified tRNAs fail to decode cognate codons efficiently, resulting in defective translation of respiratory chain proteins in mitochondria. To restore the mitochondrial activity of MELAS patient cells, we overexpressed MTO1, a τm5U-modifying enzyme, in patient-derived myoblasts. We used a newly developed primer extension method and showed that MTO1 overexpression almost completely restored the τm5U modification of the MELAS mutant mt-tRNALeu(UUR). An increase in mitochondrial protein synthesis and oxygen consumption rate suggested that the mitochondrial function of MELAS patient cells can be activated by restoring the τm5U of the mutant tRNA. In addition, we confirmed that MTO1 expression restored the τm5s2U of the mutant mt-tRNALys in MERRF patient cells. These findings pave the way for epitranscriptomic therapies for mitochondrial diseases.
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Affiliation(s)
- Ena Tomoda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yuki Shirai
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kana Asano
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | | | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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14
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Ueda S, Yagi M, Tomoda E, Matsumoto S, Ueyanagi Y, Do Y, Setoyama D, Matsushima Y, Nagao A, Suzuki T, Ide T, Mori Y, Oyama N, Kang D, Uchiumi T. Mitochondrial haplotype mutation alleviates respiratory defect of MELAS by restoring taurine modification in tRNA with 3243A > G mutation. Nucleic Acids Res 2023; 51:7480-7495. [PMID: 37439353 PMCID: PMC10415116 DOI: 10.1093/nar/gkad591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 07/14/2023] Open
Abstract
The 3243A > G in mtDNA is a representative mutation in mitochondrial diseases. Mitochondrial protein synthesis is impaired due to decoding disorder caused by severe reduction of 5-taurinomethyluridine (τm5U) modification of the mutant mt-tRNALeu(UUR) bearing 3243A > G mutation. The 3243A > G heteroplasmy in peripheral blood reportedly decreases exponentially with age. Here, we found three cases with mild respiratory symptoms despite bearing high rate of 3243A > G mutation (>90%) in blood mtDNA. These patients had the 3290T > C haplotypic mutation in addition to 3243A > G pathogenic mutation in mt-tRNALeu(UUR) gene. We generated cybrid cells of these cases to examine the effects of the 3290T > C mutation on mitochondrial function and found that 3290T > C mutation improved mitochondrial translation, formation of respiratory chain complex, and oxygen consumption rate of pathogenic cells associated with 3243A > G mutation. We measured τm5U frequency of mt-tRNALeu(UUR) with 3243A > G mutation in the cybrids by a primer extension method assisted with chemical derivatization of τm5U, showing that hypomodification of τm5U was significantly restored by the 3290T > C haplotypic mutation. We concluded that the 3290T > C is a haplotypic mutation that suppresses respiratory deficiency of mitochondrial disease by restoring hypomodified τm5U in mt-tRNALeu(UUR) with 3243A > G mutation, implying a potential therapeutic measure for mitochondrial disease associated with pathogenic mutations in mt-tRNAs.
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Affiliation(s)
- Saori Ueda
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mikako Yagi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Ena Tomoda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shinya Matsumoto
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yasushi Ueyanagi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yura Do
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Daiki Setoyama
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuichi Matsushima
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Japan
| | - Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tomomi Ide
- Department of Cardiovascular Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yusuke Mori
- Department of Internal Medicine Kitakyushu City Yahata Hospital, 2-6-2 Ogura, Yahatahigashi-ku, Kitakyushu 805-8534, Japan
| | - Noriko Oyama
- Department of Endocrinology and Metabolism, Fukuoka Children's Hospital, 5-1-1 Kashiiteriha, Higashi-ku, Fukuoka 813-0017, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takeshi Uchiumi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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15
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Mullin NK, Voigt AP, Flamme-Wiese MJ, Liu X, Riker MJ, Varzavand K, Stone EM, Tucker BA, Mullins RF. Multimodal single-cell analysis of nonrandom heteroplasmy distribution in human retinal mitochondrial disease. JCI Insight 2023; 8:e165937. [PMID: 37289546 PMCID: PMC10443808 DOI: 10.1172/jci.insight.165937] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 06/02/2023] [Indexed: 06/10/2023] Open
Abstract
Variants within the high copy number mitochondrial genome (mtDNA) can disrupt organelle function and lead to severe multisystem disease. The wide range of manifestations observed in patients with mitochondrial disease results from varying fractions of abnormal mtDNA molecules in different cells and tissues, a phenomenon termed heteroplasmy. However, the landscape of heteroplasmy across cell types within tissues and its influence on phenotype expression in affected patients remains largely unexplored. Here, we identify nonrandom distribution of a pathogenic mtDNA variant across a complex tissue using single-cell RNA-Seq, mitochondrial single-cell ATAC sequencing, and multimodal single-cell sequencing. We profiled the transcriptome, chromatin accessibility state, and heteroplasmy in cells from the eyes of a patient with mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) and from healthy control donors. Utilizing the retina as a model for complex multilineage tissues, we found that the proportion of the pathogenic m.3243A>G allele was neither evenly nor randomly distributed across diverse cell types. All neuroectoderm-derived neural cells exhibited a high percentage of the mutant variant. However, a subset of mesoderm-derived lineage, namely the vasculature of the choroid, was near homoplasmic for the WT allele. Gene expression and chromatin accessibility profiles of cell types with high and low proportions of m.3243A>G implicate mTOR signaling in the cellular response to heteroplasmy. We further found by multimodal single-cell sequencing of retinal pigment epithelial cells that a high proportion of the pathogenic mtDNA variant was associated with transcriptionally and morphologically abnormal cells. Together, these findings show the nonrandom nature of mitochondrial variant partitioning in human mitochondrial disease and underscore its implications for mitochondrial disease pathogenesis and treatment.
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Affiliation(s)
- Nathaniel K. Mullin
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
- Medical Scientist Training Program, University of Iowa, Iowa City, Iowa, USA
| | - Andrew P. Voigt
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
- Medical Scientist Training Program, University of Iowa, Iowa City, Iowa, USA
| | - Miles J. Flamme-Wiese
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Xiuying Liu
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Megan J. Riker
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Katayoun Varzavand
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Edwin M. Stone
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Budd A. Tucker
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
| | - Robert F. Mullins
- University of Iowa Institute for Vision Research, Iowa City, Iowa, USA
- Department of Ophthalmology and Visual Sciences and
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16
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Rahmadanthi FR, Maksum IP. Transfer RNA Mutation Associated with Type 2 Diabetes Mellitus. BIOLOGY 2023; 12:871. [PMID: 37372155 DOI: 10.3390/biology12060871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
Transfer RNA (tRNA) genes in the mitochondrial DNA genome play an important role in protein synthesis. The 22 tRNA genes carry the amino acid that corresponds to that codon but changes in the genetic code often occur such as gene mutations that impact the formation of adenosine triphosphate (ATP). Insulin secretion does not occur because the mitochondria cannot work optimally. tRNA mutation may also be caused by insulin resistance. In addition, the loss of tRNA modification can cause pancreatic β cell dysfunction. Therefore, both can be indirectly associated with diabetes mellitus because diabetes mellitus, especially type 2, is caused by insulin resistance and the body cannot produce insulin. In this review, we will discuss tRNA in detail, several diseases related to tRNA mutations, how tRNA mutations can lead to type 2 diabetes mellitus, and one example of a point mutation that occurs in tRNA.
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Affiliation(s)
- Fanny Rizki Rahmadanthi
- Departement of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, Indonesia
| | - Iman Permana Maksum
- Departement of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, Indonesia
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17
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Dixon TAM, Rhyno ELM, El N, McGaw SP, Otley NA, Parker KS, Buldo EC, Pabody CM, Savoie M, Cockshutt A, Morash AJ, Lamarre SG, MacCormack TJ. Taurine depletion impairs cardiac function and affects tolerance to hypoxia and high temperatures in brook char (Salvelinus fontinalis). J Exp Biol 2023; 226:286891. [PMID: 36728502 DOI: 10.1242/jeb.245092] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/20/2023] [Indexed: 02/03/2023]
Abstract
Physiological and environmental stressors can cause osmotic stress in fish hearts, leading to a reduction in intracellular taurine concentration. Taurine is a β-amino acid known to regulate cardiac function in other animal models but its role in fish has not been well characterized. We generated a model of cardiac taurine deficiency (TD) by feeding brook char (Salvelinus fontinalis) a diet enriched in β-alanine, which inhibits cardiomyocyte taurine uptake. Cardiac taurine levels were reduced by 21% and stress-induced changes in normal taurine handling were observed in TD brook char. Responses to exhaustive exercise and acute thermal and hypoxia tolerance were then assessed using a combination of in vivo, in vitro and biochemical approaches. Critical thermal maximum was higher in TD brook char despite significant reductions in maximum heart rate. In vivo, TD brook char exhibited a lower resting heart rate, blunted hypoxic bradycardia and a severe reduction in time to loss of equilibrium under hypoxia. In vitro function was similar between control and TD hearts under oxygenated conditions, but stroke volume and cardiac output were severely compromised in TD hearts under severe hypoxia. Aspects of mitochondrial structure and function were also impacted in TD permeabilized cardiomyocytes, but overall effects were modest. High levels of intracellular taurine are required to achieve maximum cardiac function in brook char and cardiac taurine efflux may be necessary to support heart function under stress. Taurine appears to play a vital, previously unrecognized role in supporting cardiovascular function and stress tolerance in fish.
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Affiliation(s)
- Toni-Anne M Dixon
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB, Canada, E4L 1E4
| | - Emma-Lee M Rhyno
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB, Canada, E4L 1E4
| | - Nir El
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB, Canada, E4L 1E4
| | - Samuel P McGaw
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB, Canada, E4L 1E4
| | - Nathan A Otley
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB, Canada, E4L 1E4
| | - Katya S Parker
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB, Canada, E4L 1E4
| | - Elena C Buldo
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB, Canada, E4L 1E4
| | - Claire M Pabody
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB, Canada, E4L 1E4
| | - Mireille Savoie
- Department of Biology, Mount Allison University, Sackville, NB, Canada, E4L 1E4
| | - Amanda Cockshutt
- Department of Chemistry, Saint Francis Xavier University, Antigonish, NS, Canada, B2G 2W5
| | - Andrea J Morash
- Department of Biology, Mount Allison University, Sackville, NB, Canada, E4L 1E4
| | - Simon G Lamarre
- Departement de Biologie, Université de Moncton, Moncton, NB, Canada, E1A 3E9
| | - Tyson J MacCormack
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB, Canada, E4L 1E4
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18
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Varghese LN, Schwenke DO, Katare R. Role of noncoding RNAs in cardiac ageing. Front Cardiovasc Med 2023; 10:1142575. [PMID: 37034355 PMCID: PMC10073704 DOI: 10.3389/fcvm.2023.1142575] [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: 01/11/2023] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
The global population is estimated to reach 9.8 billion by 2050, of which 2.1 billion will comprise individuals above 60 years of age. As the number of elderly is estimated to double from 2017, it is a victory of the modern healthcare system but also worrisome as ageing, and the onset of chronic disease are correlated. Among other chronic conditions, cardiovascular diseases (CVDs) are the leading cause of death in the aged population. While the underlying cause of the age-associated development of CVDs is not fully understood, studies indicate the role of non-coding RNAs such as microRNAs (miRNAs) and long noncoding RNAs (lnc-RNAs) in the development of age-associated CVDs. miRNAs and lnc-RNAs are non-coding RNAs which control gene expression at the post-transcriptional level. The expression of specific miRNAs and lnc-RNAs are reportedly dysregulated with age, leading to cardiovascular system changes and ultimately causing CVDs. Since miRNAs and lnc-RNAs play several vital roles in maintaining the normal functioning of the cardiovascular system, they are also being explored for their therapeutic potential as a treatment for CVDs. This review will first explore the pathophysiological changes associated with ageing. Next, we will review the known mechanisms underlying the development of CVD in ageing with a specific focus on miRNA and lnc-RNAs. Finally, we will discuss the therapeutic options and future challenges towards healthy cardiac ageing. With the global ageing population on the rise, this review will provide a fundamental understanding of some of the underlying molecular mechanisms of cardiac ageing.
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Shiraishi W, Tateishi T, Hashimoto Y, Yamasaki R, Kira JI, Isobe N. [Chronic progressive external ophthalmoplegia that could not be diagnosed by biceps muscle biopsy, but was genetically diagnosed by extraocular muscle biopsy]. Rinsho Shinkeigaku 2022; 62:946-951. [PMID: 36450492 DOI: 10.5692/clinicalneurol.cn-001798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
A 48-year-old Japanese male experienced slowly progressive diplopia. He had no family history and was negative for the edrophonium chloride test. Blood analysis showed elevated lactic acid and pyruvic acid levels, suggesting mitochondrial disease. A muscle biopsy from the biceps brachii was performed, but no pathological or genetical mitochondrial abnormalities were detected. Subsequently, he underwent muscle plication for diplopia in which the right inferior rectus muscle was biopsied. Genetic examination of genomic DNA extracted from the extraocular muscle tissue revealed multiple mitochondrial gene deletions, with a heteroplasmy rate of approximately 35%, resulting in the diagnosis of chronic progressive external ophthalmoplegia. In mitochondrial diseases, the tissue distribution of mitochondria with disease-associated variants in mtDNA should be noted, and it is important to select the affected muscle when performing a biopsy for an accurate diagnosis.
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Affiliation(s)
- Wataru Shiraishi
- Department of Neurology, Neurological Institute, Graduate School of Medical Sciences, Kyushu University
- Department of Neurology, Kokura Memorial Hospital
- Shiraishi Internal Medicine Clinic
| | - Takahisa Tateishi
- Department of Neurology, Neurological Institute, Graduate School of Medical Sciences, Kyushu University
- Department of Medicine, Kurume University School of Medicine
| | - Yu Hashimoto
- Department of Neurology, Neurological Institute, Graduate School of Medical Sciences, Kyushu University
| | - Ryo Yamasaki
- Department of Neurology, Neurological Institute, Graduate School of Medical Sciences, Kyushu University
| | - Jun-Ichi Kira
- Department of Neurology, Neurological Institute, Graduate School of Medical Sciences, Kyushu University
- Translational Neuroscience Center, Graduate School of Medicine, and School of Pharmacy at Fukuoka, International University of Health and Welfare
- Department of Neurology, Brain and Nerve Center, Fukuoka Central Hospital
| | - Noriko Isobe
- Department of Neurology, Neurological Institute, Graduate School of Medical Sciences, Kyushu University
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Kotammagari TK, Tähtinen P, Lönnberg T. Oligonucleotides Featuring a Covalently Mercurated 6-Phenylcarbazole Residue as High-Affinity Hybridization Probes for Thiopyrimidine-Containing Sequences. Chemistry 2022; 28:e202202530. [PMID: 36108095 PMCID: PMC10092508 DOI: 10.1002/chem.202202530] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Indexed: 12/14/2022]
Abstract
Short oligonucleotides incorporating either 1-mercuri-6-phenylcarbazole, 8-mercuri-6-phenylcarbazole, or 1,8-dimercuri-6-phenylcarbazole C-nucleoside in the middle of the chain have been synthesized and studied for their potential as hybridization probes for sequences containing thiopyrimidine nucleobases. All of these oligonucleotides formed very stable duplexes with complementary sequences pairing the organometallic moiety with either 2- or 4-thiothymine. The isomeric monomercurated oligonucleotides were also able to discriminate between 2- and 4-thiothymine based on the different melting temperatures of the respective duplexes. DFT-optimized structures of the most stable mononuclear HgII -mediated base pairs featured a coordinated covalent bond between HgII and either S2 or S4 and a hydrogen bond between the carbazole nitrogen and N3. The dinuclear HgII -mediated base pairs, in turn, were geometrically very similar to the one previously reported to form between 1,8-dimercuri-6-phenylcarbazole and thymine and had one HgII ion coordinated to a thio and the other one to an oxo substituent.
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Affiliation(s)
- Tharun K Kotammagari
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Petri Tähtinen
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
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Abstract
tRNAs are key adaptor molecules that decipher the genetic code during translation of mRNAs in protein synthesis. In contrast to the traditional view of tRNAs as ubiquitously expressed housekeeping molecules, awareness is now growing that tRNA-encoding genes display tissue-specific and cell type-specific patterns of expression, and that tRNA gene expression and function are both dynamically regulated by post-transcriptional RNA modifications. Moreover, dysregulation of tRNAs, mediated by alterations in either their abundance or function, can have deleterious consequences that contribute to several distinct human diseases, including neurological disorders and cancer. Accumulating evidence shows that reprogramming of mRNA translation through altered tRNA activity can drive pathological processes in a codon-dependent manner. This Review considers the emerging evidence in support of the precise control of functional tRNA levels as an important regulatory mechanism that coordinates mRNA translation and protein expression in physiological cell homeostasis, and highlights key examples of human diseases that are linked directly to tRNA dysregulation.
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Affiliation(s)
- Esteban A Orellana
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Elisabeth Siegal
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
- Harvard Initiative for RNA Medicine, Harvard University, Boston, MA, USA.
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Wang L, Lin S. Emerging functions of tRNA modifications in mRNA translation and diseases. J Genet Genomics 2022; 50:223-232. [PMID: 36309201 DOI: 10.1016/j.jgg.2022.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
Abstract
tRNAs are essential modulators that recognize mRNA codons and bridge amino acids for mRNA translation. The tRNAs are heavily modified, which is essential for forming a complex secondary structure that facilitates codon recognition and mRNA translation. In recent years, studies have identified the regulatory roles of tRNA modifications in mRNA translation networks. Misregulation of tRNA modifications is closely related to the progression of developmental diseases and cancers. In this review, we summarize the tRNA biogenesis process and then discuss the effects and mechanisms of tRNA modifications on tRNA processing and mRNA translation. Finally, we provide a comprehensive overview of tRNA modifications' physiological and pathological functions, focusing on diseases including cancers.
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Affiliation(s)
- Lu Wang
- Department of Medical Laboratory, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong 510515, China; Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Shuibin Lin
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510080, China.
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Bommisetti P, Young A, Bandarian V. Elucidation of the substrate of tRNA-modifying enzymes MnmEG leads to in vitro reconstitution of an evolutionarily conserved uridine hypermodification. J Biol Chem 2022; 298:102548. [PMID: 36181794 PMCID: PMC9626948 DOI: 10.1016/j.jbc.2022.102548] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 12/02/2022] Open
Abstract
The evolutionarily conserved bacterial proteins MnmE and MnmG collectively install a carboxymethylaminomethyl (cmnm) group at the fifth position of wobble uridines of several tRNA species. While the reaction catalyzed by MnmEG is one of the central steps in the biosynthesis of the methylaminomethyl (mnm) posttranscriptional tRNA modification, details of the reaction remain elusive. Glycine is known to be the source of the carboxy methylamino moiety of cmnm, and a tetrahydrofolate (THF) analog is thought to supply the one carbon that is appended to the fifth position of U. However, the nature of the folate analog remains unknown. This article reports the in vitro biochemical reconstitution of the MnmEG reaction. Using isotopically labeled methyl and methylene THF analogs, we demonstrate that methylene THF is the true substrate. We also show that reduced FAD is required for the reaction and that DTT can replace the NADH in its role as a reductant. We discuss the implications of these methylene-THF and reductant requirements on the mechanism of this key tRNA modification catalyzed by MnmEG.
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Affiliation(s)
- Praneeth Bommisetti
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Anthony Young
- Soliome Inc, 479 Jessie Street, San Francisco, CA 94103, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States.
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Cellular and mitochondrial taurine depletion in bile duct ligated rats: a justification for taurine supplementation in cholestasis/cirrhosis. Clin Exp Hepatol 2022; 8:195-210. [PMID: 36685263 PMCID: PMC9850306 DOI: 10.5114/ceh.2022.119216] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/05/2022] [Indexed: 01/25/2023] Open
Abstract
Taurine (TAU) is a free amino acid abundant in the human body. Various physiological roles have been attributed to TAU. At the subcellular level, mitochondria are the primary targets for TAU function. Meanwhile, it has been found that TAU depletion is associated with severe pathologies. Cholestasis is a severe clinical complication that can progress to liver fibrosis, cirrhosis, and hepatic failure. Bile duct ligation (BDL) is a reliable model for assessing cholestasis/cirrhosis and related complications. The current study was designed to investigate the effects of cholestasis/cirrhosis on tissue and mitochondrial TAU reservoirs. Cholestatic rats were monitored (14 and 42 days after BDL surgery), and TAU levels were assessed in various tissues and isolated mitochondria. There was a significant decrease in TAU in the brain, heart, liver, kidney, skeletal muscle, intestine, lung, testis, and ovary of the BDL animals (14 and 42 days after surgery). Mitochondrial levels of TAU were also significantly depleted in BDL animals. Tissue and mitochondrial TAU levels in cirrhotic animals (42 days after the BDL operation) were substantially lower than those in the cholestatic rats (14 days after BDL surgery). These data indicate an essential role for tissue and mitochondrial TAU in preventing organ injury induced by cholestasis/cirrhosis and could justify TAU supplementation for therapeutic purposes.
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Kishimoto-Urata M, Urata S, Fujimoto C, Yamasoba T. Role of Oxidative Stress and Antioxidants in Acquired Inner Ear Disorders. Antioxidants (Basel) 2022; 11:antiox11081469. [PMID: 36009187 PMCID: PMC9405327 DOI: 10.3390/antiox11081469] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 01/27/2023] Open
Abstract
Oxygen metabolism in the mitochondria is essential for biological activity, and reactive oxygen species (ROS) are produced simultaneously in the cell. Once an imbalance between ROS production and degradation (oxidative stress) occurs, cells are damaged. Sensory organs, especially those for hearing, are constantly exposed during daily life. Therefore, almost all mammalian species are liable to hearing loss depending on their environment. In the auditory pathway, hair cells, spiral ganglion cells, and the stria vascularis, where mitochondria are abundant, are the main targets of ROS. Excessive generation of ROS in auditory sensory organs is widely known to cause sensorineural hearing loss, and mitochondria-targeted antioxidants are candidates for treatment. This review focuses on the relationship between acquired hearing loss and antioxidant use to provide an overview of novel antioxidants, namely medicines, supplemental nutrients, and natural foods, based on clinical, animal, and cultured-cell studies.
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Belal S, Goudenège D, Bocca C, Dumont F, Chao De La Barca JM, Desquiret-Dumas V, Gueguen N, Geffroy G, Benyahia R, Kane S, Khiati S, Bris C, Aranyi T, Stockholm D, Inisan A, Renaud A, Barth M, Simard G, Reynier P, Letournel F, Lenaers G, Bonneau D, Chevrollier A, Procaccio V. Glutamate-Induced Deregulation of Krebs Cycle in Mitochondrial Encephalopathy Lactic Acidosis Syndrome Stroke-Like Episodes (MELAS) Syndrome Is Alleviated by Ketone Body Exposure. Biomedicines 2022; 10:biomedicines10071665. [PMID: 35884972 PMCID: PMC9312837 DOI: 10.3390/biomedicines10071665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/19/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
(1) Background: The development of mitochondrial medicine has been severely impeded by a lack of effective therapies. (2) Methods: To better understand Mitochondrial Encephalopathy Lactic Acidosis Syndrome Stroke-like episodes (MELAS) syndrome, neuronal cybrid cells carrying different mutation loads of the m.3243A > G mitochondrial DNA variant were analysed using a multi-omic approach. (3) Results: Specific metabolomic signatures revealed that the glutamate pathway was significantly increased in MELAS cells with a direct correlation between glutamate concentration and the m.3243A > G heteroplasmy level. Transcriptomic analysis in mutant cells further revealed alterations in specific gene clusters, including those of the glutamate, gamma-aminobutyric acid pathways, and tricarboxylic acid (TCA) cycle. These results were supported by post-mortem brain tissue analysis from a MELAS patient, confirming the glutamate dysregulation. Exposure of MELAS cells to ketone bodies significantly reduced the glutamate level and improved mitochondrial functions, reducing the accumulation of several intermediate metabolites of the TCA cycle and alleviating the NADH-redox imbalance. (4) Conclusions: Thus, a multi-omic integrated approach to MELAS cells revealed glutamate as a promising disease biomarker, while also indicating that a ketogenic diet should be tested in MELAS patients.
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Affiliation(s)
- Sophie Belal
- MitoLab Team, UMR CNRS 6015-INSERM U1083, Unité MitoVasc, SFR ICAT, Université d’Angers, 49933 Angers, France; (S.B.); (D.G.); (C.B.); (J.M.C.D.L.B.); (V.D.-D.); (N.G.); (G.G.); (R.B.); (S.K.); (S.K.); (C.B.); (A.I.); (A.R.); (P.R.); (G.L.); (D.B.); (A.C.)
| | - David Goudenège
- MitoLab Team, UMR CNRS 6015-INSERM U1083, Unité MitoVasc, SFR ICAT, Université d’Angers, 49933 Angers, France; (S.B.); (D.G.); (C.B.); (J.M.C.D.L.B.); (V.D.-D.); (N.G.); (G.G.); (R.B.); (S.K.); (S.K.); (C.B.); (A.I.); (A.R.); (P.R.); (G.L.); (D.B.); (A.C.)
- Biochemistry and Genetics Department, University Hospital of Angers, 49933 Angers, France; (M.B.); (G.S.)
| | - Cinzia Bocca
- MitoLab Team, UMR CNRS 6015-INSERM U1083, Unité MitoVasc, SFR ICAT, Université d’Angers, 49933 Angers, France; (S.B.); (D.G.); (C.B.); (J.M.C.D.L.B.); (V.D.-D.); (N.G.); (G.G.); (R.B.); (S.K.); (S.K.); (C.B.); (A.I.); (A.R.); (P.R.); (G.L.); (D.B.); (A.C.)
- Biochemistry and Genetics Department, University Hospital of Angers, 49933 Angers, France; (M.B.); (G.S.)
| | - Florent Dumont
- Signalling and Cardiovascular Pathophysiology, INSERM UMR-S 1180, University of Paris-Saclay, 92296 Châtenay-Malabry, France;
| | - Juan Manuel Chao De La Barca
- MitoLab Team, UMR CNRS 6015-INSERM U1083, Unité MitoVasc, SFR ICAT, Université d’Angers, 49933 Angers, France; (S.B.); (D.G.); (C.B.); (J.M.C.D.L.B.); (V.D.-D.); (N.G.); (G.G.); (R.B.); (S.K.); (S.K.); (C.B.); (A.I.); (A.R.); (P.R.); (G.L.); (D.B.); (A.C.)
- Biochemistry and Genetics Department, University Hospital of Angers, 49933 Angers, France; (M.B.); (G.S.)
| | - Valérie Desquiret-Dumas
- MitoLab Team, UMR CNRS 6015-INSERM U1083, Unité MitoVasc, SFR ICAT, Université d’Angers, 49933 Angers, France; (S.B.); (D.G.); (C.B.); (J.M.C.D.L.B.); (V.D.-D.); (N.G.); (G.G.); (R.B.); (S.K.); (S.K.); (C.B.); (A.I.); (A.R.); (P.R.); (G.L.); (D.B.); (A.C.)
- Biochemistry and Genetics Department, University Hospital of Angers, 49933 Angers, France; (M.B.); (G.S.)
| | - Naïg Gueguen
- MitoLab Team, UMR CNRS 6015-INSERM U1083, Unité MitoVasc, SFR ICAT, Université d’Angers, 49933 Angers, France; (S.B.); (D.G.); (C.B.); (J.M.C.D.L.B.); (V.D.-D.); (N.G.); (G.G.); (R.B.); (S.K.); (S.K.); (C.B.); (A.I.); (A.R.); (P.R.); (G.L.); (D.B.); (A.C.)
- Biochemistry and Genetics Department, University Hospital of Angers, 49933 Angers, France; (M.B.); (G.S.)
| | - Guillaume Geffroy
- MitoLab Team, UMR CNRS 6015-INSERM U1083, Unité MitoVasc, SFR ICAT, Université d’Angers, 49933 Angers, France; (S.B.); (D.G.); (C.B.); (J.M.C.D.L.B.); (V.D.-D.); (N.G.); (G.G.); (R.B.); (S.K.); (S.K.); (C.B.); (A.I.); (A.R.); (P.R.); (G.L.); (D.B.); (A.C.)
| | - Rayane Benyahia
- MitoLab Team, UMR CNRS 6015-INSERM U1083, Unité MitoVasc, SFR ICAT, Université d’Angers, 49933 Angers, France; (S.B.); (D.G.); (C.B.); (J.M.C.D.L.B.); (V.D.-D.); (N.G.); (G.G.); (R.B.); (S.K.); (S.K.); (C.B.); (A.I.); (A.R.); (P.R.); (G.L.); (D.B.); (A.C.)
| | - Selma Kane
- MitoLab Team, UMR CNRS 6015-INSERM U1083, Unité MitoVasc, SFR ICAT, Université d’Angers, 49933 Angers, France; (S.B.); (D.G.); (C.B.); (J.M.C.D.L.B.); (V.D.-D.); (N.G.); (G.G.); (R.B.); (S.K.); (S.K.); (C.B.); (A.I.); (A.R.); (P.R.); (G.L.); (D.B.); (A.C.)
| | - Salim Khiati
- MitoLab Team, UMR CNRS 6015-INSERM U1083, Unité MitoVasc, SFR ICAT, Université d’Angers, 49933 Angers, France; (S.B.); (D.G.); (C.B.); (J.M.C.D.L.B.); (V.D.-D.); (N.G.); (G.G.); (R.B.); (S.K.); (S.K.); (C.B.); (A.I.); (A.R.); (P.R.); (G.L.); (D.B.); (A.C.)
| | - Céline Bris
- MitoLab Team, UMR CNRS 6015-INSERM U1083, Unité MitoVasc, SFR ICAT, Université d’Angers, 49933 Angers, France; (S.B.); (D.G.); (C.B.); (J.M.C.D.L.B.); (V.D.-D.); (N.G.); (G.G.); (R.B.); (S.K.); (S.K.); (C.B.); (A.I.); (A.R.); (P.R.); (G.L.); (D.B.); (A.C.)
- Biochemistry and Genetics Department, University Hospital of Angers, 49933 Angers, France; (M.B.); (G.S.)
| | - Tamas Aranyi
- Institute of Enzymology, Research Center for Natural Sciences, H-1519 Budapest, Hungary;
- Department of Molecular Biology, Semmelweis University of Medicine, H-1519 Budapest, Hungary
| | - Daniel Stockholm
- Ecole Pratique des Hautes Etudes, PSL Research University, 75014 Paris, France;
- Centre de Recherche Saint-Antoine, UMRS-938, INSERM, Sorbonne Université, F-75012 Paris, France
| | - Aurore Inisan
- MitoLab Team, UMR CNRS 6015-INSERM U1083, Unité MitoVasc, SFR ICAT, Université d’Angers, 49933 Angers, France; (S.B.); (D.G.); (C.B.); (J.M.C.D.L.B.); (V.D.-D.); (N.G.); (G.G.); (R.B.); (S.K.); (S.K.); (C.B.); (A.I.); (A.R.); (P.R.); (G.L.); (D.B.); (A.C.)
| | - Aurélie Renaud
- MitoLab Team, UMR CNRS 6015-INSERM U1083, Unité MitoVasc, SFR ICAT, Université d’Angers, 49933 Angers, France; (S.B.); (D.G.); (C.B.); (J.M.C.D.L.B.); (V.D.-D.); (N.G.); (G.G.); (R.B.); (S.K.); (S.K.); (C.B.); (A.I.); (A.R.); (P.R.); (G.L.); (D.B.); (A.C.)
| | - Magalie Barth
- Biochemistry and Genetics Department, University Hospital of Angers, 49933 Angers, France; (M.B.); (G.S.)
| | - Gilles Simard
- Biochemistry and Genetics Department, University Hospital of Angers, 49933 Angers, France; (M.B.); (G.S.)
| | - Pascal Reynier
- MitoLab Team, UMR CNRS 6015-INSERM U1083, Unité MitoVasc, SFR ICAT, Université d’Angers, 49933 Angers, France; (S.B.); (D.G.); (C.B.); (J.M.C.D.L.B.); (V.D.-D.); (N.G.); (G.G.); (R.B.); (S.K.); (S.K.); (C.B.); (A.I.); (A.R.); (P.R.); (G.L.); (D.B.); (A.C.)
- Biochemistry and Genetics Department, University Hospital of Angers, 49933 Angers, France; (M.B.); (G.S.)
| | - Franck Letournel
- Department of Neurobiology-Neuropathology, Angers Hospital, 49933 Angers, France;
- UMR INSERM 1066-CNRS 6021, MINT Laboratory, 49933 Angers, France
| | - Guy Lenaers
- MitoLab Team, UMR CNRS 6015-INSERM U1083, Unité MitoVasc, SFR ICAT, Université d’Angers, 49933 Angers, France; (S.B.); (D.G.); (C.B.); (J.M.C.D.L.B.); (V.D.-D.); (N.G.); (G.G.); (R.B.); (S.K.); (S.K.); (C.B.); (A.I.); (A.R.); (P.R.); (G.L.); (D.B.); (A.C.)
- Service de Neurologie, CHU d'Angers, 49933 Angers, France
| | - Dominique Bonneau
- MitoLab Team, UMR CNRS 6015-INSERM U1083, Unité MitoVasc, SFR ICAT, Université d’Angers, 49933 Angers, France; (S.B.); (D.G.); (C.B.); (J.M.C.D.L.B.); (V.D.-D.); (N.G.); (G.G.); (R.B.); (S.K.); (S.K.); (C.B.); (A.I.); (A.R.); (P.R.); (G.L.); (D.B.); (A.C.)
- Biochemistry and Genetics Department, University Hospital of Angers, 49933 Angers, France; (M.B.); (G.S.)
| | - Arnaud Chevrollier
- MitoLab Team, UMR CNRS 6015-INSERM U1083, Unité MitoVasc, SFR ICAT, Université d’Angers, 49933 Angers, France; (S.B.); (D.G.); (C.B.); (J.M.C.D.L.B.); (V.D.-D.); (N.G.); (G.G.); (R.B.); (S.K.); (S.K.); (C.B.); (A.I.); (A.R.); (P.R.); (G.L.); (D.B.); (A.C.)
| | - Vincent Procaccio
- MitoLab Team, UMR CNRS 6015-INSERM U1083, Unité MitoVasc, SFR ICAT, Université d’Angers, 49933 Angers, France; (S.B.); (D.G.); (C.B.); (J.M.C.D.L.B.); (V.D.-D.); (N.G.); (G.G.); (R.B.); (S.K.); (S.K.); (C.B.); (A.I.); (A.R.); (P.R.); (G.L.); (D.B.); (A.C.)
- Biochemistry and Genetics Department, University Hospital of Angers, 49933 Angers, France; (M.B.); (G.S.)
- Correspondence:
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Surai PF, Earle-Payne K, Kidd MT. Taurine as a Natural Antioxidant: From Direct Antioxidant Effects to Protective Action in Various Toxicological Models. Antioxidants (Basel) 2021; 10:1876. [PMID: 34942978 PMCID: PMC8698923 DOI: 10.3390/antiox10121876] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/21/2021] [Accepted: 11/23/2021] [Indexed: 12/18/2022] Open
Abstract
Natural antioxidants have received tremendous attention over the last 3 decades. At the same time, the attitude to free radicals is slowly changing, and their signalling role in adaptation to stress has recently received a lot of attention. Among many different antioxidants in the body, taurine (Tau), a sulphur-containing non-proteinogenic β-amino acid, is shown to have a special place as an important natural modulator of the antioxidant defence networks. Indeed, Tau is synthesised in most mammals and birds, and the Tau requirement is met by both synthesis and food/feed supply. From the analysis of recent data, it could be concluded that the direct antioxidant effect of Tau due to scavenging free radicals is limited and could be expected only in a few mammalian/avian tissues (e.g., heart and eye) with comparatively high (>15-20 mM) Tau concentrations. The stabilising effects of Tau on mitochondria, a prime site of free radical formation, are characterised and deserve more attention. Tau deficiency has been shown to compromise the electron transport chain in mitochondria and significantly increase free radical production. It seems likely that by maintaining the optimal Tau status of mitochondria, it is possible to control free radical production. Tau's antioxidant protective action is of great importance in various stress conditions in human life, and is related to commercial animal and poultry production. In various in vitro and in vivo toxicological models, Tau showed AO protective effects. The membrane-stabilizing effects, inhibiting effects on ROS-producing enzymes, as well as the indirect AO effects of Tau via redox balance maintenance associated with the modulation of various transcription factors (e.g., Nrf2 and NF-κB) and vitagenes could also contribute to its protective action in stress conditions, and thus deserve more attention.
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Affiliation(s)
- Peter F. Surai
- Vitagene and Health Research Centre, Bristol BS4 2RS, UK
- Department of Microbiology and Biochemistry, Faculty of Veterinary Medicine, Trakia University, 6000 Stara Zagora, Bulgaria
- Biochemistry and Physiology Department, Saint-Petersburg State University of Veterinary Medicine, 196084 St. Petersburg, Russia
- Department of Animal Nutrition, Faculty of Agricultural and Environmental Sciences, Szent Istvan University, H-2103 Gödöllo, Hungary
| | - Katie Earle-Payne
- NHS Greater Glasgow and Clyde, Renfrewshire Health and Social Care Centre, 10 Ferry Road, Renfrew PA4 8RU, UK;
| | - Michael T. Kidd
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA;
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28
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Chen WT, Tseng HY, Jiang CL, Lee CY, Chi P, Chen LY, Lo KY, Wang IC, Lin FJ. Elp1 facilitates RAD51-mediated homologous recombination repair via translational regulation. J Biomed Sci 2021; 28:81. [PMID: 34819065 PMCID: PMC8613991 DOI: 10.1186/s12929-021-00773-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 11/02/2021] [Indexed: 11/25/2022] Open
Abstract
Background RAD51-dependent homologous recombination (HR) is one of the most important pathways for repairing DNA double-strand breaks (DSBs), and its regulation is crucial to maintain genome integrity. Elp1 gene encodes IKAP/ELP1, a core subunit of the Elongator complex, which has been implicated in translational regulation. However, how ELP1 contributes to genome maintenance is unclear. Methods To investigate the function of Elp1, Elp1-deficient mouse embryonic fibroblasts (MEFs) were generated. Metaphase chromosome spreading, immunofluorescence, and comet assays were used to access chromosome abnormalities and DSB formation. Functional roles of Elp1 in MEFs were evaluated by cell viability, colony forming capacity, and apoptosis assays. HR-dependent DNA repair was assessed by reporter assay, immunofluorescence, and western blot. Polysome profiling was used to evaluate translational efficiency. Differentially expressed proteins and signaling pathways were identified using a label-free liquid chromatography–tandem mass spectrometry (LC–MS/MS) proteomics approach. Results Here, we report that Elp1 depletion enhanced genomic instability, manifested as chromosome breakage and genotoxic stress-induced genomic DNA fragmentation upon ionizing radiation (IR) exposure. Elp1-deficient cells were hypersensitive to DNA damage and exhibited impaired cell proliferation and defective HR repair. Moreover, Elp1 depletion reduced the formation of IR-induced RAD51 foci and decreased RAD51 protein levels. Polysome profiling analysis revealed that ELP1 regulated RAD51 expression by promoting its translation in response to DNA damage. Notably, the requirement for ELP1 in DSB repair could be partially rescued in Elp1-deficient cells by reintroducing RAD51, suggesting that Elp1-mediated HR-directed repair of DSBs is RAD51-dependent. Finally, using proteome analyses, we identified several proteins involved in cancer pathways and DNA damage responses as being differentially expressed upon Elp1 depletion. Conclusions Our study uncovered a molecular mechanism underlying Elp1-mediated regulation of HR activity and provides a novel link between translational regulation and genome stability. Supplementary Information The online version contains supplementary material available at 10.1186/s12929-021-00773-z.
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Affiliation(s)
- Wei-Ting Chen
- Department of Biochemical Science and Technology, National Taiwan University, No.1, Sec.4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Huan-Yi Tseng
- Department of Biochemical Science and Technology, National Taiwan University, No.1, Sec.4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Chung-Lin Jiang
- Department of Biochemical Science and Technology, National Taiwan University, No.1, Sec.4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Chih-Ying Lee
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan.,Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Liuh-Yow Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Kai-Yin Lo
- Department of Agricultural Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - I-Ching Wang
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Fu-Jung Lin
- Department of Biochemical Science and Technology, National Taiwan University, No.1, Sec.4, Roosevelt Rd., Taipei, 10617, Taiwan. .,Research Center for Development Biology and Regenerative Medicine, National Taiwan University, Taipei, 10617, Taiwan.
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29
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Biosynthesis and Degradation of Sulfur Modifications in tRNAs. Int J Mol Sci 2021; 22:ijms222111937. [PMID: 34769366 PMCID: PMC8584467 DOI: 10.3390/ijms222111937] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/30/2021] [Accepted: 11/01/2021] [Indexed: 12/23/2022] Open
Abstract
Various sulfur-containing biomolecules include iron–sulfur clusters that act as cofactors for enzymes, sulfur-containing vitamins such as thiamin, and sulfur-modified nucleosides in RNA, in addition to methionine and cysteine in proteins. Sulfur-containing nucleosides are post-transcriptionally introduced into tRNA molecules, where they ensure precise codon recognition or stabilization of tRNA structure, thereby maintaining cellular proteome integrity. Modulating sulfur modification controls the translation efficiency of specific groups of genes, allowing organisms to adapt to specific environments. The biosynthesis of tRNA sulfur nucleosides involves elaborate ‘sulfur trafficking systems’ within cellular sulfur metabolism and ‘modification enzymes’ that incorporate sulfur atoms into tRNA. This review provides an up-to-date overview of advances in our knowledge of the mechanisms involved. It covers the functions, biosynthesis, and biodegradation of sulfur-containing nucleosides as well as the reaction mechanisms of biosynthetic enzymes catalyzed by the iron–sulfur clusters, and identification of enzymes involved in the de-modification of sulfur atoms of RNA. The mechanistic similarity of these opposite reactions is discussed. Mutations in genes related to these pathways can cause human diseases (e.g., cancer, diabetes, and mitochondrial diseases), emphasizing the importance of these pathways.
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30
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Dorsey S, Ahmed F. Developments in distinguishing secondary vascular headache from primary headache disorders in clinical practice. Expert Rev Neurother 2021; 21:1357-1369. [PMID: 34553658 DOI: 10.1080/14737175.2021.1984882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Vascular headaches are secondary headache disorders with potentially devastating consequences if missed. Clinicians often struggle to distinguish these from primary headache disorders whereby there is no underlying structural pathology. Here, the authors describe the advancement in our understanding of vascular headache disorders, their clinical presentation and the developments in neuroimaging that facilitate diagnosis. AREAS COVERED Here the authors discuss the definition of primary and secondary headache disorders. They review the literature on the presentation, choice of neuroimaging and diagnostic tools that can be used to diagnose specific vascular headaches including Carotid or Vertebral artery dissection, Stroke, Temporal Arteritis, subarachnoid hemorrhage, cerebral venous thrombosis, Reversible Cerebral Vasoconstriction syndrome, Primary angiitis, AV malformation and Genetic vasculopathy. The authors discuss the influence of Covid-19 on the management of patients with headache. EXPERT OPINION Whilst developments in neuroimaging have been of paramount importance in the diagnosis of vascular headache disorders, there is no substitute for meticulous history taking and examination. Research has aided our understanding of clinical presentation, however further studies are needed as well as increased education of neurologists and acute physicians.
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Affiliation(s)
- Sophie Dorsey
- Department of Neurology, Hull University Teaching Hospitals, Hull, UK
| | - Fayyaz Ahmed
- Department of Neurology, Hull University Teaching Hospitals, Hull, UK.,Department of Neurosciences, Hull York Medical School, Hull, UK
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31
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Shaukat AN, Kaliatsi EG, Stamatopoulou V, Stathopoulos C. Mitochondrial tRNA-Derived Fragments and Their Contribution to Gene Expression Regulation. Front Physiol 2021; 12:729452. [PMID: 34539450 PMCID: PMC8446549 DOI: 10.3389/fphys.2021.729452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/09/2021] [Indexed: 01/14/2023] Open
Abstract
Mutations in human mitochondrial tRNAs (mt-tRNAs) are responsible for several and sometimes severe clinical phenotypes, classified among mitochondrial diseases. In addition, post-transcriptional modifications of mt-tRNAs in correlation with several stress signals can affect their stability similarly to what has been described for their nuclear-encoded counterparts. Many of the perturbations related to either point mutations or aberrant modifications of mt-tRNAs can lead to specific cleavage and the production of mitochondrial tRNA-derived fragments (mt-tRFs). Although mt-tRFs have been detected in several studies, the exact biogenesis steps and biological role remain, to a great extent, unexplored. Several mt-tRFs are produced because of the excessive oxidative stress which predominantly affects mitochondrial DNA integrity. In addition, mt-tRFs have been detected in various diseases with possible detrimental consequences, but also their production may represent a response mechanism to external stimuli, including infections from pathogens. Finally, specific point mutations on mt-tRNAs have been reported to impact the pool of the produced mt-tRFs and there is growing evidence suggesting that mt-tRFs can be exported and act in the cytoplasm. In this review, we summarize current knowledge on mitochondrial tRNA-deriving fragments and their possible contribution to gene expression regulation.
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Affiliation(s)
| | - Eleni G Kaliatsi
- Department of Biochemistry, School of Medicine, University of Patras, Patras, Greece
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32
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The Role of Taurine in Mitochondria Health: More Than Just an Antioxidant. Molecules 2021; 26:molecules26164913. [PMID: 34443494 PMCID: PMC8400259 DOI: 10.3390/molecules26164913] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/08/2021] [Accepted: 08/10/2021] [Indexed: 12/21/2022] Open
Abstract
Taurine is a naturally occurring sulfur-containing amino acid that is found abundantly in excitatory tissues, such as the heart, brain, retina and skeletal muscles. Taurine was first isolated in the 1800s, but not much was known about this molecule until the 1990s. In 1985, taurine was first approved as the treatment among heart failure patients in Japan. Accumulating studies have shown that taurine supplementation also protects against pathologies associated with mitochondrial defects, such as aging, mitochondrial diseases, metabolic syndrome, cancer, cardiovascular diseases and neurological disorders. In this review, we will provide a general overview on the mitochondria biology and the consequence of mitochondrial defects in pathologies. Then, we will discuss the antioxidant action of taurine, particularly in relation to the maintenance of mitochondria function. We will also describe several reported studies on the current use of taurine supplementation in several mitochondria-associated pathologies in humans.
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33
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Zheng YY, Wu Y, Begley TJ, Sheng J. Sulfur modification in natural RNA and therapeutic oligonucleotides. RSC Chem Biol 2021; 2:990-1003. [PMID: 34458821 PMCID: PMC8341892 DOI: 10.1039/d1cb00038a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/22/2021] [Indexed: 11/21/2022] Open
Abstract
Sulfur modifications have been discovered on both DNA and RNA. Sulfur substitution of oxygen atoms at nucleobase or backbone locations in the nucleic acid framework led to a wide variety of sulfur-modified nucleosides and nucleotides. While the discovery, regulation and functions of DNA phosphorothioate (PS) modification, where one of the non-bridging oxygen atoms is replaced by sulfur on the DNA backbone, are important topics, this review focuses on the sulfur modification in natural cellular RNAs and therapeutic nucleic acids. The sulfur modifications on RNAs exhibit diversity in terms of modification location and cellular function, but the various sulfur modifications share common biosynthetic strategies across RNA species, cell types and domains of life. The first section reviews the post-transcriptional sulfur modifications on nucleobases with an emphasis on thiouridine on tRNA and phosphorothioate modification on RNA backbones, as well as the functions of the sulfur modifications on different species of cellular RNAs. The second section reviews the biosynthesis of different types of sulfur modifications and summarizes the general strategy for the biosynthesis of sulfur-containing RNA residues. One of the main goals of investigating sulfur modifications is to aid the genomic drug development pipeline and enhance our understandings of the rapidly growing nucleic acid-based gene therapies. The last section of the review focuses on the current drug development strategies employing sulfur substitution of oxygen atoms in therapeutic RNAs.
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Affiliation(s)
- Ya Ying Zheng
- Department of Chemistry, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
| | - Ying Wu
- Department of Chemistry, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
| | - Thomas J Begley
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- Department of Biological Science, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
| | - Jia Sheng
- Department of Chemistry, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
- The RNA Institute, University at Albany, State University of New York 1400 Washington Ave. Albany NY 12222 USA
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34
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Baliou S, Adamaki M, Ioannou P, Pappa A, Panayiotidis MI, Christodoulou I, Spandidos DA, Kyriakopoulos AM, Zoumpourlis V. Ameliorative effect of taurine against diabetes and renal-associated disorders (Review). MEDICINE INTERNATIONAL 2021; 1:3. [PMID: 36699147 PMCID: PMC9855276 DOI: 10.3892/mi.2021.3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/25/2021] [Indexed: 01/28/2023]
Abstract
To develop novel therapeutic methods for both diabetic and renal disorders, scientists had initially focused on elucidating the molecular mechanisms of taurine in established cell lines and mouse models. Although a large amount of data have been revealed, taurine has been confirmed to be the next step of novel promising therapeutic interventions against diabetic disorders. Taurine appears to ameliorate diabetes 1-related complications in various organs through its antioxidant, anti-inflammatory and anti-hormonal actions. In type 2 diabetes, taurine has been positively implicated in glucose homeostasis, exerting potent hypoglycemic, anti-obesity, hypotensive and hypolipidemic effects. Of particular interest is that taurine provides protection against renal dysfunction, including hypertension and proteinuria, specific glomerular and tubular disorders, acute and chronic renal conditions, and diabetic nephropathy. The ameliorative effects of taurine against renal disorders are based on its osmoregulatory properties, its association with signaling pathways and its association with the renin-angiotensin-aldosterone system (RAAS). Further clinical studies are required to ensure the importance of research findings.
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Affiliation(s)
- Stella Baliou
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Maria Adamaki
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Petros Ioannou
- Department of Internal Medicine and Infectious Diseases, University Hospital of Heraklion, 71110 Heraklion, Greece
| | - Aglaia Pappa
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Mihalis I. Panayiotidis
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus,Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus
| | - Ioannis Christodoulou
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71409 Heraklion, Greece
| | | | - Vassilis Zoumpourlis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece,Correspondence to: Dr Vassilis Zoumpourlis, Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vas. Konstantinou Avenue, 11635 Athens, Greece
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35
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Peng GX, Zhang Y, Wang QQ, Li QR, Xu H, Wang ED, Zhou XL. The human tRNA taurine modification enzyme GTPBP3 is an active GTPase linked to mitochondrial diseases. Nucleic Acids Res 2021; 49:2816-2834. [PMID: 33619562 PMCID: PMC7969015 DOI: 10.1093/nar/gkab104] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 01/03/2023] Open
Abstract
GTPBP3 and MTO1 cooperatively catalyze 5-taurinomethyluridine (τm5U) biosynthesis at the 34th wobble position of mitochondrial tRNAs. Mutations in tRNAs, GTPBP3 or MTO1, causing τm5U hypomodification, lead to various diseases. However, efficient in vitro reconstitution and mechanistic study of τm5U modification have been challenging, in part due to the lack of pure and active enzymes. A previous study reported that purified human GTPBP3 (hGTPBP3) is inactive in GTP hydrolysis. Here, we identified the mature form of hGTPBP3 and showed that hGTPBP3 is an active GTPase in vitro that is critical for tRNA modification in vivo. Unexpectedly, the isolated G domain and a mutant with the N-terminal domain truncated catalyzed GTP hydrolysis to only a limited extent, exhibiting high Km values compared with that of the mature enzyme. We further described several important pathogenic mutations of hGTPBP3, associated with alterations in hGTPBP3 localization, structure and/or function in vitro and in vivo. Moreover, we discovered a novel cytoplasm-localized isoform of hGTPBP3, indicating an unknown potential noncanonical function of hGTPBP3. Together, our findings established, for the first time, the GTP hydrolysis mechanism of hGTPBP3 and laid a solid foundation for clarifying the τm5U modification mechanism and etiology of τm5U deficiency-related diseases.
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Affiliation(s)
- Gui-Xin Peng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, 393 Middle Hua Xia Road, Shanghai 201210, China
| | - Yong Zhang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Qin-Qin Wang
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Hua Xia Road, Shanghai 201210, China
| | - Qing-Run Li
- CAS Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Sciences, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Hong Xu
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai Municipal Key Clinical Specialty, the International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 910 Heng Shan Road, Shanghai 200030, China
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, 393 Middle Hua Xia Road, Shanghai 201210, China
| | - Xiao-Long Zhou
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
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36
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Sanchez Caballero L, Gorgogietas V, Arroyo MN, Igoillo-Esteve M. Molecular mechanisms of β-cell dysfunction and death in monogenic forms of diabetes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 359:139-256. [PMID: 33832649 DOI: 10.1016/bs.ircmb.2021.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Monogenetic forms of diabetes represent 1%-5% of all diabetes cases and are caused by mutations in a single gene. These mutations, that affect genes involved in pancreatic β-cell development, function and survival, or insulin regulation, may be dominant or recessive, inherited or de novo. Most patients with monogenic diabetes are very commonly misdiagnosed as having type 1 or type 2 diabetes. The severity of their symptoms depends on the nature of the mutation, the function of the affected gene and, in some cases, the influence of additional genetic or environmental factors that modulate severity and penetrance. In some patients, diabetes is accompanied by other syndromic features such as deafness, blindness, microcephaly, liver and intestinal defects, among others. The age of diabetes onset may also vary from neonatal until early adulthood manifestations. Since the different mutations result in diverse clinical presentations, patients usually need different treatments that range from just diet and exercise, to the requirement of exogenous insulin or other hypoglycemic drugs, e.g., sulfonylureas or glucagon-like peptide 1 analogs to control their glycemia. As a consequence, awareness and correct diagnosis are crucial for the proper management and treatment of monogenic diabetes patients. In this chapter, we describe mutations causing different monogenic forms of diabetes associated with inadequate pancreas development or impaired β-cell function and survival, and discuss the molecular mechanisms involved in β-cell demise.
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Affiliation(s)
- Laura Sanchez Caballero
- ULB Center for Diabetes Research (UCDR), Université Libre de Bruxelles, Brussels, Belgium. http://www.ucdr.be/
| | - Vyron Gorgogietas
- ULB Center for Diabetes Research (UCDR), Université Libre de Bruxelles, Brussels, Belgium. http://www.ucdr.be/
| | - Maria Nicol Arroyo
- ULB Center for Diabetes Research (UCDR), Université Libre de Bruxelles, Brussels, Belgium. http://www.ucdr.be/
| | - Mariana Igoillo-Esteve
- ULB Center for Diabetes Research (UCDR), Université Libre de Bruxelles, Brussels, Belgium. http://www.ucdr.be/.
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37
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Kazuhito T, Wei FY. Posttranscriptional modifications in mitochondrial tRNA and its implication in mitochondrial translation and disease. J Biochem 2021; 168:435-444. [PMID: 32818253 DOI: 10.1093/jb/mvaa098] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 08/03/2020] [Indexed: 12/17/2022] Open
Abstract
A fundamental aspect of mitochondria is that they possess DNA and protein translation machinery. Mitochondrial DNA encodes 22 tRNAs that translate mitochondrial mRNAs to 13 polypeptides of respiratory complexes. Various chemical modifications have been identified in mitochondrial tRNAs via complex enzymatic processes. A growing body of evidence has demonstrated that these modifications are essential for translation by regulating tRNA stability, structure and mRNA binding, and can be dynamically regulated by the metabolic environment. Importantly, the hypomodification of mitochondrial tRNA due to pathogenic mutations in mitochondrial tRNA genes or nuclear genes encoding modifying enzymes can result in life-threatening mitochondrial diseases in humans. Thus, the mitochondrial tRNA modification is a fundamental mechanism underlying the tight regulation of mitochondrial translation and is essential for life. In this review, we focus on recent findings on the physiological roles of 5-taurinomethyl modification (herein referred as taurine modification) in mitochondrial tRNAs. We summarize the findings in human patients and animal models with a deficiency of taurine modifications and provide pathogenic links to mitochondrial diseases. We anticipate that this review will help understand the complexity of mitochondrial biology and disease.
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Affiliation(s)
- Tomizawa Kazuhito
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo-ku, Kumamoto-shi, Kumamoto 860-8556, Japan
| | - Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Honjo 1-1-1, Chuo-ku, Kumamoto-shi, Kumamoto 860-8556, Japan.,Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, Seriyo-machi 4-1, Aoba-ku, Sendai-shi, Miyagi 980-8575, Japan
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38
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The expanding world of tRNA modifications and their disease relevance. Nat Rev Mol Cell Biol 2021; 22:375-392. [PMID: 33658722 DOI: 10.1038/s41580-021-00342-0] [Citation(s) in RCA: 263] [Impact Index Per Article: 87.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2021] [Indexed: 02/08/2023]
Abstract
Transfer RNA (tRNA) is an adapter molecule that links a specific codon in mRNA with its corresponding amino acid during protein synthesis. tRNAs are enzymatically modified post-transcriptionally. A wide variety of tRNA modifications are found in the tRNA anticodon, which are crucial for precise codon recognition and reading frame maintenance, thereby ensuring accurate and efficient protein synthesis. In addition, tRNA-body regions are also frequently modified and thus stabilized in the cell. Over the past two decades, 16 novel tRNA modifications were discovered in various organisms, and the chemical space of tRNA modification continues to expand. Recent studies have revealed that tRNA modifications can be dynamically altered in response to levels of cellular metabolites and environmental stresses. Importantly, we now understand that deficiencies in tRNA modification can have pathological consequences, which are termed 'RNA modopathies'. Dysregulation of tRNA modification is involved in mitochondrial diseases, neurological disorders and cancer.
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39
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Richter U, McFarland R, Taylor RW, Pickett SJ. The molecular pathology of pathogenic mitochondrial tRNA variants. FEBS Lett 2021; 595:1003-1024. [PMID: 33513266 PMCID: PMC8600956 DOI: 10.1002/1873-3468.14049] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/14/2021] [Accepted: 01/18/2021] [Indexed: 12/16/2022]
Abstract
Mitochondrial diseases are clinically and genetically heterogeneous disorders, caused by pathogenic variants in either the nuclear or mitochondrial genome. This heterogeneity is particularly striking for disease caused by variants in mitochondrial DNA‐encoded tRNA (mt‐tRNA) genes, posing challenges for both the treatment of patients and understanding the molecular pathology. In this review, we consider disease caused by the two most common pathogenic mt‐tRNA variants: m.3243A>G (within MT‐TL1, encoding mt‐tRNALeu(UUR)) and m.8344A>G (within MT‐TK, encoding mt‐tRNALys), which together account for the vast majority of all mt‐tRNA‐related disease. We compare and contrast the clinical disease they are associated with, as well as their molecular pathologies, and consider what is known about the likely molecular mechanisms of disease. Finally, we discuss the role of mitochondrial–nuclear crosstalk in the manifestation of mt‐tRNA‐associated disease and how research in this area not only has the potential to uncover molecular mechanisms responsible for the vast clinical heterogeneity associated with these variants but also pave the way to develop treatment options for these devastating diseases.
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Affiliation(s)
- Uwe Richter
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, UK.,Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland.,Newcastle University Biosciences Institute, Newcastle University, UK
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, UK.,Newcastle University Translational and Clinical Research Institute, Newcastle University, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, UK.,Newcastle University Translational and Clinical Research Institute, Newcastle University, UK
| | - Sarah J Pickett
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, UK.,Newcastle University Translational and Clinical Research Institute, Newcastle University, UK
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40
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Chujo T, Tomizawa K. Human transfer RNA modopathies: diseases caused by aberrations in transfer RNA modifications. FEBS J 2021; 288:7096-7122. [PMID: 33513290 PMCID: PMC9255597 DOI: 10.1111/febs.15736] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/13/2020] [Accepted: 01/27/2021] [Indexed: 12/14/2022]
Abstract
tRNA molecules are post-transcriptionally modified by tRNA modification enzymes. Although composed of different chemistries, more than 40 types of human tRNA modifications play pivotal roles in protein synthesis by regulating tRNA structure and stability as well as decoding genetic information on mRNA. Many tRNA modifications are conserved among all three kingdoms of life, and aberrations in various human tRNA modification enzymes cause life-threatening diseases. Here, we describe the class of diseases and disorders caused by aberrations in tRNA modifications as 'tRNA modopathies'. Aberrations in over 50 tRNA modification enzymes are associated with tRNA modopathies, which most frequently manifest as dysfunctions of the brain and/or kidney, mitochondrial diseases, and cancer. However, the molecular mechanisms that link aberrant tRNA modifications to human diseases are largely unknown. In this review, we provide a comprehensive compilation of human tRNA modification functions, tRNA modification enzyme genes, and tRNA modopathies, and we summarize the elucidated pathogenic mechanisms underlying several tRNA modopathies. We will also discuss important questions that need to be addressed in order to understand the molecular pathogenesis of tRNA modopathies.
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Affiliation(s)
- Takeshi Chujo
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Japan
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Bai H, Li T, Yu Y, Zhou N, Kou H, Guo Y, Yang L, Yan P. Cytoprotective Effects of Taurine on Heat-Induced Bovine Mammary Epithelial Cells In Vitro. Cells 2021; 10:cells10020258. [PMID: 33525569 PMCID: PMC7912084 DOI: 10.3390/cells10020258] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 02/07/2023] Open
Abstract
It is a widely known that heat stress induces a reduction in milk production in cows and impairs their overall health. Studies have shown that taurine protects tissues and organs under heat stress. However, there have yet to be studies showing the functions of taurine in mammary alveolar cells-large T antigen (MAC-T) (a bovine mammary epithelial cell line) cells under heat shock. Therefore, different concentrations of taurine (10 mM, 50 mM, and 100 mM) were tested to determine the effects on heat-induced MAC-T cells. The results showed that taurine protected the cells against heat-induced damage as shown by morphological observations in conjunction with suppressed the translocation and expression of heat shock factor 1 (HSF1). Moreover, taurine not only reversed the decline in antioxidase (superoxide dismutase (SOD) and glutathione peroxidase (GSH-PX)) activities but also attenuated the accumulation of malondialdehyde (MDA). Meanwhile, mitochondrial damage (morphology and complex I activity) resulting from heat exposure was mitigated. Taurine also alleviated the rates of cell apoptosis and markedly depressed the mRNA expressions of BCL2 associated X, apoptosis regulator (BAX) and caspase3. Furthermore, compared with the heat stress (HS) group, the protein levels of caspase3 and cleaved caspase3 were decreased in all taurine groups. In summary, taurine improves the antioxidant and anti-apoptosis ability of MAC-T cells thereby alleviates damage of cells due to heat insults.
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Affiliation(s)
- Hui Bai
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (H.B.); (T.L.); (Y.Y.); (Y.G.); (L.Y.)
- Ulanqab Animal Husbandry Workstation, Ulanqab 012000, China; (N.Z.); (H.K.)
| | - Tingting Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (H.B.); (T.L.); (Y.Y.); (Y.G.); (L.Y.)
| | - Yan Yu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (H.B.); (T.L.); (Y.Y.); (Y.G.); (L.Y.)
| | - Ningcong Zhou
- Ulanqab Animal Husbandry Workstation, Ulanqab 012000, China; (N.Z.); (H.K.)
| | - Huijuan Kou
- Ulanqab Animal Husbandry Workstation, Ulanqab 012000, China; (N.Z.); (H.K.)
| | - Yingying Guo
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (H.B.); (T.L.); (Y.Y.); (Y.G.); (L.Y.)
| | - Liang Yang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (H.B.); (T.L.); (Y.Y.); (Y.G.); (L.Y.)
| | - Peishi Yan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (H.B.); (T.L.); (Y.Y.); (Y.G.); (L.Y.)
- Correspondence: ; Tel.: +86-13912967680
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Vila-Sanjurjo A, Smith PM, Elson JL. Heterologous Inferential Analysis (HIA) and Other Emerging Concepts: In Understanding Mitochondrial Variation In Pathogenesis: There is no More Low-Hanging Fruit. Methods Mol Biol 2021; 2277:203-245. [PMID: 34080154 DOI: 10.1007/978-1-0716-1270-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Here we summarize our latest efforts to elucidate the role of mtDNA variants affecting the mitochondrial translation machinery, namely variants mapping to the mt-rRNA and mt-tRNA genes. Evidence is accumulating to suggest that the cellular response to interference with mitochondrial translation is different from that occurring as a result of mutations in genes encoding OXPHOS proteins. As a result, it appears safe to state that a complete view of mitochondrial disease will not be obtained until we understand the effect of mt-rRNA and mt-tRNA variants on mitochondrial protein synthesis. Despite the identification of a large number of potentially pathogenic variants in the mitochondrially encoded rRNA (mt-rRNA) genes, we lack direct methods to firmly establish their pathogenicity. In the absence of such methods, we have devised an indirect approach named heterologous inferential analysis (HIA ) that can be used to make predictions concerning the disruptive potential of a large subset of mt-rRNA variants. We have used HIA to explore the mutational landscape of 12S and 16S mt-rRNA genes. Our HIA studies include a thorough classification of all rare variants reported in the literature as well as others obtained from studies performed in collaboration with physicians. HIA has also been used with non-mammalian mt-rRNA genes to elucidate how mitotypes influence the interaction of the individual and the environment. Regarding mt-tRNA variations, rapidly growing evidence shows that the spectrum of mutations causing mitochondrial disease might differ between the different mitochondrial haplogroups seen in human populations.
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Affiliation(s)
- Antón Vila-Sanjurjo
- Departamento de Bioloxía, Facultade de Ciencias, Centro de Investigacións en Ciencias Avanzadas (CICA), Universidade da Coruña, A Coruña, Spain.
| | - Paul M Smith
- Department of Paediatrics, Royal Aberdeen Children's Hospital, Aberdeen, UK
| | - Joanna L Elson
- Biosciences Institute Newcastle, Newcastle University, Newcastle upon Tyne, UK.
- Human Metabolomics, North-West University, Potchefstroom, South Africa.
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Northern Blotting Technique for Detection and Expression Analysis of mRNAs and Small RNAs. Methods Mol Biol 2021; 2170:155-183. [PMID: 32797458 DOI: 10.1007/978-1-0716-0743-5_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Northern analysis is a conventional but gold standard method for detection and quantification of gene expression changes. It not only detects the presence of a transcript but also indicates size and relative comparison of transcript abundance on a single membrane. In recent years it has been aptly adapted to validate and study the size and expression of small noncoding RNAs. Here, we describe protocols employed in our laboratory for conventional northern analysis with total RNA/mRNA to study gene expression and validation of small noncoding RNAs using low molecular weight fraction of RNAs. A brief account on the recent advancements for improving the sensitivity and efficiency of northern blot detection is also included in this chapter.
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Kripps KA, Friederich MW, Chen T, Larson AA, Mirsky DM, Wang Y, Tanji K, Knight KM, Wong LJ, Van Hove JLK. A novel acceptor stem variant in mitochondrial tRNA Tyr impairs mitochondrial translation and is associated with a severe phenotype. Mol Genet Metab 2020; 131:398-404. [PMID: 33279411 PMCID: PMC7749820 DOI: 10.1016/j.ymgme.2020.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 11/25/2022]
Abstract
Genetic defects in mitochondrial DNA encoded tRNA genes impair mitochondrial translation with resultant defects in the mitochondrial respiratory chain and oxidative phosphorylation system. The phenotypic spectrum of disease seen in mitochondrial tRNA defects is variable and proving pathogenicity of new variants is challenging. Only three pathogenic variants have been described previously in the mitochondrial tRNATyr gene MT-TY, with the reported phenotypes consisting largely of adult onset myopathy and ptosis. We report a patient with a novel MT-TY acceptor stem variant m.5889A>G at high heteroplasmy in muscle, low in blood, and absent in the mother's blood. The phenotype consisted of a childhood-onset severe multi-system disorder characterized by a neurodegenerative course including ataxia and seizures, failure-to-thrive, combined myopathy and neuropathy, and hearing and vision loss. Brain imaging showed progressive atrophy and basal ganglia calcifications. Mitochondrial biomarkers lactate and GDF15 were increased. Functional studies showed a deficient activity of the respiratory chain enzyme complexes containing mtDNA-encoded subunits I, III and IV. There were decreased steady state levels of these mitochondrial complex proteins, and presence of incompletely assembled complex V forms in muscle. These changes are typical of a mitochondrial translational defect. These data support the pathogenicity of this novel variant. Careful review of variants in MT-TY additionally identified two other pathogenic variants, one likely pathogenic variant, nine variants of unknown significance, five likely benign and four benign variants.
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Affiliation(s)
- Kimberly A Kripps
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | - Marisa W Friederich
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, CO, USA; Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, 13121 East 16th Avenue, Aurora, CO, USA
| | - Ting Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Endocrinology, Genetics and Metabolism, Children's Hospital of Soochow University, Suzhou, China
| | - Austin A Larson
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | - David M Mirsky
- Department of Radiology, University of Colorado, and Children's Hospital Colorado, Aurora, CO, USA
| | - Yue Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kurenai Tanji
- Division of Neuropathology, Columbia University Medical Center, New York, NY, USA
| | - Kaz M Knight
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Johan L K Van Hove
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, CO, USA; Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, 13121 East 16th Avenue, Aurora, CO, USA.
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45
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Chemical reversal of abnormalities in cells carrying mitochondrial DNA mutations. Nat Chem Biol 2020; 17:335-343. [PMID: 33168978 DOI: 10.1038/s41589-020-00676-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 08/30/2020] [Accepted: 09/16/2020] [Indexed: 12/24/2022]
Abstract
Mitochondrial DNA (mtDNA) mutations are the major cause of mitochondrial diseases. Cells harboring disease-related mtDNA mutations exhibit various phenotypic abnormalities, such as reduced respiration and elevated lactic acid production. Induced pluripotent stem cell (iPSC) lines derived from patients with mitochondrial disease, with high proportions of mutated mtDNA, exhibit defects in maturation into neurons or cardiomyocytes. In this study, we have discovered a small-molecule compound, which we name tryptolinamide (TLAM), that activates mitochondrial respiration in cybrids generated from patient-derived mitochondria and fibroblasts from patient-derived iPSCs. We found that TLAM inhibits phosphofructokinase-1 (PFK1), which in turn activates AMPK-mediated fatty-acid oxidation to promote oxidative phosphorylation, and redirects carbon flow from glycolysis toward the pentose phosphate pathway to reinforce anti-oxidative potential. Finally, we found that TLAM rescued the defect in neuronal differentiation of iPSCs carrying a high ratio of mutant mtDNA, suggesting that PFK1 represents a potential therapeutic target for mitochondrial diseases.
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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: 136] [Impact Index Per Article: 34.0] [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.
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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.
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Baliou S, Kyriakopoulos AM, Goulielmaki M, Panayiotidis MI, Spandidos DA, Zoumpourlis V. Significance of taurine transporter (TauT) in homeostasis and its layers of regulation (Review). Mol Med Rep 2020; 22:2163-2173. [PMID: 32705197 PMCID: PMC7411481 DOI: 10.3892/mmr.2020.11321] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/09/2020] [Indexed: 11/05/2022] Open
Abstract
Taurine (2‑aminoethanesulfonic acid) contributes to homeostasis, mainly through its antioxidant and osmoregulatory properties. Taurine's influx and efflux are mainly mediated through the ubiquitous expression of the sodium/chloride‑dependent taurine transporter, located on the plasma membrane. The significance of the taurine transporter has been shown in various organ malfunctions in taurine‑transporter‑null mice. The taurine transporter differentially responds to various cellular stimuli including ionic environment, electrochemical charge, and pH changes. The renal system has been used as a model to evaluate the factors that significantly determine the regulation of taurine transporter regulation.
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Affiliation(s)
- Stella Baliou
- National Hellenic Research Foundation, 11635 Athens, Greece
| | | | | | - Michalis I Panayiotidis
- Department of Electron Microscopy and Molecular Pathology, The Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71003 Heraklion, Greece
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Liu H, Ren D, Jiang L, Li X, Yao Y, Mi L, Chen W, Mo A, Jiang N, Yang J, Chen P, Ma H, Luo X, Lu P. A Natural Variation in PLEIOTROPIC DEVELOPMENTAL DEFECTS Uncovers a Crucial Role for Chloroplast tRNA Modification in Translation and Plant Development. THE PLANT CELL 2020; 32:2345-2366. [PMID: 32327539 PMCID: PMC7346568 DOI: 10.1105/tpc.19.00660] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 03/30/2020] [Accepted: 04/15/2020] [Indexed: 05/28/2023]
Abstract
The modification of tRNA is important for accurate, efficient protein translation. A number of tRNA-modifying enzymes were found to influence various developmental processes in distinct organisms. However, few genetic or molecular studies have focused on genes encoding tRNA-modifying enzymes in green plant organelles. Here, we discovered that PDD OL , a natural variation allele of PLEIOTROPIC DEVELOPMENTAL DEFECTS (PDD), leads to pleiotropic developmental defects in a near-isogenic line (NIL) generated by introgressing the wild rice Oryza longistaminata into the rice (Oryza sativa) cv 187R. Map-based cloning revealed that PDD encodes an evolutionarily conserved tRNA-modifying GTPase belonging to the tRNA modification E family. The function of PDD was further confirmed by genetic complementation experiments and mutant analysis. PDD mRNA is primarily expressed in leaves, and PDD is localized to chloroplasts. Biochemical analyses indicated that PDD187R forms homodimers and has strong GTPase activity, whereas PDDOL fails to form homodimers and has weak GTPase activity. Liquid chromatography-coupled tandem quadrupole mass spectrometry revealed that PDD is associated with the 5-methylaminomethyl-2-thiouridine modification of chloroplast tRNA. Furthermore, compared to 187R, NIL-PDD OL has severely reduced levels of proteins involved in photosynthesis and ribosome biogenesis but increased levels of plastid-encoded RNA polymerase subunits. Finally, we demonstrate that the defect due to PDD OL alters chloroplast gene expression, thereby affecting communication between the chloroplast and the nucleus.
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Affiliation(s)
- Hui Liu
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ding Ren
- School of Life Sciences, Fudan University, Shanghai 200433, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Ling Jiang
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xiaojing Li
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yuan Yao
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Limin Mi
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Wanli Chen
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Aowei Mo
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ning Jiang
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jinshui Yang
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Peng Chen
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong Ma
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Xiaojin Luo
- School of Life Sciences, Fudan University, Shanghai 200433, China
- MOE Engineering Research Center of Gene Technology, Fudan University, Shanghai 200433, China
| | - Pingli Lu
- School of Life Sciences, Fudan University, Shanghai 200433, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
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DALRD3 encodes a protein mutated in epileptic encephalopathy that targets arginine tRNAs for 3-methylcytosine modification. Nat Commun 2020; 11:2510. [PMID: 32427860 PMCID: PMC7237682 DOI: 10.1038/s41467-020-16321-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 04/24/2020] [Indexed: 12/24/2022] Open
Abstract
In mammals, a subset of arginine tRNA isoacceptors are methylated in the anticodon loop by the METTL2 methyltransferase to form the 3-methylcytosine (m3C) modification. However, the mechanism by which METTL2 identifies specific tRNA arginine species for m3C formation as well as the biological role of m3C in mammals is unknown. Here, we show that human METTL2 forms a complex with DALR anticodon binding domain containing 3 (DALRD3) protein to recognize particular arginine tRNAs destined for m3C modification. DALRD3-deficient human cells exhibit nearly complete loss of the m3C modification in tRNA-Arg species. Notably, we identify a homozygous nonsense mutation in the DALRD3 gene that impairs m3C formation in human patients exhibiting developmental delay and early-onset epileptic encephalopathy. These findings uncover an unexpected function for the DALRD3 protein in the targeting of distinct arginine tRNAs for m3C modification and suggest a crucial biological role for DALRD3-dependent tRNA modification in proper neurological development.
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50
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Perli E, Pisano A, Pignataro MG, Campese AF, Pelullo M, Genovese I, de Turris V, Ghelli AM, Cerbelli B, Giordano C, Colotti G, Morea V, d'Amati G. Exogenous peptides are able to penetrate human cell and mitochondrial membranes, stabilize mitochondrial tRNA structures, and rescue severe mitochondrial defects. FASEB J 2020; 34:7675-7686. [PMID: 32304340 DOI: 10.1096/fj.201903270r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 03/04/2020] [Accepted: 03/24/2020] [Indexed: 12/14/2022]
Abstract
Mutations in mitochondrial transfer RNA (mt-tRNA) genes are responsible for a wide range of syndromes, for which no effective treatment is available. We previously reported that transfection of the nucleotide sequence encoding for the 16-residue β32_33 peptide from mitochondrial leucyl-tRNA synthetase ameliorates the cell phenotype caused by the mitochondrial tRNA mutations. In this work, we demonstrated that both the β32_33 peptide linked with the known (L)-Phe-(D)-Arg-(L)-Phe-(L)-Lys (FrFK) mitochondrial penetrating sequence and, strikingly, the β32_33 peptide per se, are able to penetrate both the plasma and mitochondrial membranes and exert the rescuing activity when exogenously administered to cells bearing the mutations m.3243A > G and m.8344A > G. These mutations are responsible for the most common and severe mt-tRNA-related diseases. In addition, we dissected the molecular determinants of constructs activity by showing that both the order of amino acids along the sequence and presence of positive charges are essential determinants of the peptide activity in cells and mt-tRNA structures stabilization in vitro. In view of future in vivo studies, this information may be required to design of β32_33 peptide-mimetic derivatives. The β32_33 and FrFK-β32_33 peptides are, therefore, promising molecules for the development of therapeutic agents against diseases caused by the mt-tRNA point mutations.
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Affiliation(s)
- Elena Perli
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome, Rome, Italy
| | - Annalinda Pisano
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome, Rome, Italy
| | - Maria Gemma Pignataro
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Maria Pelullo
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Ilaria Genovese
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Valeria de Turris
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Anna Maria Ghelli
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
| | - Bruna Cerbelli
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University, Latina, Italy
| | - Carla Giordano
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome, Rome, Italy
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology, National Research Council of Italy, Rome, Italy
| | - Veronica Morea
- Institute of Molecular Biology and Pathology, National Research Council of Italy, Rome, Italy
| | - Giulia d'Amati
- Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome, Rome, Italy
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